Citrus Sinensis ID: 026737

---

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----
Protein Sequence
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIVNN
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEEEEEEEEcccccEEEEccHHHHHHHHcccccccEEEcEEEcEEEEEccccccccccEEEEEcEEccccccccccccccccEEEEEEEEEEccccEEEEEccccccccHHHHHHHHccccEEEEEEEEEEEcEEEEEEcccEEEEEEccccccccccccccccccccccEEccEEEEEEcccccccccHHHHHHcHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccEEEEccEEEEEEEEEccccccEEEEEccccHHHHHHHcccccEEEccEEEEEEEccccccccccEEEEEcccccccccccccHEEEcccEEEEEEEEEcccccEEEEEEHcccccHHHHHHHHHcccccEEEEEEEEccccEEEEEccccEEEEEEEEccccccccccccEEEEEccEEEEEEEEEcHHHHHHHHcHHHcccccHHHHHHcccccc
Coil and Loop (DISEMBL)
mspshsckepqKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWnkyssrvnvedifvgrdygafihlrfpdglyhlTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKqleedpllETLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKRVVSQDLQLwlsnappsgkkFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIVNN
Flexible Loop (DISEMBL)
mspshsckepQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDilnegdevrvkvikidreksritlsikqleedplleTLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFhetaivnn
Low Complexity Region (SEG)
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIVNN
Disordered region (IsUnstruct)
***************EIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIV**
Disordered Region (DISOPRED)
*SPSH**KEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIV**
Disordered Region (DISEMBL)
***********KSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIVNN
Disordered Region (DISPRO)
*************IHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAI***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIVNN
Positional Conservation
no confident homologs detected

---

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	234	2.2.26 [Sep-21-2011]
P73530	328	30S ribosomal protein S1	N/A	no	0.495	0.353	0.338	1e-12
Q89AJ3	566	30S ribosomal protein S1	yes	no	0.461	0.190	0.333	4e-12
P37985	557	30S ribosomal protein S1	yes	no	0.316	0.132	0.432	8e-12
P0AG70	557	30S ribosomal protein S1	yes	no	0.316	0.132	0.432	8e-12
P0AG67	557	30S ribosomal protein S1	N/A	no	0.316	0.132	0.432	8e-12
P0AG68	557	30S ribosomal protein S1	yes	no	0.316	0.132	0.432	8e-12
P0AG69	557	30S ribosomal protein S1	N/A	no	0.316	0.132	0.432	8e-12
P14128	378	30S ribosomal protein S1	N/A	no	0.316	0.195	0.432	9e-12
P29344	411	30S ribosomal protein S1,	N/A	no	0.435	0.248	0.324	2e-11
Q83E09	551	30S ribosomal protein S1	yes	no	0.269	0.114	0.478	3e-11

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

 Score = 73.2 bits (178), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 43/127 (33%), Positives = 71/127 (55%), Gaps = 11/127 (8%)

Query: 13  SIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDY 67
           S  E  + L G  + +K ++ +EE  +LV S + A+  +  + + V  + VG     + Y
Sbjct: 150 SAREAKEDLVGEDLPLKFLEVDEERNRLVLSHRRALVERKMNGLEVAQVVVGSVRGIKPY 209

Query: 68  GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127
           GAFI +        ++GL+H+SE+S D I     + N  DE++V +I +D E+ RI+LS 
Sbjct: 210 GAFIDIG------GVSGLLHISEISHDHIDTPHSVFNVNDEIKVMIIDLDAERGRISLST 263

Query: 128 KQLEEDP 134
           KQLE +P
Sbjct: 264 KQLEPEP 270

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

>sp|Q89AJ3|RS1_BUCBP 30S ribosomal protein S1 OS=Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) GN=rpsA PE=3 SV=2

 Score = 71.6 bits (174), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 42/126 (33%), Positives = 73/126 (57%), Gaps = 18/126 (14%)

Query: 21  LTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNV------EDIFVG------RDYG 68
           L G  +  KVI+ +++   +V S +  + ++Y++  N+      E + V        DYG
Sbjct: 147 LEGKELEFKVIKLDQKRNNVVVSRRAVIESEYNAERNLLLETLQEGLIVSGIVKNLTDYG 206

Query: 69  AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
           AF+ L   DGL H+T      +++W  ++   +I+N GDEV++K++K DREK R++L +K
Sbjct: 207 AFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNIGDEVKIKILKFDREKIRVSLGLK 260

Query: 129 QLEEDP 134
           QL +DP
Sbjct: 261 QLSDDP 266

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

Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) (taxid: 224915)

>sp|P37985|RS1_DICD3 30S ribosomal protein S1 OS=Dickeya dadantii (strain 3937) GN=rpsA PE=3 SV=2

 Score = 70.9 bits (172), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 54/81 (66%), Gaps = 7/81 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L
Sbjct: 204 DYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSL 257

Query: 126 SIKQLEEDPLLETLEKVIPQG 146
            +KQL EDP +  + K  P+G
Sbjct: 258 GLKQLGEDPWV-AIAKRYPEG 277

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

Dickeya dadantii (strain 3937) (taxid: 198628)

>sp|P0AG70|RS1_SHIFL 30S ribosomal protein S1 OS=Shigella flexneri GN=rpsA PE=3 SV=1

 Score = 70.9 bits (172), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 54/81 (66%), Gaps = 7/81 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L
Sbjct: 204 DYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSL 257

Query: 126 SIKQLEEDPLLETLEKVIPQG 146
            +KQL EDP +  + K  P+G
Sbjct: 258 GLKQLGEDPWV-AIAKRYPEG 277

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

Shigella flexneri (taxid: 623)

>sp|P0AG67|RS1_ECOLI 30S ribosomal protein S1 OS=Escherichia coli (strain K12) GN=rpsA PE=1 SV=1

 Score = 70.9 bits (172), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 54/81 (66%), Gaps = 7/81 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L
Sbjct: 204 DYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSL 257

Query: 126 SIKQLEEDPLLETLEKVIPQG 146
            +KQL EDP +  + K  P+G
Sbjct: 258 GLKQLGEDPWV-AIAKRYPEG 277

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

Escherichia coli (strain K12) (taxid: 83333)

>sp|P0AG68|RS1_ECOL6 30S ribosomal protein S1 OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=rpsA PE=3 SV=1

 Score = 70.9 bits (172), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 54/81 (66%), Gaps = 7/81 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L
Sbjct: 204 DYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSL 257

Query: 126 SIKQLEEDPLLETLEKVIPQG 146
            +KQL EDP +  + K  P+G
Sbjct: 258 GLKQLGEDPWV-AIAKRYPEG 277

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

Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (taxid: 199310)

>sp|P0AG69|RS1_ECO57 30S ribosomal protein S1 OS=Escherichia coli O157:H7 GN=rpsA PE=3 SV=1

 Score = 70.9 bits (172), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 54/81 (66%), Gaps = 7/81 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L
Sbjct: 204 DYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSL 257

Query: 126 SIKQLEEDPLLETLEKVIPQG 146
            +KQL EDP +  + K  P+G
Sbjct: 258 GLKQLGEDPWV-AIAKRYPEG 277

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

Escherichia coli O157:H7 (taxid: 83334)

>sp|P14128|RS1_PROSP 30S ribosomal protein S1 (Fragment) OS=Providencia sp. GN=rpsA PE=3 SV=1

 Score = 70.5 bits (171), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 54/81 (66%), Gaps = 7/81 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L
Sbjct: 99  DYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSL 152

Query: 126 SIKQLEEDPLLETLEKVIPQG 146
            +KQL EDP +  + K  P+G
Sbjct: 153 GLKQLGEDPWV-AIAKRYPEG 172

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

Providencia sp (taxid: 589)

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

 Score = 69.7 bits (169), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 66/114 (57%), Gaps = 12/114 (10%)

Query: 26  ISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLY 80
           I +K ++ +EE  +LV S + A+ +   +++ +  +  G     + YGAFI +       
Sbjct: 229 IPLKFVEVDEEQSRLVMSNRKAMADS-QAQLGIGSVVTGTVQSLKPYGAFIDIG------ 281

Query: 81  HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
            + GL+HVS++S D + DI  +L  GD ++V ++  DRE+ R++LS K+LE  P
Sbjct: 282 GINGLLHVSQISHDRVSDIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 335

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|Q83E09|RS1_COXBU 30S ribosomal protein S1 OS=Coxiella burnetii (strain RSA 493 / Nine Mile phase I) GN=rpsA PE=1 SV=1

 Score = 68.9 bits (167), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 33/69 (47%), Positives = 47/69 (68%), Gaps = 6/69 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   D+LN GDEV VKV+K DR+K R++L
Sbjct: 200 DYGAFVDLGGVDGLLHIT------DMAWGRVKHPSDLLNVGDEVHVKVLKFDRDKKRVSL 253

Query: 126 SIKQLEEDP 134
            +KQL +DP
Sbjct: 254 GMKQLADDP 262

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

Coxiella burnetii (strain RSA 493 / Nine Mile phase I) (taxid: 227377)

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	234
225433644	390	PREDICTED: 30S ribosomal protein S1 homo	0.927	0.556	0.666	5e-84
224131510	299	predicted protein [Populus trichocarpa]	0.927	0.725	0.664	2e-83
147802809	418	hypothetical protein VITISV_006784 [Viti	0.927	0.519	0.599	1e-79
356569689	378	PREDICTED: 40S ribosomal protein S1-like	0.927	0.574	0.650	2e-79
449484641	379	PREDICTED: 30S ribosomal protein S1-like	0.927	0.572	0.640	2e-79
449468800	378	PREDICTED: 30S ribosomal protein S1-like	0.927	0.574	0.640	4e-79
356538073	383	PREDICTED: 30S ribosomal protein S1 homo	0.927	0.566	0.638	7e-78
18403854	392	ribosomal protein S1-like RNA-binding do	0.927	0.553	0.636	4e-77
297835412	392	S1 RNA-binding domain-containing protein	0.927	0.553	0.628	1e-75
357462911	399	Polyribonucleotide nucleotidyltransferas	0.927	0.543	0.594	2e-72

>gi|225433644|ref|XP_002264430.1| PREDICTED: 30S ribosomal protein S1 homolog [Vitis vinifera] gi|296089601|emb|CBI39420.3| unnamed protein product [Vitis vinifera]

 Score =  316 bits (809), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 166/249 (66%), Positives = 194/249 (77%), Gaps = 32/249 (12%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPSHSCKEP K+I EIAKGL GS+ISVKVI A+EE +KL+FSEK+A W K+S ++N+ D
Sbjct: 136 LSPSHSCKEPHKTIQEIAKGLIGSLISVKVILADEEKRKLIFSEKEAAWLKFSKQINIGD 195

Query: 61  IF---VG--RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           IF   VG   DYGAF+HLRFPDGLYHLTGLVHVSEVSWDL+QD+RD+LNEGDEVRVK++K
Sbjct: 196 IFEAMVGSVEDYGAFVHLRFPDGLYHLTGLVHVSEVSWDLVQDVRDVLNEGDEVRVKIVK 255

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQ---------------------GLEPYLKSF 154
           +DR KSRITLSIKQLEEDPLLETL+KVIPQ                     GLE   +  
Sbjct: 256 VDRVKSRITLSIKQLEEDPLLETLDKVIPQDGSTGPDSLRTSDSYDIEPLPGLETIFEEL 315

Query: 155 YKK--MDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL-- 210
            ++  + DVRI+RQGFEKRVVSQDLQLWLSNAP   K+FTLLARAGRQVQEIQL+ SL  
Sbjct: 316 LQEEGISDVRISRQGFEKRVVSQDLQLWLSNAPAVDKQFTLLARAGRQVQEIQLTTSLDQ 375

Query: 211 --IRKASKR 217
             I+KA +R
Sbjct: 376 EGIKKALQR 384

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224131510|ref|XP_002321102.1| predicted protein [Populus trichocarpa] gi|222861875|gb|EEE99417.1| predicted protein [Populus trichocarpa]

 Score =  314 bits (805), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 166/250 (66%), Positives = 194/250 (77%), Gaps = 33/250 (13%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPSHSCK+PQK+IHEIAK LTG +ISVKVI A EE +KL+FSEK+AVW+K+S  +NV +
Sbjct: 44  LSPSHSCKDPQKTIHEIAKDLTGLLISVKVIHAEEENRKLIFSEKEAVWSKFSKGINVGE 103

Query: 61  IFVGR-----DYGAFIHLRFPDG-LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 114
           IF GR     DYGAFIH+RFPDG LYHLTGLVHVSEVSWDL+QD+RDILN GDEV VK+I
Sbjct: 104 IFAGRVGSVEDYGAFIHMRFPDGSLYHLTGLVHVSEVSWDLVQDVRDILNVGDEVTVKII 163

Query: 115 KIDREKSRITLSIKQLEEDPLLETLEKVIPQ---------------------GLEPYLKS 153
            ID+ KSRITLSIKQLEEDPLLETL+KVIPQ                     GLE   + 
Sbjct: 164 DIDQGKSRITLSIKQLEEDPLLETLDKVIPQDGSIAPDPLSMHNSITIEPLPGLESIFQE 223

Query: 154 FYKK--MDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL- 210
             ++  +DD+RI+RQGFEKRVVSQDLQLWLSNAPP  +KFTLLARAGRQVQEIQL+ +L 
Sbjct: 224 LTREDGIDDIRISRQGFEKRVVSQDLQLWLSNAPPINRKFTLLARAGRQVQEIQLTTTLD 283

Query: 211 ---IRKASKR 217
              I+KA +R
Sbjct: 284 QGGIKKALQR 293

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147802809|emb|CAN68483.1| hypothetical protein VITISV_006784 [Vitis vinifera]

 Score =  301 bits (771), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 166/277 (59%), Positives = 194/277 (70%), Gaps = 60/277 (21%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPSHSCKEP K+I EIAKGL GS+ISVKVI A+EE +KL+FSEK+A W K+S ++N+ D
Sbjct: 136 LSPSHSCKEPHKTIQEIAKGLIGSLISVKVILADEEKRKLIFSEKEAAWLKFSKQINIGD 195

Query: 61  IF---VG--RDYGAFIHLRFPDG----------LYHLTGLVHVSEVSWDLIQDIRDILNE 105
           IF   VG   DYGAF+HLRFPDG          LYHLTGLVHVSEVSWDL+QD+RD+LNE
Sbjct: 196 IFEAMVGSVEDYGAFVHLRFPDGTSFSVTYITGLYHLTGLVHVSEVSWDLVQDVRDVLNE 255

Query: 106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ-------------------- 145
           GDEVRVK++K+DR KSRITLSIKQLEEDPLLETL+KVIPQ                    
Sbjct: 256 GDEVRVKIVKVDRVKSRITLSIKQLEEDPLLETLDKVIPQIIFLLHRTKSSDVSHLLQDG 315

Query: 146 -------------------GLEPYLKSFYKK--MDDVRITRQGFEKRVVSQDLQLWLSNA 184
                              GLE   +   ++  + DVRI+RQGFEKRVVSQDLQLWLSNA
Sbjct: 316 STGPDSLRTSDSYDIEPLPGLETIFEELLQEEGISDVRISRQGFEKRVVSQDLQLWLSNA 375

Query: 185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKR 217
           P   K+FTLLARAGRQVQEIQL+ SL    I+KA +R
Sbjct: 376 PAVDKQFTLLARAGRQVQEIQLTTSLDQEGIKKALQR 412

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356569689|ref|XP_003553029.1| PREDICTED: 40S ribosomal protein S1-like [Glycine max]

 Score =  301 bits (770), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 162/249 (65%), Positives = 190/249 (76%), Gaps = 32/249 (12%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SP H+ KEP+KSI EIA+GL GSI+SVKVI A+E+ KKL+FSEK+A W+KYS +VNV D
Sbjct: 124 LSPVHASKEPEKSIQEIAQGLIGSIMSVKVILADEDNKKLIFSEKEAAWSKYSKQVNVGD 183

Query: 61  IF---VG--RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           IF   VG   DYGAF+HLRFPDGLYHLTGL+HVSEVSWDLIQD+RDIL  GDEVR KV+ 
Sbjct: 184 IFEVRVGYVEDYGAFVHLRFPDGLYHLTGLIHVSEVSWDLIQDVRDILKVGDEVRAKVVG 243

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQ---------------------GLEPYLKSF 154
           ID  KSRI LSI+QLEEDPLLETL+KVIPQ                     GLE  L+  
Sbjct: 244 IDWGKSRINLSIRQLEEDPLLETLDKVIPQDGSADPDSMSGGDSGSIEPLPGLETILEEL 303

Query: 155 YKK--MDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL-- 210
            ++  + DVRI+RQGFEKRVVSQDLQLWLSNAPP+ ++FTLLARAGRQVQEI L+ SL  
Sbjct: 304 LQEDGIYDVRISRQGFEKRVVSQDLQLWLSNAPPTNQRFTLLARAGRQVQEIHLTTSLDQ 363

Query: 211 --IRKASKR 217
             IR+A +R
Sbjct: 364 EGIRRALQR 372

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449484641|ref|XP_004156938.1| PREDICTED: 30S ribosomal protein S1-like [Cucumis sativus]

 Score =  300 bits (769), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 157/245 (64%), Positives = 184/245 (75%), Gaps = 28/245 (11%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPSHSCKEP KSI +IAK L GS+ISVKVIQA+E+ +KL+FSEK+A  +K+S +V V D
Sbjct: 125 LSPSHSCKEPYKSIQDIAKSLIGSLISVKVIQADEKNRKLIFSEKEAARSKFSGQVAVGD 184

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           ++ G+     DYGAF+HLR  DGLYHLTGLVHVSEVSWDL+QD+RDIL+EGDEV VKVI 
Sbjct: 185 VYEGKVGSVEDYGAFVHLRLSDGLYHLTGLVHVSEVSWDLVQDVRDILSEGDEVTVKVIN 244

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMD---------------- 159
           +++ KSRITLSI+QLEEDPLLETL+KVIPQ       SF  K D                
Sbjct: 245 VNKNKSRITLSIRQLEEDPLLETLDKVIPQDSSAEPDSFGPKGDSEIIPLPGLETIIEEL 304

Query: 160 -------DVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIR 212
                  DVR+ RQGFEKRVVSQDLQLWLSNAPP  KKFTLLARAGRQVQEIQL+ SL +
Sbjct: 305 LQEEGIVDVRVNRQGFEKRVVSQDLQLWLSNAPPVEKKFTLLARAGRQVQEIQLTTSLDQ 364

Query: 213 KASKR 217
           +  KR
Sbjct: 365 EGIKR 369

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468800|ref|XP_004152109.1| PREDICTED: 30S ribosomal protein S1-like [Cucumis sativus]

 Score =  300 bits (767), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 157/245 (64%), Positives = 184/245 (75%), Gaps = 28/245 (11%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPSHSCKEP KSI +IAK L GS+ISVKVIQA+E+ +KL+FSEK+A  +K+S +V V D
Sbjct: 124 LSPSHSCKEPYKSIQDIAKSLIGSLISVKVIQADEKNRKLIFSEKEAARSKFSGQVAVGD 183

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           ++ G+     DYGAF+HLR  DGLYHLTGLVHVSEVSWDL+QD+RDIL+EGDEV VKVI 
Sbjct: 184 VYEGKVGSVEDYGAFVHLRLSDGLYHLTGLVHVSEVSWDLVQDVRDILSEGDEVTVKVIN 243

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMD---------------- 159
           +++ KSRITLSI+QLEEDPLLETL+KVIPQ       SF  K D                
Sbjct: 244 VNKNKSRITLSIRQLEEDPLLETLDKVIPQESSAEPDSFGPKGDSEIIPLPGLETIIEEL 303

Query: 160 -------DVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIR 212
                  DVR+ RQGFEKRVVSQDLQLWLSNAPP  KKFTLLARAGRQVQEIQL+ SL +
Sbjct: 304 LQEEGIVDVRVNRQGFEKRVVSQDLQLWLSNAPPVEKKFTLLARAGRQVQEIQLTTSLDQ 363

Query: 213 KASKR 217
           +  KR
Sbjct: 364 EGIKR 368

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538073|ref|XP_003537529.1| PREDICTED: 30S ribosomal protein S1 homolog [Glycine max]

 Score =  295 bits (756), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 159/249 (63%), Positives = 188/249 (75%), Gaps = 32/249 (12%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SP H+ KEP+KSI EIA+GL GSI+SVKVI A+E+ KKL+FSEK+A W+K+S +VNV D
Sbjct: 129 LSPVHASKEPEKSIQEIAQGLIGSIMSVKVILADEDNKKLIFSEKEAAWSKFSKQVNVGD 188

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           IF  R     DYGAF+HLRFPDGLY LTGL+HVSEVSWDLIQD+RDIL  GDEVRVKV+ 
Sbjct: 189 IFEVRVGYVEDYGAFVHLRFPDGLYRLTGLIHVSEVSWDLIQDVRDILKVGDEVRVKVVG 248

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQ---------------------GLEPYLKSF 154
           ID  KSRI LSI+QLEEDPLLETL+KVIPQ                     GLE  L+  
Sbjct: 249 IDWGKSRINLSIRQLEEDPLLETLDKVIPQDGSADPDSMSGGDSGSIEPLPGLETILEEL 308

Query: 155 YKK--MDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL-- 210
            ++  + DVRI+RQGFEKRVVSQDLQLWL NAPP+ ++FTLLARAGRQVQEI L+ SL  
Sbjct: 309 LQEDGIYDVRISRQGFEKRVVSQDLQLWLCNAPPTNQRFTLLARAGRQVQEIHLTTSLDQ 368

Query: 211 --IRKASKR 217
             I+KA +R
Sbjct: 369 EGIKKALQR 377

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18403854|ref|NP_566737.1| ribosomal protein S1-like RNA-binding domain-containing protein [Arabidopsis thaliana] gi|9293944|dbj|BAB01847.1| unnamed protein product [Arabidopsis thaliana] gi|15146284|gb|AAK83625.1| AT3g23700/MYM9_3 [Arabidopsis thaliana] gi|22655022|gb|AAM98102.1| At3g23700/MYM9_3 [Arabidopsis thaliana] gi|332643282|gb|AEE76803.1| ribosomal protein S1-like RNA-binding domain-containing protein [Arabidopsis thaliana]

 Score =  293 bits (750), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 156/245 (63%), Positives = 180/245 (73%), Gaps = 28/245 (11%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPS SCKEPQKSIHEIAK L GS + VKV+QA+EE +KL+ SEK A+W KYS  VNV D
Sbjct: 138 LSPSRSCKEPQKSIHEIAKTLVGSKLPVKVVQADEENRKLILSEKLALWPKYSQNVNVGD 197

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           +F GR     DYGAFIHLRF DGLYHLTGLVHVSEVSWD +QD+RD+L +GDEVRV V  
Sbjct: 198 VFNGRVGSVEDYGAFIHLRFDDGLYHLTGLVHVSEVSWDYVQDVRDVLRDGDEVRVIVTN 257

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQ---------------------GLEPYLKSF 154
           ID+EKSRITLSIKQLE+DPLLETL+KVI +                     GLE  L+  
Sbjct: 258 IDKEKSRITLSIKQLEDDPLLETLDKVILKDSSTGSPSLSSNNGDTIEPLPGLETILEEL 317

Query: 155 YKK--MDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIR 212
            K+  ++ V+I RQGFEKRVVSQDLQLWLSN PPS  KF LLARAGRQVQEI L+ SL +
Sbjct: 318 LKEDGIEAVKINRQGFEKRVVSQDLQLWLSNTPPSDGKFVLLARAGRQVQEIHLTTSLEQ 377

Query: 213 KASKR 217
              K+
Sbjct: 378 GGIKK 382

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297835412|ref|XP_002885588.1| S1 RNA-binding domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297331428|gb|EFH61847.1| S1 RNA-binding domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  288 bits (738), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 154/245 (62%), Positives = 179/245 (73%), Gaps = 28/245 (11%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPS SCKEPQKSIHEIAK L GS + VKV+QA+EE +KL+ SEK A+W KYS  V+V D
Sbjct: 138 LSPSRSCKEPQKSIHEIAKTLVGSKLPVKVVQADEENRKLILSEKLALWPKYSQNVSVGD 197

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           +F GR     DYGAFIHLRF DGLYHLTGLVHVSEVSWD +QD+RD+L +GDEVRV V  
Sbjct: 198 VFTGRVGSVEDYGAFIHLRFDDGLYHLTGLVHVSEVSWDYVQDVRDVLRDGDEVRVIVTN 257

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQ---------------------GLEPYLKSF 154
           ID+EKSRITLSIKQLE+DPLLETL+KVI +                     GLE  L+  
Sbjct: 258 IDKEKSRITLSIKQLEDDPLLETLDKVILKDSSSGSPSLSSNNGDTIEPLPGLETILEEL 317

Query: 155 YKK--MDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIR 212
            K+  ++ V+I RQGFEKRVVSQDLQLWLSN PPS  KF LLARAGRQVQEI L+  L +
Sbjct: 318 LKEDGIEAVKINRQGFEKRVVSQDLQLWLSNTPPSDGKFVLLARAGRQVQEIHLTTFLEQ 377

Query: 213 KASKR 217
              K+
Sbjct: 378 GGIKK 382

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357462911|ref|XP_003601737.1| Polyribonucleotide nucleotidyltransferase [Medicago truncatula] gi|355490785|gb|AES71988.1| Polyribonucleotide nucleotidyltransferase [Medicago truncatula]

 Score =  277 bits (709), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 148/249 (59%), Positives = 182/249 (73%), Gaps = 32/249 (12%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SP HSC+EP ++I E A+ L G+I+SVKVI  +EE +KLV SEK+A W K+S  +N+ D
Sbjct: 145 LSPVHSCQEPDQTIKERARELIGAILSVKVIIVDEEKRKLVLSEKEASWFKHSKHINIGD 204

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           +F GR     DYGAF+HLRFPDGLYHLTGL+H+SEVSWDL+QD+RD L EG+EVRVKVI 
Sbjct: 205 LFEGRVGSVEDYGAFVHLRFPDGLYHLTGLIHISEVSWDLVQDVRDFLREGEEVRVKVIS 264

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQ---------------------GLEPYLKSF 154
           ID  K R+TLSIKQLEEDPLLETL+KVI Q                     GL+  L+  
Sbjct: 265 IDTVKMRLTLSIKQLEEDPLLETLDKVIRQDGSGVPNSISSTTSSPIDPLPGLDTILEEL 324

Query: 155 YKK--MDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL-- 210
            ++  +++ RI+RQGFEKRVVSQDLQLWLSNAPP  ++FTLLARAGRQVQEI L  SL  
Sbjct: 325 LQEDGINEARISRQGFEKRVVSQDLQLWLSNAPPMDQRFTLLARAGRQVQEIHLKTSLDQ 384

Query: 211 --IRKASKR 217
             I+KA +R
Sbjct: 385 EGIKKAIQR 393

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	234
TAIR|locus:2095203	392	AT3G23700 [Arabidopsis thalian	0.611	0.364	0.736	2.3e-74
TIGR_CMR|NSE_0408	553	NSE_0408 "ribosomal protein S1	0.717	0.303	0.301	1.3e-13
TIGR_CMR|SO_2402	555	SO_2402 "ribosomal protein S1"	0.410	0.172	0.394	7.4e-13
UNIPROTKB|P0AG67	557	rpsA "30S ribosomal subunit pr	0.508	0.213	0.333	1.2e-12
TIGR_CMR|ECH_0402	567	ECH_0402 "putative ribosomal p	0.790	0.326	0.267	1.3e-12
TAIR|locus:2145860	416	RPS1 "ribosomal protein S1" [A	0.5	0.281	0.333	6.2e-12
TIGR_CMR|APH_0273	542	APH_0273 "ribosomal protein S1	0.709	0.306	0.321	1e-11
TIGR_CMR|CPS_2335	553	CPS_2335 "ribosomal protein S1	0.508	0.215	0.326	1.1e-11
UNIPROTKB|Q9KQT3	556	VC_1915 "30S ribosomal protein	0.410	0.172	0.365	3.6e-11
TIGR_CMR|VC_1915	556	VC_1915 "ribosomal protein S1"	0.410	0.172	0.365	3.6e-11

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

 Score = 551 (199.0 bits), Expect = 2.3e-74, Sum P(2) = 2.3e-74
 Identities = 109/148 (73%), Positives = 124/148 (83%)

Query:     1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
             +SPS SCKEPQKSIHEIAK L GS + VKV+QA+EE +KL+ SEK A+W KYS  VNV D
Sbjct:   138 LSPSRSCKEPQKSIHEIAKTLVGSKLPVKVVQADEENRKLILSEKLALWPKYSQNVNVGD 197

Query:    61 IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
             +F GR     DYGAFIHLRF DGLYHLTGLVHVSEVSWD +QD+RD+L +GDEVRV V  
Sbjct:   198 VFNGRVGSVEDYGAFIHLRFDDGLYHLTGLVHVSEVSWDYVQDVRDVLRDGDEVRVIVTN 257

Query:   116 IDREKSRITLSIKQLEEDPLLETLEKVI 143
             ID+EKSRITLSIKQLE+DPLLETL+KVI
Sbjct:   258 IDKEKSRITLSIKQLEDDPLLETLDKVI 285

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

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0005634 "nucleus" evidence=IDA

GO:0009409 "response to cold" evidence=IEP;RCA

GO:0009570 "chloroplast stroma" evidence=IDA

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

GO:0006364 "rRNA processing" evidence=RCA

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

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

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

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0042742 "defense response to bacterium" evidence=RCA

GO:0042793 "transcription from plastid promoter" evidence=RCA

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

 Score = 186 (70.5 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 54/179 (30%), Positives = 90/179 (50%)

Query:    38 KKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92
             +K + +  +A  ++Y S +   DI  GR      YG F+ +   D +  + GL++V+++S
Sbjct:   195 RKALGAVHEAARSEYISTIKEGDIIDGRVKSIASYGVFVQIHESDKVGVVDGLLYVNDIS 254

Query:    93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLK 152
             W  +     I + G EVRVKVI +D EK RI+L +KQL E+P  +  +K  P  + P + 
Sbjct:   255 WARVTHPSSIYSVGQEVRVKVIAVDPEKGRISLGVKQLTENPWKDVSKKYTPGNVYPGVV 314

Query:   153 SFYKKMDD-VRITRQGFEKRVVSQDLQLWLSNAP---PSGKKFTLLARAGRQVQEIQLS 207
             +  +     VR+  +G E  V S ++  W    P   P+ K   +L     +  +I LS
Sbjct:   315 TSVEDYGIFVRL-EEGVEGLVHSGEIS-WTREKPLFLPNSKVNVMLLSVDEEGHKIALS 371

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

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

 Score = 179 (68.1 bits), Expect = 7.4e-13, P = 7.4e-13
 Identities = 41/104 (39%), Positives = 63/104 (60%)

Query:    43 SEKDAVWNKYSSRVNVEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRD 101
             +E+DA+         V+ I     DYGAF+ L   DGL H+T      +++W  ++   +
Sbjct:   180 AERDALLENLQEGQAVKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSE 233

Query:   102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ 145
             I+N GDE+ VKV+K DRE++R++L +KQL EDP LE + K  P+
Sbjct:   234 IVNVGDEINVKVLKYDRERTRVSLGLKQLGEDPWLE-ISKRYPE 276

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

GO:0006412 "translation" evidence=ISS

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

 Score = 177 (67.4 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 46/138 (33%), Positives = 75/138 (54%)

Query:    21 LTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVNVEDIFVG-RDYG 68
             L G  +  KVI+ +++   +V S           E+D +       + V+ I     DYG
Sbjct:   147 LEGKELEFKVIKLDQKRNNVVVSRRAVIESENSAERDQLLENLQEGMEVKGIVKNLTDYG 206

Query:    69 AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
             AF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L +K
Sbjct:   207 AFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSLGLK 260

Query:   129 QLEEDPLLETLEKVIPQG 146
             QL EDP +  + K  P+G
Sbjct:   261 QLGEDPWV-AIAKRYPEG 277

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

GO:0003729 "mRNA binding" evidence=IDA

GO:0016020 "membrane" evidence=IDA

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

GO:0003723 "RNA binding" evidence=IDA

GO:0006412 "translation" evidence=IMP

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

GO:0005737 "cytoplasm" evidence=IDA

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

 Score = 177 (67.4 bits), Expect = 1.3e-12, P = 1.3e-12
 Identities = 53/198 (26%), Positives = 91/198 (45%)

Query:    38 KKLVFSEKDA-VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV 91
             +K +  E  A   + Y S++N  DI  G+      YG FI +     +  + GL+H++++
Sbjct:   209 RKAILEESLADAKSLYLSQLNEGDIIEGKVKSITKYGVFIEIHESPSVGVVDGLLHITDI 268

Query:    92 SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYL 151
             SW  +     + + G  V+ K+IKIDRE  +I+L +KQLEE P    +EK  P  ++   
Sbjct:   269 SWSRVSHPSAVFSCGQTVKTKIIKIDRENKKISLGVKQLEESPW-SNIEKKYP--VDSIH 325

Query:   152 KSFYKKMDDVRI---TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSH 208
             K     +++  +      G E  V   ++  W  N+ P  + F        +V  I  + 
Sbjct:   326 KGIVTSIEEYGVFVELETGIEGLVHVSEVS-WTKNSLPINQLFMRGEEIQVKVLSIDTAK 384

Query:   209 SLIRKASKRHCNEYWNVF 226
             S +  + KR  +  W  F
Sbjct:   385 SRMSLSMKRCQDNPWQAF 402

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

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

 Score = 171 (65.3 bits), Expect = 6.2e-12, P = 6.2e-12
 Identities = 43/129 (33%), Positives = 73/129 (56%)

Query:    11 QKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----R 65
             Q S    A+ L    I +K ++ +EE  KLV S + AV +   +++ +  + +G     +
Sbjct:   217 QISSKAAAEELLEKEIPLKFVEVDEEQTKLVLSNRKAVADS-QAQLGIGSVVLGVVQSLK 275

Query:    66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
              YGAFI +    G+    GL+HVS++S D + DI  +L  GD ++V ++  DR++ R++L
Sbjct:   276 PYGAFIDI---GGI---NGLLHVSQISHDRVSDIATVLQPGDTLKVMILSHDRDRGRVSL 329

Query:   126 SIKQLEEDP 134
             S K+LE  P
Sbjct:   330 STKKLEPTP 338

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

GO:0005739 "mitochondrion" evidence=ISM

GO:0009507 "chloroplast" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

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

GO:0006364 "rRNA processing" evidence=RCA

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

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

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

GO:0034660 "ncRNA metabolic process" evidence=RCA

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

 Score = 171 (65.3 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 62/193 (32%), Positives = 90/193 (46%)

Query:    15 HEIAKGLTGSIISVKVIQANEEMKKLVFSEK---DAVWNKYSSRVNVEDIFVG-----RD 66
             H  A    G  +  K+I+ + E +K+    K   ++ W     R  V  I  G      D
Sbjct:   251 HPSAVFSCGQTVRAKIIRIDRENRKISLGVKQLEESPWANVEERYPVGSIHKGTVTSIED 310

Query:    67 YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-DIRDILNEGDEVRVKVIKIDREKSRITL 125
             YG F+ L    G+    GL+HVSEVSW      +  +   G+E+ VKV+ ID  K+R++L
Sbjct:   311 YGIFVELE--TGV---EGLIHVSEVSWVRSHLPVNQLFMRGEEIEVKVLSIDATKNRMSL 365

Query:   126 SIKQLEEDPLLETLEKVIPQG--LEPYLKS------FYKKMDDVRITRQGFEKRVVSQDL 177
             SIK+ +E+P    +EK  P G  +   +KS      F    DD   T  G E  + S +L
Sbjct:   366 SIKRCKENPWEAFIEKH-PVGSIVNTKVKSIGNLGMFVSLTDDD--TNSGIEGLIRSTEL 422

Query:   178 QLWLSNAPPSGKK 190
               W S +P S  K
Sbjct:   423 S-W-SGSPESALK 433

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

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

 Score = 171 (65.3 bits), Expect = 1.1e-11, P = 1.1e-11
 Identities = 45/138 (32%), Positives = 75/138 (54%)

Query:    21 LTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVNVEDIFVG-RDYG 68
             L G  +  KVI+ +++   +V S           E+D +    +    V+ I     DYG
Sbjct:   147 LEGKPLEFKVIKLDQKRNNVVVSRRAVIEAEGSAERDELLESLAEGQEVKGIVKNLTDYG 206

Query:    69 AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
             AF+ L   DGL H+T      +++W  ++   +I+N GDE++VKV+K DRE++R++L +K
Sbjct:   207 AFVDLGGIDGLLHIT------DMAWKRVKHPSEIVNVGDEIQVKVLKFDRERTRVSLGMK 260

Query:   129 QLEEDPLLETLEKVIPQG 146
             QL EDP +    +  P+G
Sbjct:   261 QLGEDPWVAIANRY-PEG 277

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

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

 Score = 169 (64.5 bits), Expect = 3.6e-11, P = 3.6e-11
 Identities = 38/104 (36%), Positives = 61/104 (58%)

Query:    44 EKDAVWNKYSSRVNVEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDI 102
             E+D +         V+ I     DYGAF+ L   DGL H+T      +++W  ++   +I
Sbjct:   181 ERDELLETLQEGTEVKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEI 234

Query:   103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQG 146
             +N GDE+ VKV+K DR+++R++L +KQL EDP +  + K  P+G
Sbjct:   235 VNVGDEILVKVLKFDRDRTRVSLGLKQLGEDPWV-AIAKRYPEG 277

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

GO:0006412 "translation" evidence=ISS

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

 Score = 169 (64.5 bits), Expect = 3.6e-11, P = 3.6e-11
 Identities = 38/104 (36%), Positives = 61/104 (58%)

Query:    44 EKDAVWNKYSSRVNVEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDI 102
             E+D +         V+ I     DYGAF+ L   DGL H+T      +++W  ++   +I
Sbjct:   181 ERDELLETLQEGTEVKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEI 234

Query:   103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQG 146
             +N GDE+ VKV+K DR+++R++L +KQL EDP +  + K  P+G
Sbjct:   235 VNVGDEILVKVLKFDRDRTRVSLGLKQLGEDPWV-AIAKRYPEG 277

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

GO:0006412 "translation" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00033518001	SubName- Full=Chromosome chr5 scaffold_67, whole genome shotgun sequence; (390 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00033192001	SubName- Full=Chromosome chr5 scaffold_64, whole genome shotgun sequence; (410 aa)			•	•				•	0.459
	GSVIVG00021597001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (488 aa)			•	•					0.442
	GSVIVG00020753001	SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (448 aa)				•					0.430
	GSVIVG00035114001	SubName- Full=Chromosome chr1 scaffold_75, whole genome shotgun sequence; (226 aa)				•					0.426
	GSVIVG00005394001	SubName- Full=Chromosome undetermined scaffold_151, whole genome shotgun sequence; (507 aa)			•	•				•	0.420
	GSVIVG00036212001	SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (397 aa)				•					0.420
	GSVIVG00003851001	SubName- Full=Chromosome chr8 scaffold_150, whole genome shotgun sequence; (518 aa)				•					0.420
	GSVIVG00011932001	SubName- Full=Chromosome undetermined scaffold_2569, whole genome shotgun sequence; (393 aa)				•					0.418
	GSVIVG00037644001	SubName- Full=Chromosome chr9 scaffold_90, whole genome shotgun sequence; (395 aa)				•					0.417
	GSVIVG00023239001	SubName- Full=Chromosome chr8 scaffold_29, whole genome shotgun sequence; (219 aa)				•					0.416

---

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	234
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-20
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	9e-20
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	9e-19
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	1e-18
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	1e-18
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	2e-18
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	3e-18
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	2e-17
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	3e-17
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	2e-16
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	2e-16
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-15
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	2e-15
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	2e-15
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	3e-15
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	4e-15
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	5e-15
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	7e-15
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-14
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	1e-14
pfam00575	74	pfam00575, S1, S1 RNA binding domain	5e-14
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	2e-13
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	4e-13
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	9e-13
PRK05807	136	PRK05807, PRK05807, hypothetical protein; Provisio	1e-12
PRK08582	139	PRK08582, PRK08582, hypothetical protein; Provisio	3e-12
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	7e-12
cd05708	77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	7e-12
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	1e-11
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	2e-11
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	9e-11
PRK03987	262	PRK03987, PRK03987, translation initiation factor	3e-10
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	4e-10
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	5e-10
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	6e-10
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-09
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	1e-09
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	2e-09
cd05691	73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	2e-09
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	3e-09
PRK07252	120	PRK07252, PRK07252, hypothetical protein; Provisio	4e-09
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	6e-09
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	9e-08
cd04461	83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	2e-07
cd05690	69	cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: R	2e-07
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	7e-07
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	2e-06
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	4e-06
cd05689	72	cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: R	4e-06
cd05686	73	cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-b	1e-05
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	2e-05
cd05698	70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	2e-05
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	4e-05
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	2e-04

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

 Score = 88.7 bits (221), Expect = 2e-20
 Identities = 40/126 (31%), Positives = 67/126 (53%), Gaps = 18/126 (14%)

Query: 21  LTGSIISVKVIQANEEMKKLVFS-------EKDAVWNKYSSRVNVEDIFVGR-----DYG 68
           L G  +  KVI+ +++   +V S       E+     +    +    +  G      DYG
Sbjct: 157 LEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYG 216

Query: 69  AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
           AF+       L  + GL+H++++SW  +    +++N GDEV+VKV+K D+EK R++L +K
Sbjct: 217 AFV------DLGGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK 270

Query: 129 QLEEDP 134
           QL EDP
Sbjct: 271 QLGEDP 276

Length = 565

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

 Score = 87.1 bits (217), Expect = 9e-20
 Identities = 41/118 (34%), Positives = 64/118 (54%), Gaps = 14/118 (11%)

Query: 26  ISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPD 77
           + VKV++ ++E K++    K      W     +  V     G+     DYGAF+ L   +
Sbjct: 251 VKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELE--E 308

Query: 78  GLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
           G+    GLVHVSE+SW    +    +++ G EV V V++ID EK RI+L +KQ +E+P
Sbjct: 309 GI---EGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENP 363

Length = 565

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

 Score = 83.4 bits (207), Expect = 9e-19
 Identities = 41/140 (29%), Positives = 72/140 (51%), Gaps = 27/140 (19%)

Query: 23  GSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVNVEDIFVG-----RD 66
           G  + VK+I+ + E  +++ S           +K+ +     S +   D+  G      D
Sbjct: 150 GKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELL----SSLKEGDVVEGTVARLTD 205

Query: 67  YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
           +GAF+ +   DGL      VH+SE+S + ++   ++++ G EV VKV+ ID E  RI+LS
Sbjct: 206 FGAFVDIGGVDGL------VHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLS 259

Query: 127 IKQLEEDPLLETLEKVIPQG 146
           +K     P  E +E+ +P+G
Sbjct: 260 LKDTLPGP-WEGVEEKLPEG 278

Length = 390

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

 Score = 84.2 bits (209), Expect = 1e-18
 Identities = 38/125 (30%), Positives = 69/125 (55%), Gaps = 19/125 (15%)

Query: 23  GSIISVKVIQANEEMKK--------LVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGA 69
           G  + VK+I+ N + +K        ++  EK+    +  + +   D+  G      D+GA
Sbjct: 434 GQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGA 493

Query: 70  FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129
           F+ +    G+    GL+HVSE+SW  ++   D+L  GDE++V ++ ID+E  +++LS+K+
Sbjct: 494 FVDI---GGV---DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK 547

Query: 130 LEEDP 134
           L  DP
Sbjct: 548 LLPDP 552

Length = 647

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

 Score = 83.5 bits (207), Expect = 1e-18
 Identities = 41/135 (30%), Positives = 72/135 (53%), Gaps = 26/135 (19%)

Query: 23  GSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVNVEDIFVGR-----D 66
           G  +  K+++ +++   +V S           +++ + NK      V ++  G      D
Sbjct: 150 GKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKL----EVGEVVEGVVKNITD 205

Query: 67  YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
           YGAF+ +        + GL+H+SE+SW  +    +++  GDEV+VKVI +D E+ R++LS
Sbjct: 206 YGAFVDI------GGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLS 259

Query: 127 IKQLEEDPLLETLEK 141
           +KQLEEDP     +K
Sbjct: 260 LKQLEEDPWEGIEKK 274

Length = 541

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

 Score = 83.1 bits (206), Expect = 2e-18
 Identities = 48/132 (36%), Positives = 68/132 (51%), Gaps = 14/132 (10%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  + VKVI  +EE  ++  S K      W     +  V D   G+     DYGAF+ + 
Sbjct: 239 GDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIE 298

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
             +G+    GLVHVSE+SW       +++  G EV VKV+ ID E+ RI+L +KQL+E+P
Sbjct: 299 --EGV---EGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENP 353

Query: 135 LLETLEKVIPQG 146
             E      P G
Sbjct: 354 -WEEFADKHPVG 364

Length = 541

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

 Score = 82.5 bits (205), Expect = 3e-18
 Identities = 45/130 (34%), Positives = 73/130 (56%), Gaps = 14/130 (10%)

Query: 22  TGSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHL 73
            G  + V V++ +EE +++    K      W +++ +  V D+  G+     D+GAF+  
Sbjct: 334 VGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFV-- 391

Query: 74  RFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 132
               G+    GLVH+S++SWD   ++  ++  +GDEV   V+K+D EK RI+L IKQLEE
Sbjct: 392 GLEGGI---DGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEE 448

Query: 133 DPLLETLEKV 142
           DP  E  +K 
Sbjct: 449 DPFEEFAKKH 458

Length = 565

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

 Score = 80.8 bits (200), Expect = 2e-17
 Identities = 44/120 (36%), Positives = 70/120 (58%), Gaps = 13/120 (10%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  I V ++  ++E KKL  S K  +   W     +  V  I +G+      +GAF+ L 
Sbjct: 524 GDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELE 583

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
              G+    GLVH+S++SW  I    D+L+EG+EV+ K++++D E+ RI LSIK++EE+P
Sbjct: 584 --PGV---DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP 638

Length = 647

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

 Score = 79.1 bits (196), Expect = 3e-17
 Identities = 42/120 (35%), Positives = 68/120 (56%), Gaps = 13/120 (10%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  + VKV+  + E +++  S KD +   W     ++   D+  G      D+GAF+ + 
Sbjct: 239 GQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEV- 297

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
              G+    GLVH+S++S   I    ++L EG EV+VKV++++ E+ RI+LSIK LEE P
Sbjct: 298 -LPGV---EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAP 353

Length = 390

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

 Score = 77.3 bits (191), Expect = 2e-16
 Identities = 46/128 (35%), Positives = 71/128 (55%), Gaps = 13/128 (10%)

Query: 22  TGSIISVKVIQANEEMKKLVFSEKDAVWN---KYSSRVNVEDIFVGR-----DYGAFIHL 73
            G  + VKV+  + E +++    K    N   +++ +  V D+  G+     D+GAF+ L
Sbjct: 324 VGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAFVEL 383

Query: 74  RFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 133
               G+    GLVH+S++SWD   +  +   +GDEV  KV+ +D+EK RI+L IKQLEE 
Sbjct: 384 --EGGI---DGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEES 438

Query: 134 PLLETLEK 141
           P  E  EK
Sbjct: 439 PWEEFSEK 446

Length = 541

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

 Score = 76.4 bits (188), Expect = 2e-16
 Identities = 42/127 (33%), Positives = 74/127 (58%), Gaps = 11/127 (8%)

Query: 13  SIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDY 67
           S  +  + L G  + +K ++ +EE  +LV S + A+  +  +R+ V ++ VG     + Y
Sbjct: 151 STRKPKEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPY 210

Query: 68  GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127
           GAFI +        ++GL+H+SE+S + I+    + N  DE++V +I +D E+ RI+LS 
Sbjct: 211 GAFIDIG------GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLST 264

Query: 128 KQLEEDP 134
           KQLE +P
Sbjct: 265 KQLEPEP 271

Length = 318

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

 Score = 75.2 bits (185), Expect = 1e-15
 Identities = 42/128 (32%), Positives = 66/128 (51%), Gaps = 14/128 (10%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  + VKVI+ ++E  ++  S K      W     +  V D   GR     DYG F+ + 
Sbjct: 234 GQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIE 293

Query: 75  FPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 133
             +G+    GLVHVSE+SW         ++ +GDEV V ++ ID E+ R++L +KQ + +
Sbjct: 294 --EGI---EGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKAN 348

Query: 134 PLLETLEK 141
           P  +  EK
Sbjct: 349 PWEQFEEK 356

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

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

 Score = 74.7 bits (185), Expect = 2e-15
 Identities = 32/83 (38%), Positives = 52/83 (62%), Gaps = 15/83 (18%)

Query: 56  VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
             V +I+ G+     D+GAF+ +  P  DGL      VH+SE++ + ++ + D+L EGDE
Sbjct: 619 PEVGEIYEGKVVRIVDFGAFVEI-LPGKDGL------VHISEIADERVEKVEDVLKEGDE 671

Query: 109 VRVKVIKIDREKSRITLSIKQLE 131
           V+VKV++ID ++ RI LS K + 
Sbjct: 672 VKVKVLEID-KRGRIRLSRKAVL 693

Length = 693

>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated

 Score = 69.7 bits (171), Expect = 2e-15
 Identities = 33/70 (47%), Positives = 47/70 (67%), Gaps = 5/70 (7%)

Query: 65  RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           + YGAF+ L   D      GLVH+SE++   ++DI D L+ GDEV+VKV+ +D EK +I+
Sbjct: 19  QPYGAFVAL---DE--ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKIS 73

Query: 125 LSIKQLEEDP 134
           LSI+  EE P
Sbjct: 74  LSIRATEEAP 83

Length = 123

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

 Score = 68.0 bits (167), Expect = 3e-15
 Identities = 27/61 (44%), Positives = 42/61 (68%), Gaps = 6/61 (9%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           D+GAF+ L   DGL      +H+S++SW  ++   +++N GDEV VKV+KID+E+ RI+L
Sbjct: 14  DFGAFVDLGGVDGL------LHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67

Query: 126 S 126
            
Sbjct: 68  G 68

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

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

 Score = 73.7 bits (182), Expect = 4e-15
 Identities = 39/119 (32%), Positives = 62/119 (52%), Gaps = 13/119 (10%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  +   V++ + E +++    K      + +++ +     I  G      D GAF+ L 
Sbjct: 422 GDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKDKGAFVEL- 480

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 133
             DG+    GL+  SE+S D ++D  ++L  GDEV  KVI IDR+  RI+LSIK L+E 
Sbjct: 481 -EDGV---EGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEA 535

Length = 565

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

 Score = 68.9 bits (169), Expect = 5e-15
 Identities = 33/69 (47%), Positives = 46/69 (66%), Gaps = 6/69 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
            YGAF+      G    TGLVH+SE++   ++DI D L  G EV+VKV+ ID E  +I+L
Sbjct: 18  PYGAFV--ELEGGK---TGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDID-ENGKISL 71

Query: 126 SIKQLEEDP 134
           SI++LEE+P
Sbjct: 72  SIRKLEEEP 80

Length = 129

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

 Score = 72.8 bits (179), Expect = 7e-15
 Identities = 41/135 (30%), Positives = 62/135 (45%), Gaps = 21/135 (15%)

Query: 16  EIAKGLTGSIISVKVIQANEEMKKLVFS-------EKDAVWNKYSSRVNVEDIFVGR--- 65
           E  +   G      + +  E  + +V S       E+      +   V   D+  G    
Sbjct: 153 EDPESYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTR 212

Query: 66  --DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS-- 121
              +GAF+ L  P     + G+VH+SE+SW  +Q   + ++ GD VRVKV+ I+R K   
Sbjct: 213 LAPFGAFVELA-PG----VEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGK 267

Query: 122 --RITLSIKQLEEDP 134
             RI+LSIKQ   DP
Sbjct: 268 GLRISLSIKQAGGDP 282

Length = 491

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

 Score = 72.1 bits (177), Expect = 1e-14
 Identities = 33/76 (43%), Positives = 49/76 (64%), Gaps = 6/76 (7%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           D+GAF+ L   DGL      +H++++SW  ++   + +  G EV+VKVIK D+EK RI+L
Sbjct: 200 DFGAFVDLGGVDGL------LHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISL 253

Query: 126 SIKQLEEDPLLETLEK 141
           S+KQL EDP     +K
Sbjct: 254 SLKQLGEDPWEAIEKK 269

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

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

 Score = 66.2 bits (162), Expect = 1e-14
 Identities = 28/63 (44%), Positives = 45/63 (71%), Gaps = 6/63 (9%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
            +GAF+ L    G+   +GLVH+S+++   ++D++D+L EGD+V+VKV+ ID    RI+L
Sbjct: 13  PFGAFVEL--GGGI---SGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG-RISL 66

Query: 126 SIK 128
           SIK
Sbjct: 67  SIK 69

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

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

 Score = 64.6 bits (158), Expect = 5e-14
 Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 10/79 (12%)

Query: 55  RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEV 109
           +    D+  G        GAF+ L        + G + +SE+S D ++D  ++L  GDEV
Sbjct: 1   KPEEGDVVKGTVTRVTKGGAFVDL-----GNGVEGFIPISEISDDRVEDPDEVLKVGDEV 55

Query: 110 RVKVIKIDREKSRITLSIK 128
            VKV+K+D+E+ RI LSI+
Sbjct: 56  EVKVLKVDKERGRIILSIR 74

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

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

 Score = 68.4 bits (168), Expect = 2e-13
 Identities = 34/82 (41%), Positives = 53/82 (64%), Gaps = 11/82 (13%)

Query: 56  VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVR 110
           V V +++ G      D+GAF+ L  P       GLVH+S+++ + ++ + D+L EGDEV+
Sbjct: 617 VEVGEVYEGTVVRIVDFGAFVEL-LPGK----DGLVHISQLAKERVEKVEDVLKEGDEVK 671

Query: 111 VKVIKIDREKSRITLSIKQLEE 132
           VKVI+ID ++ RI LSIK + E
Sbjct: 672 VKVIEID-KQGRIRLSIKAVLE 692

Length = 692

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

 Score = 67.4 bits (165), Expect = 4e-13
 Identities = 39/121 (32%), Positives = 64/121 (52%), Gaps = 14/121 (11%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  + V ++  + E ++L    K      W ++  +  V D   G+     D+GAF+ L 
Sbjct: 321 GDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELE 380

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNE-GDEVRVKVIKIDREKSRITLSIKQLEED 133
              G+    GL+H+S++SWD      D L + GDE+   V+ +D+EK RI+L +KQL E+
Sbjct: 381 --GGI---DGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTEN 435

Query: 134 P 134
           P
Sbjct: 436 P 436

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

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

 Score = 61.1 bits (149), Expect = 9e-13
 Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 10/77 (12%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
            V D+  G        GAF+ L        + GL+ +SE+S   ++D  ++L  GDEV+V
Sbjct: 1   EVGDVVEGTVTEITPGGAFVDL-----GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKV 55

Query: 112 KVIKIDREKSRITLSIK 128
           KV+ +D EK RI LS+K
Sbjct: 56  KVLSVDEEKGRIILSLK 72

Length = 72

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

 Score = 62.8 bits (153), Expect = 1e-12
 Identities = 31/68 (45%), Positives = 47/68 (69%), Gaps = 7/68 (10%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           ++GAF+ +   +G    TGLVH+SEV+   ++DIR+ L E D+V+VKVI ID +  +I+L
Sbjct: 18  NFGAFVEV---EGK---TGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISL 70

Query: 126 SIKQLEED 133
           SIKQ  + 
Sbjct: 71  SIKQAMKQ 78

Length = 136

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

 Score = 61.6 bits (150), Expect = 3e-12
 Identities = 31/69 (44%), Positives = 48/69 (69%), Gaps = 6/69 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           ++GAF+ L  P+G    TGLVH+SEV+ + ++DI D L  GDEV VKV+ ++ +  +I L
Sbjct: 18  NFGAFVEL--PEGK---TGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDD-GKIGL 71

Query: 126 SIKQLEEDP 134
           SIK+ ++ P
Sbjct: 72  SIKKAKDRP 80

Length = 139

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

 Score = 64.0 bits (156), Expect = 7e-12
 Identities = 44/135 (32%), Positives = 67/135 (49%), Gaps = 18/135 (13%)

Query: 23  GSIISVKV--IQANEEMK--KLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAF 70
           G  + VKV  I+  ++ K  ++  S K A    W+    R+   D   G+      +GAF
Sbjct: 250 GDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAF 309

Query: 71  IHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129
           + +     L  + GLVHVSE+SW   +    D++  GD V VK+  ID  K RI+LS++ 
Sbjct: 310 VEI-----LPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRD 364

Query: 130 LEEDPLLETLEKVIP 144
            E DP  +  E+  P
Sbjct: 365 AEGDPWADVAERFAP 379

Length = 491

>gnl|CDD|240213 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

 Score = 58.9 bits (143), Expect = 7e-12
 Identities = 29/63 (46%), Positives = 41/63 (65%), Gaps = 4/63 (6%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYG FI +   DG  +++GL H SE+S + + D   +   GD+VR KV+KID EK RI+L
Sbjct: 15  DYGVFIDI---DGT-NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISL 70

Query: 126 SIK 128
            +K
Sbjct: 71  GLK 73

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

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

 Score = 63.3 bits (155), Expect = 1e-11
 Identities = 30/79 (37%), Positives = 49/79 (62%), Gaps = 15/79 (18%)

Query: 54  SRVNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEG 106
           +   V  I+ G+     D+GAF+ +  P  DGL      VH+SE++ + ++ + D+L EG
Sbjct: 614 AEPEVGKIYEGKVVRIMDFGAFVEI-LPGKDGL------VHISEIANERVEKVEDVLKEG 666

Query: 107 DEVRVKVIKIDREKSRITL 125
           DEV+VKV++ID+ + RI L
Sbjct: 667 DEVKVKVLEIDK-QGRIKL 684

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

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

 Score = 57.4 bits (139), Expect = 2e-11
 Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 5/61 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
            +G F+ L        + GLVH+SE+S   ++D  ++   GDEV VKV+++D EK RI+L
Sbjct: 10  KFGVFVEL-----EDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64

Query: 126 S 126
           S
Sbjct: 65  S 65

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

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

 Score = 55.6 bits (135), Expect = 9e-11
 Identities = 29/73 (39%), Positives = 47/73 (64%), Gaps = 11/73 (15%)

Query: 60  DIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 114
            I+ G+     D+GAF+ +  P       GLVH+SE+S + ++ + D+L  GDEV+VKVI
Sbjct: 2   KIYEGKVVKIKDFGAFVEI-LPGK----DGLVHISELSDERVEKVEDVLKVGDEVKVKVI 56

Query: 115 KIDREKSRITLSI 127
           ++D ++ RI+LS 
Sbjct: 57  EVD-DRGRISLSR 68

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo. Length = 68

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

 Score = 57.9 bits (141), Expect = 3e-10
 Identities = 28/78 (35%), Positives = 47/78 (60%), Gaps = 8/78 (10%)

Query: 57  NVEDIFVGRDYGAFIHL-RFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
            V+++    D+GAF+ L  +P       G +H+SEV+   +++IRD + EG +V  KVI+
Sbjct: 15  TVKEVK---DFGAFVTLDEYPG----KEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIR 67

Query: 116 IDREKSRITLSIKQLEED 133
           +D  K  I LS+K++ E 
Sbjct: 68  VDPRKGHIDLSLKRVNEH 85

Length = 262

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

 Score = 58.5 bits (142), Expect = 4e-10
 Identities = 32/82 (39%), Positives = 47/82 (57%), Gaps = 15/82 (18%)

Query: 53  SSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVK 112
           SS VN         +GAF+ L   DGL      VHVSE+SW  I    +++  G EV V+
Sbjct: 217 SSIVN---------FGAFVDLGGVDGL------VHVSELSWKHIDHPSEVVEVGQEVTVE 261

Query: 113 VIKIDREKSRITLSIKQLEEDP 134
           V+ +D ++ R++LS+K  +EDP
Sbjct: 262 VLDVDMDRERVSLSLKATQEDP 283

Length = 486

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

 Score = 53.8 bits (130), Expect = 5e-10
 Identities = 24/61 (39%), Positives = 39/61 (63%), Gaps = 5/61 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           D+GAF+ +    G+    GL+H+S+++   +    D+++ GD V VKVI ID E+ RI+L
Sbjct: 13  DFGAFVDI----GV-KQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISL 67

Query: 126 S 126
           S
Sbjct: 68  S 68

The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea. Length = 68

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

 Score = 58.2 bits (140), Expect = 6e-10
 Identities = 58/221 (26%), Positives = 98/221 (44%), Gaps = 31/221 (14%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  I +KVI+ ++  K++  S K      W ++ ++  V D+  GR     D+GAFI L 
Sbjct: 540 GQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIEL- 598

Query: 75  FPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 133
             +G+    GL H+SE SW        D++  GDEV   ++  D +  R++L +KQ+  +
Sbjct: 599 -AEGI---EGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTAN 654

Query: 134 PLLETLEKVIPQGLEPYLKSFYKKMDDVRIT--------RQGFEKRVVSQDLQLWLSNAP 185
           P  E +E   P G       F +++  V++T         +G +  +   DL  W+    
Sbjct: 655 P-WEEIEARYPVG-----ARFTRRI--VKVTNAGAFIEMEEGIDGFLHVDDLS-WVKRTR 705

Query: 186 PSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVF 226
           P+  +  +       V E       IR   K+  +  W VF
Sbjct: 706 PADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVF 746

Length = 863

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

 Score = 57.4 bits (139), Expect = 1e-09
 Identities = 34/114 (29%), Positives = 60/114 (52%), Gaps = 13/114 (11%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVG-----RDYGAFIHLR 74
           G  I   V+  ++E K++    K      W K++++  V  +  G     +D+GAF+   
Sbjct: 408 GDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFV--E 465

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
            P G+    GL+  SE+S +  +D  D +  GDEV  KV+ ID++  +++LS+K
Sbjct: 466 LPGGV---EGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516

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

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

 Score = 56.9 bits (138), Expect = 1e-09
 Identities = 26/86 (30%), Positives = 50/86 (58%), Gaps = 6/86 (6%)

Query: 56  VNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
             V+ +    DYGA++ L    G     G +H+SEV+   +++IRD + EG +V  KV++
Sbjct: 17  GTVKQVA---DYGAYVELDEYPGK---EGFIHISEVASGWVKNIRDYVKEGQKVVAKVLR 70

Query: 116 IDREKSRITLSIKQLEEDPLLETLEK 141
           +D ++  I LS+K++ E    + +++
Sbjct: 71  VDPKRGHIDLSLKRVTEHQRRKKIQE 96

Length = 269

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

 Score = 57.0 bits (138), Expect = 2e-09
 Identities = 29/67 (43%), Positives = 43/67 (64%), Gaps = 5/67 (7%)

Query: 67  YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
           +GAF+  R  +G+    GLVH+SE++   ++    ++  GDEV VKVI ID E+ RI+LS
Sbjct: 307 FGAFV--RVEEGI---EGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLS 361

Query: 127 IKQLEED 133
           +KQ  E 
Sbjct: 362 LKQANEG 368

Length = 486

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

 Score = 51.9 bits (125), Expect = 2e-09
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 81  HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131
            + G +  +E+S D ++D  +    GDEV  K+  +DR+  +I+LSIK  E
Sbjct: 23  GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE 73

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

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

 Score = 51.8 bits (125), Expect = 3e-09
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 8/75 (10%)

Query: 56  VNVEDIFVGRDYGAFIHL-RFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 114
           V V+ I    D GA++ L  + +    + G++ +SE+S   I+ IR ++  G +  VKVI
Sbjct: 9   VTVKSIA---DMGAYVSLLEYGN----IEGMILLSELSRRRIRSIRKLVKVGRKEVVKVI 61

Query: 115 KIDREKSRITLSIKQ 129
           ++D+EK  I LS K+
Sbjct: 62  RVDKEKGYIDLSKKR 76

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

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

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 25/67 (37%), Positives = 39/67 (58%), Gaps = 5/67 (7%)

Query: 67  YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
           YGAF+ L         TGL+H+SE+    I +I  +L  G+EV V+V+  D    + +LS
Sbjct: 17  YGAFVALENGT-----TGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLS 71

Query: 127 IKQLEED 133
           ++ LEE+
Sbjct: 72  LRTLEEE 78

Length = 120

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

 Score = 55.5 bits (133), Expect = 6e-09
 Identities = 31/92 (33%), Positives = 53/92 (57%), Gaps = 11/92 (11%)

Query: 51  KYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNE 105
           ++ + V++ED   G       +GAFI L   DGL      +HV+++SW  +   R+ + +
Sbjct: 486 EFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGL------LHVNDMSWGHVARPREFVKK 539

Query: 106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLE 137
           G  + +KVI++D+ + RI LS+K  + DP LE
Sbjct: 540 GQTIELKVIRLDQAEKRINLSLKHFQPDPWLE 571

Length = 863

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

 Score = 48.0 bits (115), Expect = 9e-08
 Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 5/64 (7%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           D+G F+ L    G     GLVH+S++S++  + +  D++  G +V+VKVI I   K  I+
Sbjct: 13  DFGCFVQLEGLKG--RKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGK--IS 68

Query: 125 LSIK 128
           LS+K
Sbjct: 69  LSMK 72

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

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 5/62 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
            YG F+   F      LTGL   S +S + + D      +G  V  KV  +D EK R  L
Sbjct: 27  PYGVFV--EFL---GGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLL 81

Query: 126 SI 127
           S+
Sbjct: 82  SL 83

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

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

 Score = 46.7 bits (111), Expect = 2e-07
 Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 6/61 (9%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           D+G F+ L    G+    GLVH+S++SW   ++   +I  +G EV   V+ ID E+ RI+
Sbjct: 13  DFGIFVGL--DGGI---DGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERIS 67

Query: 125 L 125
           L
Sbjct: 68  L 68

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

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

 Score = 48.8 bits (117), Expect = 7e-07
 Identities = 38/129 (29%), Positives = 60/129 (46%), Gaps = 20/129 (15%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVG-----RDYGAFIHLR 74
           G  +  KV+  ++E +++    K      W ++S +     +  G     +D GAF+   
Sbjct: 411 GDEVEAKVLAVDKEKERISLGIKQLEESPWEEFSEKYKKGSVVKGKVKSVKDKGAFV--E 468

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
              G+    GL+ +SE+S       RD+L  GDEV   V+ ID++  +I LSIK LE   
Sbjct: 469 LGGGV---EGLIRLSELS-------RDVLKVGDEVEAVVVSIDKKNRKILLSIKALERKE 518

Query: 135 LLETLEKVI 143
             E LE   
Sbjct: 519 EKEALESYN 527

Length = 541

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

 Score = 47.6 bits (114), Expect = 2e-06
 Identities = 27/67 (40%), Positives = 45/67 (67%), Gaps = 5/67 (7%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           D+GAF+ +    G+ H  GLVH+S++S   ++D  +++  GD V+VKVI++D  + RI L
Sbjct: 671 DFGAFVDI----GV-HQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIAL 725

Query: 126 SIKQLEE 132
           S++  EE
Sbjct: 726 SMRLDEE 732

Length = 780

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

 Score = 46.9 bits (112), Expect = 4e-06
 Identities = 17/59 (28%), Positives = 36/59 (61%)

Query: 83  TGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK 141
            G++ + E++ D I  +++ +  GDE+ VKV+K++ E   + LS K+ + +   + LE+
Sbjct: 327 EGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEE 385

Length = 647

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

 Score = 43.3 bits (102), Expect = 4e-06
 Identities = 27/62 (43%), Positives = 39/62 (62%), Gaps = 8/62 (12%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR--DILNEGDEVRVKVIKIDREKSRI 123
           DYG F+ L   +G+    GLVHVSE+ W   ++I    +++ GDEV V V+ ID E+ RI
Sbjct: 16  DYGCFVELE--EGV---EGLVHVSEMDWT-NKNIHPSKVVSLGDEVEVMVLDIDEERRRI 69

Query: 124 TL 125
           +L
Sbjct: 70  SL 71

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

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

 Score = 41.7 bits (98), Expect = 1e-05
 Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 5/63 (7%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           +YGAF+ +    G     GLVH S +S   + D  ++++ G++V VKVI  +  K ++ L
Sbjct: 16  EYGAFVKI---PG-CRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE-MKDKMKL 70

Query: 126 SIK 128
           S+ 
Sbjct: 71  SLS 73

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

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

 Score = 44.5 bits (106), Expect = 2e-05
 Identities = 21/58 (36%), Positives = 39/58 (67%)

Query: 84  GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK 141
           G++ +SE+S D I+DI D++  GDE+ V V+K++  +  + LS ++LE +   + LE+
Sbjct: 44  GVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEE 101

Length = 390

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 65  RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           +  G  +   F + +    G +  SE+S   I+D  +    G  V+VKV+  D E+ R+ 
Sbjct: 12  KPNGCIV--SFYNNV---KGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLL 66

Query: 125 LSIK 128
           LS K
Sbjct: 67  LSCK 70

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

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

 Score = 40.2 bits (95), Expect = 4e-05
 Identities = 16/45 (35%), Positives = 29/45 (64%)

Query: 84  GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
           G++ +SE S D I++  D +  GDEV V V++++ E+  + LS +
Sbjct: 26  GIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70

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

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

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 30/136 (22%), Positives = 57/136 (41%), Gaps = 14/136 (10%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-DYGAFIHLR 74
           G  ++VK+   +   +++  S +DA       V  +++    V      R  +G F++L 
Sbjct: 341 GDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLA 400

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE-ED 133
            P     +TGL+  S +S        + L  GD V + V +ID  K +I+L+        
Sbjct: 401 -PG----VTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGAAGSG 455

Query: 134 PLLETLEKVIPQGLEP 149
              +  ++  P+   P
Sbjct: 456 ADDDDWKQFAPKKSAP 471

Length = 491

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	234
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.97
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.97
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.97
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.97
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.97
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.96
PRK07400	318	30S ribosomal protein S1; Reviewed	99.96
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.95
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.95
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.93
PRK07400	318	30S ribosomal protein S1; Reviewed	99.85
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.71
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.7
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.56
PRK08582	139	hypothetical protein; Provisional	99.56
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.5
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.5
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.49
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.48
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.48
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.47
PHA02945	88	interferon resistance protein; Provisional	99.45
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.45
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.45
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.44
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.44
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.42
PRK07252	120	hypothetical protein; Provisional	99.42
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.41
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.41
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.4
PRK08059	123	general stress protein 13; Validated	99.39
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.39
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.39
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.36
PRK05807	136	hypothetical protein; Provisional	99.36
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.36
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.36
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.35
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.34
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.31
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.31
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.3
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.29
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.24
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.22
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.21
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.2
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.2
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.19
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.18
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.18
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.17
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.15
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.12
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.11
PRK08582	139	hypothetical protein; Provisional	99.09
COG2183	780	Tex Transcriptional accessory protein [Transcripti	99.07
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	99.06
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.04
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.03
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	99.0
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.99
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.94
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.89
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.88
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.87
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.85
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	98.84
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	98.84
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	98.75
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	98.7
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	98.69
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.69
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.69
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.65
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.65
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	98.64
PRK05807	136	hypothetical protein; Provisional	98.63
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.62
PRK07252	120	hypothetical protein; Provisional	98.62
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.61
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.59
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	98.58
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.56
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.56
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	98.56
PRK08059	123	general stress protein 13; Validated	98.55
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.54
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	98.54
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.53
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.53
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	98.52
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.49
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.48
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.44
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.43
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.4
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.4
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	98.39
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.35
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.34
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	98.33
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.32
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.32
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	98.29
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	98.26
PRK11642	813	exoribonuclease R; Provisional	98.25
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.25
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.22
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.22
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.22
TIGR01953	341	NusA transcription termination factor NusA. This m	98.22
PHA02945	88	interferon resistance protein; Provisional	98.21
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.12
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.11
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.09
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.08
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.07
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	98.06
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	98.04
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.0
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	97.96
KOG2916	304	consensus Translation initiation factor 2, alpha s	97.96
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	97.92
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	97.88
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	97.83
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	97.72
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	97.61
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	97.57
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.5
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.41
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.39
PRK05054	644	exoribonuclease II; Provisional	97.36
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	97.31
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	97.24
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.22
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	97.22
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	97.2
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	97.09
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	96.95
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	96.85
COG0557	706	VacB Exoribonuclease R [Transcription]	96.82
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	96.78
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	96.78
COG2183	780	Tex Transcriptional accessory protein [Transcripti	96.77
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	96.69
PRK11642	813	exoribonuclease R; Provisional	96.48
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	96.47
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	96.39
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	96.38
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.2
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.16
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	96.11
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.04
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	96.02
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	95.7
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	95.39
KOG2916	304	consensus Translation initiation factor 2, alpha s	95.29
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	94.74
PRK11712	489	ribonuclease G; Provisional	94.74
PRK10811	1068	rne ribonuclease E; Reviewed	94.72
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	94.69
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.09
PRK12327	362	nusA transcription elongation factor NusA; Provisi	93.72
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	93.51
TIGR01953	341	NusA transcription termination factor NusA. This m	93.04
PRK05054	644	exoribonuclease II; Provisional	91.09
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	88.98
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	87.92
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	87.07
COG0557	706	VacB Exoribonuclease R [Transcription]	86.03
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	85.85
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	84.4
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	82.76
COG4044	247	Uncharacterized protein conserved in archaea [Func	80.77

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

Probab=100.00  E-value=1.5e-42  Score=324.43  Aligned_cols=195  Identities=26%  Similarity=0.488  Sum_probs=176.5

Q ss_pred             hhcccCCCCEEEEEEEEEeCCCCEEEEEechhh-------HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeE
Q 026737           16 EIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLT   83 (234)
Q Consensus        16 ~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~~-------~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~   83 (234)
                      +++.+++|+++.|+|+++|.+++++++|+|...       .+.+++++++|+++.|+     +|||||+|+      |++
T Consensus       143 ~d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdig------Gvd  216 (541)
T COG0539         143 RDLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIG------GVD  216 (541)
T ss_pred             ccccccCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEec------Cee
Confidence            345678999999999999999999999999752       45678999999999999     999999997      699


Q ss_pred             EEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceee
Q 026737           84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLK  152 (234)
Q Consensus        84 glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV  152 (234)
                      ||+|++++||.++.+|.++|++||+|+|+|+++|++++|++||+|++.++||.....+ ++.|..           ||||
T Consensus       217 GLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~-~~~g~~v~G~Vt~i~~~GafV  295 (541)
T COG0539         217 GLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKK-YPVGDKVEGKVTNLTDYGAFV  295 (541)
T ss_pred             eEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhh-cCCCCEEEEEEEEeecCcEEE
Confidence            9999999999999999999999999999999999999999999999999999866555 777631           9999


Q ss_pred             eecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHH
Q 026737          153 SFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFH  227 (234)
Q Consensus       153 ~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~  227 (234)
                      ++.+|++||+ +|++            +|....     .++.++++||.|+|+||++|+    ||||+||+.+|||+.|+
T Consensus       296 ei~~GvEGlvhvSEi------------sw~~~~-----~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~  358 (541)
T COG0539         296 EIEEGVEGLVHVSEI------------SWTKKN-----VPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFA  358 (541)
T ss_pred             EecCCccceeechhh------------cccccC-----CHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhh
Confidence            9999999999 8999            555433     266799999999999999996    99999999999999999


Q ss_pred             hhcccCC
Q 026737          228 ETAIVNN  234 (234)
Q Consensus       228 ~~~~~~~  234 (234)
                      ++|++|.
T Consensus       359 ~~~~~g~  365 (541)
T COG0539         359 DKHPVGD  365 (541)
T ss_pred             hhcCCCC
Confidence            9999874

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

Probab=100.00  E-value=4.6e-41  Score=314.38  Aligned_cols=203  Identities=30%  Similarity=0.452  Sum_probs=185.7

Q ss_pred             CCCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhhcCCCCCcEEEEE-----EeeEEEE
Q 026737            1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH   72 (234)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G~fV~   72 (234)
                      |||.| ..||+..+.      +||+|+|+|+++|.+++|++||+|+.   +|+.+..++++|+.+.|+     +|||||+
T Consensus       224 iS~~r-v~~P~~vvk------vGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVe  296 (541)
T COG0539         224 ISWKR-VDHPSEVVK------VGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVE  296 (541)
T ss_pred             ccccc-cCCHHHhcc------cCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEE
Confidence            68888 899999987      99999999999999999999999986   699999999999999999     9999999


Q ss_pred             EecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc----
Q 026737           73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE----  148 (234)
Q Consensus        73 l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~----  148 (234)
                      +.     +|++||+|+||+||.+...|.+++++||+|.|+|+++|++++||+||+|++..|||..+.+. ++.|..    
T Consensus       297 i~-----~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~-~~~g~~v~g~  370 (541)
T COG0539         297 IE-----EGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADK-HPVGDVVEGK  370 (541)
T ss_pred             ec-----CCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhh-cCCCCeEEEE
Confidence            98     58999999999999998889999999999999999999999999999999999999987776 788742    


Q ss_pred             -------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737          149 -------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK  216 (234)
Q Consensus       149 -------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K  216 (234)
                             |+||++++|++||+ .|.+            +|....     +....++.|++++++||.+|.    |+||+|
T Consensus       371 v~~~t~~g~fv~le~gidG~vh~~d~------------sw~~~~-----~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiK  433 (541)
T COG0539         371 VKSITDFGAFVELEGGIDGLVHLSDL------------SWDRPG-----EEAEKYKKGDEVEAKVLAVDKEKERISLGIK  433 (541)
T ss_pred             EeeecccceEEccCCCccceEEHHhc------------CccccC-----cHHHhhccCcEEEEEEEEEecccceeeeehh
Confidence                   99999999999999 6766            554332     223378999999999999997    999999


Q ss_pred             ccccchhHHHHhhcccC
Q 026737          217 RHCNEYWNVFHETAIVN  233 (234)
Q Consensus       217 ~~~~~p~~~~~~~~~~~  233 (234)
                      |+.++||+.+.+.|++|
T Consensus       434 ql~~~p~~~~~~~~~~~  450 (541)
T COG0539         434 QLEESPWEEFSEKYKKG  450 (541)
T ss_pred             hhccCchhhhHhhccCC
Confidence            99999999999999987

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=2.5e-36  Score=298.09  Aligned_cols=205  Identities=26%  Similarity=0.489  Sum_probs=178.7

Q ss_pred             CCCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhhcCCCCCcEEEEE-----EeeEEEE
Q 026737            1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH   72 (234)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G~fV~   72 (234)
                      |||++ ..+|...+.      +||+++|+|+++|++++++.||+|+.   +|+.+.+.+++|++++|+     +||+||+
T Consensus       525 iS~~~-v~~~~~~~k------vGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVe  597 (863)
T PRK12269        525 MSWGH-VARPREFVK------KGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIE  597 (863)
T ss_pred             ccccc-cCCHHHhcc------CCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEE
Confidence            34555 456655443      99999999999999999999999975   588888999999999999     9999999


Q ss_pred             EecCCCcceeEEEEEceeccc-ccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc---
Q 026737           73 LRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE---  148 (234)
Q Consensus        73 l~~~~g~~g~~glv~isels~-~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~---  148 (234)
                      |+     +|++||+|+|+++| .++.+|.+.|++||+|+|+|+++|++++|++||+|++.+|||..+.++ +++|.+   
T Consensus       598 L~-----~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~-~~vG~~v~G  671 (863)
T PRK12269        598 LA-----EGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEAR-YPVGARFTR  671 (863)
T ss_pred             ec-----CCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHh-CCCCCEEEE
Confidence            97     47999999999999 578999999999999999999999999999999999999999877665 677732   


Q ss_pred             --------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhh
Q 026737          149 --------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKAS  215 (234)
Q Consensus       149 --------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~  215 (234)
                              |+||+|.+|++||+ +|++            +|....    .+++..+++||.|+|+|+++|.    |+||+
T Consensus       672 ~V~~i~~~G~fV~l~~gV~GlIh~sel------------s~~~~~----~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~  735 (863)
T PRK12269        672 RIVKVTNAGAFIEMEEGIDGFLHVDDL------------SWVKRT----RPADHELEVGKEIECMVIECDPQARRIRLGV  735 (863)
T ss_pred             EEEEEecceEEEEeCCCcEEEEEhHHh------------hccccc----cchhhccCCCCEEEEEEEEEeccCCEEEEEe
Confidence                    99999999999999 6776            454432    2344579999999999999986    99999


Q ss_pred             cccccchhHHHHhhcccCC
Q 026737          216 KRHCNEYWNVFHETAIVNN  234 (234)
Q Consensus       216 K~~~~~p~~~~~~~~~~~~  234 (234)
                      |++.++||+.|.++|++|.
T Consensus       736 K~l~~dpw~~~~~~~~vG~  754 (863)
T PRK12269        736 KQLSDNPWQVFANAYGVGS  754 (863)
T ss_pred             cccccChHHHHHhhCCCCC
Confidence            9999999999999999874

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=1.5e-33  Score=265.85  Aligned_cols=193  Identities=24%  Similarity=0.388  Sum_probs=170.0

Q ss_pred             cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEE
Q 026737           20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH   87 (234)
Q Consensus        20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~   87 (234)
                      .++|++++|+|+++|++++++.||+++.       .|+.+..++++|++++|+     ++|+||+|+     ++++||||
T Consensus       157 ~~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~-----~gv~g~v~  231 (491)
T PRK13806        157 SYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELA-----PGVEGMVH  231 (491)
T ss_pred             HcCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcC-----CCcEEEEE
Confidence            4699999999999999999999999865       366777889999999998     999999996     37999999


Q ss_pred             ceecccccccchhhhhCCCCEEEEEEEEEeCCC----CeEEEEEeecccCcchhhhhcccccccc-----------ceee
Q 026737           88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK----SRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLK  152 (234)
Q Consensus        88 isels~~~~~~~~~~~~vGd~v~vkVl~id~~~----~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV  152 (234)
                      +++++|.++.++.+.|++||.++|+|+++|.++    .|+.||+|++.++||..+.++ ++.|.+           |+||
T Consensus       232 ~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~-~~~G~~v~G~V~~v~~~G~fV  310 (491)
T PRK13806        232 ISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDR-LKAGDKVTGKVVRLAPFGAFV  310 (491)
T ss_pred             HHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhcc-CCCCCEEEEEEEEEeCceEEE
Confidence            999999999999999999999999999999876    479999999999999876665 566632           9999


Q ss_pred             eecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHH
Q 026737          153 SFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFH  227 (234)
Q Consensus       153 ~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~  227 (234)
                      ++.+|++||+ +|+++            |....    .++...+++||.|+|+|+++|.    |+||+|++.++||+.+.
T Consensus       311 ~l~~gv~Glvh~sels------------~~~~~----~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~  374 (491)
T PRK13806        311 EILPGIEGLVHVSEMS------------WTRRV----NKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVA  374 (491)
T ss_pred             EeCCCcEEEEEHHHcC------------ccccc----CCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhh
Confidence            9999999999 78884            42221    3456689999999999999985    99999999999999999


Q ss_pred             hhcccCC
Q 026737          228 ETAIVNN  234 (234)
Q Consensus       228 ~~~~~~~  234 (234)
                      +.|++|.
T Consensus       375 ~~~~vG~  381 (491)
T PRK13806        375 ERFAPGT  381 (491)
T ss_pred             hhCCCCC
Confidence            9999884

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=6.4e-33  Score=261.55  Aligned_cols=197  Identities=25%  Similarity=0.409  Sum_probs=167.6

Q ss_pred             CCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCC----CEEEEEechh---hHhhhhcCCCCCcEEEEE-----EeeE
Q 026737            2 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM----KKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGA   69 (234)
Q Consensus         2 ~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~----~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G~   69 (234)
                      +|++ ..+|...+.      +||.+.|+|+++|.++    +++.||+|++   +|+.+..++++|+++.|+     +||+
T Consensus       236 s~~~-~~~~~~~~~------vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~  308 (491)
T PRK13806        236 SWSR-VQKADEAVS------VGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGA  308 (491)
T ss_pred             CCcc-ccChhHhcC------CCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceE
Confidence            4444 445554443      9999999999999876    4799999986   698999999999999999     9999


Q ss_pred             EEEEecCCCcceeEEEEEceeccc-ccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc
Q 026737           70 FIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE  148 (234)
Q Consensus        70 fV~l~~~~g~~g~~glv~isels~-~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~  148 (234)
                      ||+++     +|++||||+|+++| .++.++.+.|++||.|+|+|+++|+++++|.||+|++..+||..+.++ +++|.+
T Consensus       309 fV~l~-----~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~-~~vG~~  382 (491)
T PRK13806        309 FVEIL-----PGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAER-FAPGTT  382 (491)
T ss_pred             EEEeC-----CCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhh-CCCCCE
Confidence            99997     47999999999999 478899999999999999999999999999999999999999987766 666632


Q ss_pred             -----------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----ch
Q 026737          149 -----------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IR  212 (234)
Q Consensus       149 -----------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~  212 (234)
                                 |+||++++|++||| +|++++++            .     .++...+++||+|+|+|+++|.    |+
T Consensus       383 v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~~------------~-----~~~~~~~~~Gd~v~~~V~~id~e~~ri~  445 (491)
T PRK13806        383 VTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAG------------K-----PATYEKLKPGDSVTLVVEEIDTAKRKIS  445 (491)
T ss_pred             EEEEEEEEecCceEEEcCCCcEEEEEHHHcCccc------------c-----cchhhcCCCCCEEEEEEEEEeCCCCEEE
Confidence                       99999999999999 78884322            1     2344578999999999999985    99


Q ss_pred             hhhccc-----ccchhHHHHh
Q 026737          213 KASKRH-----CNEYWNVFHE  228 (234)
Q Consensus       213 ls~K~~-----~~~p~~~~~~  228 (234)
                      ||+|++     ..+||+.+..
T Consensus       446 Ls~~~~~~~~~~~~~~~~~~~  466 (491)
T PRK13806        446 LAPAGAAGSGADDDDWKQFAP  466 (491)
T ss_pred             EEeehhhhhhhhhhHHHhhcc
Confidence            999987     3589999853

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=6e-33  Score=274.14  Aligned_cols=195  Identities=22%  Similarity=0.426  Sum_probs=169.9

Q ss_pred             hcccCCCCEEEEEEEEEeC-----CCCEEEEEechhh-------HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCc
Q 026737           17 IAKGLTGSIISVKVIQANE-----EMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGL   79 (234)
Q Consensus        17 ~~~~~vG~~v~~~Vi~id~-----~~~~i~lS~k~~~-------~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~   79 (234)
                      +++.++|++++|+|+++|+     +++++++|+|...       .+++++++++|++++|+     +||+||+++     
T Consensus       440 ~~~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~-----  514 (863)
T PRK12269        440 APESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLG-----  514 (863)
T ss_pred             chHHhCCCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEEC-----
Confidence            3456799999999999975     3468999998742       34567889999999998     899999996     


Q ss_pred             ceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------
Q 026737           80 YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------  148 (234)
Q Consensus        80 ~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------  148 (234)
                       |++||||+|+++|.++.+|.+.|++||+++|+|+++|++++++.||+|++.++||..+.++ +++|.+           
T Consensus       515 -Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~-~~vG~iV~G~V~~I~~f  592 (863)
T PRK12269        515 -GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENK-FGVNDVVKGRVTKIADF  592 (863)
T ss_pred             -CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhcc-CCCCCEEEEEEEEEeCC
Confidence             6999999999999999999999999999999999999999999999999999999876665 666632           


Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchh
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYW  223 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~  223 (234)
                      |+||+|.+|++||+ +|+++            |....    .++...+++||+|+|+|+++|.    |+||+|++.+|||
T Consensus       593 G~fVeL~~gveGLvhiSEls------------~~~~~----~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw  656 (863)
T PRK12269        593 GAFIELAEGIEGLAHISEFS------------WVKKT----SKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPW  656 (863)
T ss_pred             eEEEEecCCceeeeEHHHhc------------Ccccc----CCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCch
Confidence            99999999999999 78884            43221    3456689999999999999995    9999999999999


Q ss_pred             HHHHhhcccCC
Q 026737          224 NVFHETAIVNN  234 (234)
Q Consensus       224 ~~~~~~~~~~~  234 (234)
                      +.|.++|++|.
T Consensus       657 ~~~~~~~~vG~  667 (863)
T PRK12269        657 EEIEARYPVGA  667 (863)
T ss_pred             HHHHHhCCCCC
Confidence            99999999874

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=5.1e-32  Score=253.82  Aligned_cols=181  Identities=23%  Similarity=0.379  Sum_probs=158.5

Q ss_pred             cccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEE
Q 026737           18 AKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL   85 (234)
Q Consensus        18 ~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~gl   85 (234)
                      ++.++|++|+|+|+++|.++++++||+|..       .|+.+..++++|++++|+     +||+||+|+      +++||
T Consensus       161 ~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg------gv~Gl  234 (486)
T PRK07899        161 LQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG------GVDGL  234 (486)
T ss_pred             hhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEE
Confidence            345799999999999999999999999852       477788899999999999     999999996      69999


Q ss_pred             EEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceeeee
Q 026737           86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLKSF  154 (234)
Q Consensus        86 v~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~l  154 (234)
                      ||+|+++|.++.+|.+.|++||.|+|+|+++|++++||.||+|++.++||..+.+. +..|.+           |+||+|
T Consensus       235 v~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~-~~vG~vv~G~V~~I~~fGvFVeL  313 (486)
T PRK07899        235 VHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFART-HAIGQIVPGKVTKLVPFGAFVRV  313 (486)
T ss_pred             EEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHh-cCCCCEEEEEEEEEeccEEEEEe
Confidence            99999999999999999999999999999999999999999999999999877665 555521           999999


Q ss_pred             cCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccch
Q 026737          155 YKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEY  222 (234)
Q Consensus       155 ~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p  222 (234)
                      .+|++||| +|+++++..                 ..+...+++||+|+|+|+++|.    |+||+|++.++-
T Consensus       314 ~~gieGLvh~SeLs~~~v-----------------~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~~~  369 (486)
T PRK07899        314 EEGIEGLVHISELAERHV-----------------EVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANEGV  369 (486)
T ss_pred             CCCcEEEEEHHHcCcccc-----------------cCccceeCCCCEEEEEEEEEECCCCEEEEEEEEcccCC
Confidence            99999999 788853221                 1234589999999999999985    999999997654

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.97  E-value=3e-31  Score=254.13  Aligned_cols=192  Identities=28%  Similarity=0.497  Sum_probs=169.7

Q ss_pred             cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEE
Q 026737           20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH   87 (234)
Q Consensus        20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~   87 (234)
                      .++|++++|+|+++|++++++.+|+|++       .|+.++.++++|++++|+     ++|+||+++      |++||+|
T Consensus       156 ~~vG~~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~------g~~glv~  229 (565)
T PRK06299        156 PLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLG------GVDGLLH  229 (565)
T ss_pred             HhCCCEEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC------CEEEEEE
Confidence            4699999999999999999999999975       366778899999999999     999999996      6999999


Q ss_pred             ceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceeeeecC
Q 026737           88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLKSFYK  156 (234)
Q Consensus        88 isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~l~~  156 (234)
                      +++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++.++||....+. ++.|.+           |+||++.+
T Consensus       230 ~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~-~~~G~~v~g~V~~i~~~G~fV~l~~  308 (565)
T PRK06299        230 ITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKK-YPVGSKVKGKVTNITDYGAFVELEE  308 (565)
T ss_pred             HHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhh-CCCCCEEEEEEEEEeCCeEEEEeCC
Confidence            999999999999999999999999999999999999999999999999876555 666632           99999999


Q ss_pred             CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcc
Q 026737          157 KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAI  231 (234)
Q Consensus       157 gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~  231 (234)
                      |++||+ +|+++|+.+            .    .++...+++||.|+|+|+++|.    |+||+|++..+||+.+.+.|+
T Consensus       309 ~v~Glv~~sel~~~~~------------~----~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~  372 (565)
T PRK06299        309 GIEGLVHVSEMSWTKK------------N----KHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYP  372 (565)
T ss_pred             CCEEEEEHHHcCcccc------------c----cCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCC
Confidence            999999 788854322            1    2344578999999999999985    999999999999999999998


Q ss_pred             cCC
Q 026737          232 VNN  234 (234)
Q Consensus       232 ~~~  234 (234)
                      +|.
T Consensus       373 ~G~  375 (565)
T PRK06299        373 VGD  375 (565)
T ss_pred             CCC
Confidence            873

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.97  E-value=1.6e-30  Score=238.85  Aligned_cols=186  Identities=24%  Similarity=0.364  Sum_probs=163.2

Q ss_pred             cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEE
Q 026737           20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH   87 (234)
Q Consensus        20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~   87 (234)
                      .++|+++.|+|+++|++++++.||+|..       .|..++.++++|++++|+     ++|+||+++      +++||||
T Consensus       147 ~~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~------~v~g~v~  220 (390)
T PRK06676        147 DFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG------GVDGLVH  220 (390)
T ss_pred             HcCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC------CeEEEEE
Confidence            4599999999999999999999999874       356677889999999998     999999996      6999999


Q ss_pred             ceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceeeeecC
Q 026737           88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLKSFYK  156 (234)
Q Consensus        88 isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~l~~  156 (234)
                      +++++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||..+.++ +..|.+           |+||++.+
T Consensus       221 ~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~-~~~G~~v~g~V~~i~~~G~fV~l~~  299 (390)
T PRK06676        221 ISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEK-LPEGDVIEGTVKRLTDFGAFVEVLP  299 (390)
T ss_pred             HHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhh-hcCCcEEEEEEEEEeCceEEEEECC
Confidence            999999999999999999999999999999999999999999999999876655 555521           99999999


Q ss_pred             CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhh
Q 026737          157 KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHET  229 (234)
Q Consensus       157 gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~  229 (234)
                      |++||+ +|++++..            .     .++...+++||.|+|+|+++|.    |+||+|++.++||+.+.++
T Consensus       300 gi~Glv~~se~~~~~------------~-----~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~~~~~~~  360 (390)
T PRK06676        300 GVEGLVHISQISHKH------------I-----ATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEEEDRR  360 (390)
T ss_pred             CCeEEEEhHHcCccc------------c-----CChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccChhhhhhhh
Confidence            999999 78774221            1     2345578999999999999985    9999999999999999776

>TIGR00717 rpsA ribosomal protein S1

Probab=99.97  E-value=1.3e-30  Score=247.10  Aligned_cols=204  Identities=27%  Similarity=0.472  Sum_probs=173.2

Q ss_pred             CCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhhcCCCCCcEEEEE-----EeeEEEEE
Q 026737            2 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHL   73 (234)
Q Consensus         2 ~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G~fV~l   73 (234)
                      ++++ ..+|...+.      +|+++.|+|+++|++++++.+|++..   +|+.+...+++|+++.|+     ++|+||++
T Consensus       220 s~~~-~~~~~~~~~------vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l  292 (516)
T TIGR00717       220 SWKR-VKHPSEYVK------VGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEI  292 (516)
T ss_pred             CCCC-CCCHHHhcc------CCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccCCCEEEEEEEEeeCCcEEEEe
Confidence            4444 445554443      99999999999999999999999965   688888889999999998     99999999


Q ss_pred             ecCCCcceeEEEEEceecccc-cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc----
Q 026737           74 RFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE----  148 (234)
Q Consensus        74 ~~~~g~~g~~glv~isels~~-~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~----  148 (234)
                      +     ++++||+|+++++|. ...++.+.|++||.++|+|+++|++++++.||+|++..+||..+.+. +..|.+    
T Consensus       293 ~-----~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~-~~~G~~v~g~  366 (516)
T TIGR00717       293 E-----EGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEK-HPVGDRVTGK  366 (516)
T ss_pred             C-----CCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHh-CCCCCEEEEE
Confidence            7     479999999999987 46778888999999999999999999999999999999999877665 555532    


Q ss_pred             -------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737          149 -------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK  216 (234)
Q Consensus       149 -------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K  216 (234)
                             |+||++.+|++||+ +|+++|...            .    .++...+++||.|.|+|+++|.    |.||+|
T Consensus       367 V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~------------~----~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K  430 (516)
T TIGR00717       367 IKKITDFGAFVELEGGIDGLIHLSDISWDKD------------G----READHLYKKGDEIEAVVLAVDKEKKRISLGVK  430 (516)
T ss_pred             EEEEecceEEEECCCCCEEEEEHHHCcCccc------------C----CCHhHccCCCCEEEEEEEEEeCcCCEEEEeec
Confidence                   99999999999999 788754321            1    1234578999999999999985    999999


Q ss_pred             ccccchhHHHHhhcccCC
Q 026737          217 RHCNEYWNVFHETAIVNN  234 (234)
Q Consensus       217 ~~~~~p~~~~~~~~~~~~  234 (234)
                      ++.++||+.+.+.|++|.
T Consensus       431 ~~~~~p~~~~~~~~~~G~  448 (516)
T TIGR00717       431 QLTENPWEKFAAKYKVGS  448 (516)
T ss_pred             cccCCchhhhhhccCcce
Confidence            999999999999888773

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

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.97  E-value=2.9e-30  Score=247.39  Aligned_cols=204  Identities=28%  Similarity=0.453  Sum_probs=174.3

Q ss_pred             CCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhhcCCCCCcEEEEE-----EeeEEEEE
Q 026737            2 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHL   73 (234)
Q Consensus         2 ~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G~fV~l   73 (234)
                      +|++ ..+|...+.      +||++.|+|+++|.+++++.||++..   +|+.+...+++|+++.|+     ++|+||++
T Consensus       234 s~~~-~~~~~~~~k------vG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l  306 (565)
T PRK06299        234 SWKR-VNHPSEVVN------VGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVEL  306 (565)
T ss_pred             cccc-cCCHhhcCC------CCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEe
Confidence            4444 445655544      99999999999999999999999965   698888899999999999     99999999


Q ss_pred             ecCCCcceeEEEEEceecccc-cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc----
Q 026737           74 RFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE----  148 (234)
Q Consensus        74 ~~~~g~~g~~glv~isels~~-~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~----  148 (234)
                      +     ++++||+|+++++|. +..+|.+.|++||.|+|+|+++|++++++.||+|++..+||..+... +..|.+    
T Consensus       307 ~-----~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~-~~~G~~v~g~  380 (565)
T PRK06299        307 E-----EGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEK-YPVGDVVEGK  380 (565)
T ss_pred             C-----CCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHh-CCCCCEEEEE
Confidence            7     479999999999987 46788899999999999999999999999999999999999877665 566621    


Q ss_pred             -------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737          149 -------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK  216 (234)
Q Consensus       149 -------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K  216 (234)
                             |+||+|.+|++|++ +|+++++.            ..    .++...+++||.|+|+|+++|.    |.||+|
T Consensus       381 V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~------------~~----~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k  444 (565)
T PRK06299        381 VKNITDFGAFVGLEGGIDGLVHLSDISWDK------------KG----EEAVELYKKGDEVEAVVLKVDVEKERISLGIK  444 (565)
T ss_pred             EEEEecceEEEECCCCCEEEEEHHHcCccc------------cc----cChHhhCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence                   99999988999999 78874321            10    2345688999999999999984    999999


Q ss_pred             ccccchhHHHHhhcccCC
Q 026737          217 RHCNEYWNVFHETAIVNN  234 (234)
Q Consensus       217 ~~~~~p~~~~~~~~~~~~  234 (234)
                      ++..+||..+.+.+++|.
T Consensus       445 ~~~~~p~~~~~~~~~~G~  462 (565)
T PRK06299        445 QLEEDPFEEFAKKHKKGS  462 (565)
T ss_pred             hhhcCchhHHHhhcCCCC
Confidence            999999999999888873

>TIGR00717 rpsA ribosomal protein S1

Probab=99.97  E-value=1.9e-29  Score=239.16  Aligned_cols=193  Identities=26%  Similarity=0.485  Sum_probs=168.1

Q ss_pred             ccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEE
Q 026737           19 KGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLV   86 (234)
Q Consensus        19 ~~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv   86 (234)
                      ..++|++++|+|+++|++++++++|+|..       .++.++..+++|++++|+     ++|+||+++      +++||+
T Consensus       141 ~~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~------g~~g~l  214 (516)
T TIGR00717       141 DSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLG------GVDGLL  214 (516)
T ss_pred             hhhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEE
Confidence            45699999999999999999999999865       255667889999999999     899999996      699999


Q ss_pred             EceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceeeeec
Q 026737           87 HVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLKSFY  155 (234)
Q Consensus        87 ~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~l~  155 (234)
                      |.++++|.++.++.+.|++||.+.|+|+++|++++++.||+|++.++||....+. +..|.+           |+||++.
T Consensus       215 p~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~-~~~G~i~~g~V~~v~~~G~fV~l~  293 (516)
T TIGR00717       215 HITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKK-FPVGDKITGRVTNLTDYGVFVEIE  293 (516)
T ss_pred             EHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhh-ccCCCEEEEEEEEeeCCcEEEEeC
Confidence            9999999999999999999999999999999999999999999999999876654 555521           9999999


Q ss_pred             CCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhc
Q 026737          156 KKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETA  230 (234)
Q Consensus       156 ~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~  230 (234)
                      +|++||+ +|+++++..            .    .++...+++||.|+|+|+++|.    |.||+|++.++||+.+.+.+
T Consensus       294 ~~v~g~v~~sels~~~~------------~----~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~  357 (516)
T TIGR00717       294 EGIEGLVHVSEMSWVKK------------N----SHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKH  357 (516)
T ss_pred             CCCEEEEEHHHcCCccc------------c----CCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhC
Confidence            9999999 688743321            1    2344578999999999999985    99999999999999999988


Q ss_pred             ccCC
Q 026737          231 IVNN  234 (234)
Q Consensus       231 ~~~~  234 (234)
                      .+|.
T Consensus       358 ~~G~  361 (516)
T TIGR00717       358 PVGD  361 (516)
T ss_pred             CCCC
Confidence            8874

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

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.96  E-value=5.4e-29  Score=233.48  Aligned_cols=184  Identities=19%  Similarity=0.368  Sum_probs=158.6

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc
Q 026737           22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (234)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels   92 (234)
                      +|++|+|+|+++|.++++++||+|++    .|+.+...++.|++++|+     ++|+||+++       ++||||.|+++
T Consensus        82 vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~VdlG-------i~gflP~Sel~  154 (486)
T PRK07899         82 VGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDIG-------LRGFLPASLVE  154 (486)
T ss_pred             CCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEEC-------CEEEEEhhHhc
Confidence            99999999999999999999999975    477777777899999998     889999994       89999999999


Q ss_pred             cccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeeccc----Ccchhhhhcccccccc-----------ceeeeecCC
Q 026737           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE----DPLLETLEKVIPQGLE-----------PYLKSFYKK  157 (234)
Q Consensus        93 ~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~----~p~~~~~~~~~~~G~~-----------G~fV~l~~g  157 (234)
                      +.++.++..+  +||.|+|+|+++|++++++.||+|.+..    ++|..++.. +..|.+           |+||+| +|
T Consensus       155 ~~~~~~~~~~--vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~-lk~G~iv~G~V~~i~~~G~FVdl-gg  230 (486)
T PRK07899        155 MRRVRDLQPY--IGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQ-LQKGQVRKGVVSSIVNFGAFVDL-GG  230 (486)
T ss_pred             ccccCChhhc--CCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHh-ccCCCEEEEEEEEEECCeEEEEE-CC
Confidence            9988888763  8999999999999999999999996543    678777665 566521           999999 58


Q ss_pred             ceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhccc
Q 026737          158 MDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAIV  232 (234)
Q Consensus       158 i~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~~  232 (234)
                      ++||+ +|+++            |-..     .++...+++||.|+++|+++|+    |+||+|++.++||+.+.++|++
T Consensus       231 v~Glv~~Sels------------~~~v-----~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~v  293 (486)
T PRK07899        231 VDGLVHVSELS------------WKHI-----DHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAI  293 (486)
T ss_pred             EEEEEEHHHCC------------Cccc-----CCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCC
Confidence            99999 78884            4221     2455689999999999999985    9999999999999999999987


Q ss_pred             C
Q 026737          233 N  233 (234)
Q Consensus       233 ~  233 (234)
                      |
T Consensus       294 G  294 (486)
T PRK07899        294 G  294 (486)
T ss_pred             C
Confidence            6

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.96  E-value=8.2e-29  Score=221.94  Aligned_cols=178  Identities=14%  Similarity=0.221  Sum_probs=148.4

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc
Q 026737           22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (234)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels   92 (234)
                      +|++++|+|+++|.+++++.||+|+.    .|+.+...+..|++++|+     ++|+||+++      |++||||+|+++
T Consensus        78 ~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~------Gv~gfip~s~ls  151 (318)
T PRK07400         78 PNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIE------GLRGFIPGSHIS  151 (318)
T ss_pred             CCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcC
Confidence            89999999999999999999999874    488888888899999998     899999996      699999999999


Q ss_pred             cccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccc-----c------ceeeeecCCceEE
Q 026737           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGL-----E------PYLKSFYKKMDDV  161 (234)
Q Consensus        93 ~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~-----~------G~fV~l~~gi~Gl  161 (234)
                      |.+..   +.+ +|+.+.++|+++|+++++|.||+|++..++   ...+ +..|.     +      |+||++ .|++||
T Consensus       152 ~~~~~---~~~-vG~~i~~kVl~id~~~~~i~lS~K~~~~~~---~~~~-~k~G~vv~G~V~~I~~~G~fV~i-~gv~Gl  222 (318)
T PRK07400        152 TRKPK---EEL-VGEELPLKFLEVDEERNRLVLSHRRALVER---KMNR-LEVGEVVVGTVRGIKPYGAFIDI-GGVSGL  222 (318)
T ss_pred             ccCCc---ccc-CCCEEEEEEEEEEcccCEEEEEhhHhhhhh---hhcc-CCCCCEEEEEEEEEECCeEEEEE-CCEEEE
Confidence            96533   333 999999999999999999999999765543   2222 45552     1      999999 599999


Q ss_pred             E-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcc
Q 026737          162 R-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAI  231 (234)
Q Consensus       162 ~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~  231 (234)
                      + +|+++++.            .     .++...+++||.|+|+|+++|.    |+||+|++.++||+.+....+
T Consensus       223 lhisels~~~------------~-----~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~~~~~  280 (318)
T PRK07400        223 LHISEISHEH------------I-----ETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQK  280 (318)
T ss_pred             EEHHHccccc------------c-----cChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhhhhhHHH
Confidence            9 78885432            1     2355689999999999999984    999999999999998876543

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

Probab=99.95  E-value=5.7e-27  Score=227.69  Aligned_cols=181  Identities=29%  Similarity=0.458  Sum_probs=158.1

Q ss_pred             cccCCCCEEEEEEEEEeCCCCE-EEEEechhh-------HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEE
Q 026737           18 AKGLTGSIISVKVIQANEEMKK-LVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTG   84 (234)
Q Consensus        18 ~~~~vG~~v~~~Vi~id~~~~~-i~lS~k~~~-------~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~g   84 (234)
                      ++.++|+++.|+|+++|+++++ +.+|+|...       ++..+.++++|+++.|+     ++|+||+++      +++|
T Consensus       429 ~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~------gv~G  502 (647)
T PRK00087        429 LSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIG------GVDG  502 (647)
T ss_pred             HHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEEC------CEEE
Confidence            3446999999999999999998 999998752       45677889999999998     899999995      6999


Q ss_pred             EEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceeee
Q 026737           85 LVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLKS  153 (234)
Q Consensus        85 lv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~  153 (234)
                      |+|+++++|.++.++.+.|++||.++++|+++|++++++.||+|++.++||....++ +..|.+           |+||+
T Consensus       503 ll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~-~~~G~~v~g~V~~i~~~G~fV~  581 (647)
T PRK00087        503 LLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEK-YPVGSIVLGKVVRIAPFGAFVE  581 (647)
T ss_pred             EEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhh-ccCCeEEEEEEEEEECCeEEEE
Confidence            999999999999999999999999999999999999999999999999999876665 555621           99999


Q ss_pred             ecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccch
Q 026737          154 FYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEY  222 (234)
Q Consensus       154 l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p  222 (234)
                      +.+|++||+ +|+++++..                 .++...+++||+|+|+|+++|.    |+||+|++.++|
T Consensus       582 l~~~i~Gli~~sel~~~~~-----------------~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~  638 (647)
T PRK00087        582 LEPGVDGLVHISQISWKRI-----------------DKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP  638 (647)
T ss_pred             ECCCCEEEEEhhhcCcccc-----------------CCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence            999999999 788743221                 2345578999999999999985    999999999999

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.95  E-value=8.5e-27  Score=214.20  Aligned_cols=185  Identities=21%  Similarity=0.332  Sum_probs=158.4

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc
Q 026737           22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (234)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels   92 (234)
                      +|++++|+|+++|.+++++.||++..    .|+.+...++.|+++.|+     ++|+||+++      |++||||+++++
T Consensus        65 vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~------G~~gflp~~el~  138 (390)
T PRK06676         65 VGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE------GVRGFIPASLIS  138 (390)
T ss_pred             CCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcC
Confidence            99999999999999999999999974    488887888999999999     889999996      589999999999


Q ss_pred             cccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeeccc----Ccchhhhhcccccccc-----------ceeeeecCC
Q 026737           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE----DPLLETLEKVIPQGLE-----------PYLKSFYKK  157 (234)
Q Consensus        93 ~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~----~p~~~~~~~~~~~G~~-----------G~fV~l~~g  157 (234)
                      +.+..++..+  +||.+.|+|+++|.+++++.||+|++..    ++|...... +..|.+           |+||++ +|
T Consensus       139 ~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~-~~~G~~v~g~V~~v~~~G~fV~l-~~  214 (390)
T PRK06676        139 TRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSS-LKEGDVVEGTVARLTDFGAFVDI-GG  214 (390)
T ss_pred             CccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhh-CCCCCEEEEEEEEEecceEEEEe-CC
Confidence            9988888764  8999999999999999999999998765    466655554 455521           999999 58


Q ss_pred             ceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhccc
Q 026737          158 MDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAIV  232 (234)
Q Consensus       158 i~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~~  232 (234)
                      ++|++ +|++++.            ..     .++...+++||.|+++|+++|.    |.||+|++.++||+.+.+.+.+
T Consensus       215 v~g~v~~sels~~------------~~-----~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~  277 (390)
T PRK06676        215 VDGLVHISELSHE------------RV-----EKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPE  277 (390)
T ss_pred             eEEEEEHHHcCcc------------cc-----CCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcC
Confidence            99999 7887432            11     2355678999999999999985    9999999999999999888887


Q ss_pred             C
Q 026737          233 N  233 (234)
Q Consensus       233 ~  233 (234)
                      |
T Consensus       278 G  278 (390)
T PRK06676        278 G  278 (390)
T ss_pred             C
Confidence            7

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

Probab=99.93  E-value=5.1e-25  Score=214.05  Aligned_cols=185  Identities=20%  Similarity=0.342  Sum_probs=158.3

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc
Q 026737           22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (234)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels   92 (234)
                      +|++++|+|+++|.+.+++.||++..    .|+.+...+++|+++.|+     ++|+||+++      +++||||.++++
T Consensus       349 vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lg------gi~gfiP~sel~  422 (647)
T PRK00087        349 VGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYG------GVRAFLPASHVE  422 (647)
T ss_pred             CCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHhC
Confidence            99999999999999999999999865    477887888999999998     889999997      599999999999


Q ss_pred             cccccchhhhhCCCCEEEEEEEEEeCCCCe-EEEEEeeccc----Ccchhhhhccccccc-----c------ceeeeecC
Q 026737           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSR-ITLSIKQLEE----DPLLETLEKVIPQGL-----E------PYLKSFYK  156 (234)
Q Consensus        93 ~~~~~~~~~~~~vGd~v~vkVl~id~~~~r-i~LS~K~~~~----~p~~~~~~~~~~~G~-----~------G~fV~l~~  156 (234)
                      +.+..++..+  +|+.++++|+++|+++++ +.+|+|.+..    ++|....++ +..|.     +      |+||++ +
T Consensus       423 ~~~~~d~~~~--vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~-l~~G~iV~g~V~~v~~~G~fV~l-~  498 (647)
T PRK00087        423 LGYVEDLSEY--KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNS-LEEGDVVEGEVKRLTDFGAFVDI-G  498 (647)
T ss_pred             ccccCCHHHh--CCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHh-CCCCCEEEEEEEEEeCCcEEEEE-C
Confidence            9998888764  899999999999998888 9999998753    566555554 44542     1      999999 8


Q ss_pred             CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcc
Q 026737          157 KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAI  231 (234)
Q Consensus       157 gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~  231 (234)
                      |++||+ +|++++.            ..     .++...+++||.|+++|+++|+    |.||+|++.++||+.+.++|+
T Consensus       499 gv~Gll~~sels~~------------~~-----~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~  561 (647)
T PRK00087        499 GVDGLLHVSEISWG------------RV-----EKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYP  561 (647)
T ss_pred             CEEEEEEHHHcCcc------------cc-----CCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhcc
Confidence            999999 7887432            11     2355679999999999999985    999999999999999999888


Q ss_pred             cC
Q 026737          232 VN  233 (234)
Q Consensus       232 ~~  233 (234)
                      +|
T Consensus       562 ~G  563 (647)
T PRK00087        562 VG  563 (647)
T ss_pred             CC
Confidence            86

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.85  E-value=1.5e-20  Score=168.68  Aligned_cols=112  Identities=37%  Similarity=0.637  Sum_probs=106.6

Q ss_pred             cCCCCEEEEEEEEEeCCCCEEEEEechhhHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc
Q 026737           20 GLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD   94 (234)
Q Consensus        20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~   94 (234)
                      .++|+++.|+|+++|+++++++||+|.+.++....++++|+++.|+     +||+||+++      |++||+|+++++|.
T Consensus       158 ~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i~------gv~Gllhisels~~  231 (318)
T PRK07400        158 ELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIG------GVSGLLHISEISHE  231 (318)
T ss_pred             ccCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcccc
Confidence            3599999999999999999999999988888888899999999999     999999996      69999999999999


Q ss_pred             cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchh
Q 026737           95 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE  137 (234)
Q Consensus        95 ~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~  137 (234)
                      ++.++.+.|++||.|+|+|+++|.++++|.||+|++.+|||+.
T Consensus       232 ~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~  274 (318)
T PRK07400        232 HIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDM  274 (318)
T ss_pred             cccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhh
Confidence            9999999999999999999999999999999999999999964

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.71  E-value=1.4e-17  Score=148.13  Aligned_cols=105  Identities=22%  Similarity=0.356  Sum_probs=90.2

Q ss_pred             cCCC-CCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           54 SRVN-VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        54 ~~~~-~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      ++++ +|++|.|+     +||+||+|.+++   |++||||+|++||.++.++++.+++||.+.|+|+++|+++++|.||+
T Consensus        12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~---gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~   88 (319)
T PTZ00248         12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYD---DIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSK   88 (319)
T ss_pred             hhCCCCCCEEEEEEEEEeCCeEEEEecCCC---CcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEe
Confidence            3455 89999998     999999996322   69999999999999999999999999999999999999999999999


Q ss_pred             eecccCcchhhhhcccccccc------------ceeee------ecCCceEEE
Q 026737          128 KQLEEDPLLETLEKVIPQGLE------------PYLKS------FYKKMDDVR  162 (234)
Q Consensus       128 K~~~~~p~~~~~~~~~~~G~~------------G~fV~------l~~gi~Gl~  162 (234)
                      |++.++||...... ++.|.+            |+|++      ..++++++.
T Consensus        89 K~v~~~pw~~~~e~-~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~g  140 (319)
T PTZ00248         89 KRVSPEDIEACEEK-FSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYG  140 (319)
T ss_pred             eecccchHHHHHHh-CcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcC
Confidence            99999999987776 666521            77776      456777776

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

Probab=99.70  E-value=2e-17  Score=126.75  Aligned_cols=75  Identities=45%  Similarity=0.756  Sum_probs=70.5

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      .+++|++++|+     +|||||+|+     .|-.|||||||+++.|++++.+++++||+|+|+|+++|. +++|+||+|.
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~-----~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~   75 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELE-----GGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRK   75 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEec-----CCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHH
Confidence            47899999998     999999998     268999999999999999999999999999999999997 9999999999


Q ss_pred             cccCcc
Q 026737          130 LEEDPL  135 (234)
Q Consensus       130 ~~~~p~  135 (234)
                      +...|-
T Consensus        76 ~~e~pe   81 (129)
T COG1098          76 LEEEPE   81 (129)
T ss_pred             hhhCcc
Confidence            998874

>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.56  E-value=8.5e-15  Score=104.51  Aligned_cols=66  Identities=26%  Similarity=0.423  Sum_probs=60.5

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccch---hhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~---~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      +++|+++.|+     +||+||+|+     ++++|+||++++||.++.++   .+.|++||.++|+|+++|+++++|.||
T Consensus         1 ~k~G~~V~g~V~~i~~~G~fV~l~-----~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS   74 (74)
T cd05705           1 IKEGQLLRGYVSSVTKQGVFFRLS-----SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeC-----CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            5789999999     999999997     47999999999999997765   588999999999999999999999886

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

>PRK08582 hypothetical protein; Provisional

Probab=99.56  E-value=1.7e-14  Score=114.92  Aligned_cols=77  Identities=40%  Similarity=0.679  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      .+++|++|.|+     +||+||+|+     ++++||||+++++|.++.++.+.|++||.|+|+|+++|. .++|.||+|+
T Consensus         2 ~~kvG~iv~G~V~~I~~fG~fV~L~-----~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~   75 (139)
T PRK08582          2 SIEVGSKLQGKVTGITNFGAFVELP-----EGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKK   75 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEEC-----CCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence            37899999998     999999997     379999999999999999999999999999999999997 5999999999


Q ss_pred             cccCcchh
Q 026737          130 LEEDPLLE  137 (234)
Q Consensus       130 ~~~~p~~~  137 (234)
                      +.++||.+
T Consensus        76 ~~~~~~~~   83 (139)
T PRK08582         76 AKDRPKRQ   83 (139)
T ss_pred             cccCchhh
Confidence            99999964

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.50  E-value=7.3e-14  Score=138.18  Aligned_cols=87  Identities=28%  Similarity=0.435  Sum_probs=78.3

Q ss_pred             HhhhhcCCCCCcEEE-EE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCe
Q 026737           49 WNKYSSRVNVEDIFV-GR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR  122 (234)
Q Consensus        49 ~~~~~~~~~~G~iv~-g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~r  122 (234)
                      ++.+....++|++|+ |+     +||+||+|.     ++.+||||+|+++|.++.++.+.|++||.|+|+|+++|. ++|
T Consensus       744 I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~-----~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~gr  817 (891)
T PLN00207        744 ISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIA-----PGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQ  817 (891)
T ss_pred             HHHHhcCcCCCcEEECcEEEEEeccEEEEEeC-----CCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCc
Confidence            445556789999995 45     999999997     479999999999999999999999999999999999997 899


Q ss_pred             EEEEEeecccCcchhhhhc
Q 026737          123 ITLSIKQLEEDPLLETLEK  141 (234)
Q Consensus       123 i~LS~K~~~~~p~~~~~~~  141 (234)
                      |.||+|++.++||.++.+.
T Consensus       818 I~LSlK~l~~~Pw~~~~~~  836 (891)
T PLN00207        818 LRLSRRALLPEANSEKSSQ  836 (891)
T ss_pred             EEEEEeccccCchhhhhhh
Confidence            9999999999999987664

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

Probab=99.50  E-value=1.1e-13  Score=98.51  Aligned_cols=65  Identities=17%  Similarity=0.305  Sum_probs=60.4

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccc--ccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~--~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      |++++|+     ++|+||+|+     ++++|+||+++++|..  ..++.+.|++||.++|+|+++|+++++|.||+|
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~-----~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k   72 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTIS-----PDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeC-----CCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            7888888     999999997     4799999999999874  889999999999999999999999999999986

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=99.49  E-value=1.2e-13  Score=97.89  Aligned_cols=66  Identities=20%  Similarity=0.305  Sum_probs=60.8

Q ss_pred             CCCCcEEEEE-----E-eeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           56 VNVEDIFVGR-----D-YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        56 ~~~G~iv~g~-----~-~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      +++|+++.|+     + +|+|++++     ++.+|++|+|+++|++..++.+.|++||.++|+|+++|.  +++.||+|
T Consensus         1 l~~G~iv~G~V~~i~~~~g~~v~l~-----~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~   72 (72)
T cd05704           1 LEEGAVTLGMVTKVIPHSGLTVQLP-----FGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR   72 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECC-----CCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence            4689999998     4 89999997     479999999999999999999999999999999999984  99999986

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

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

Probab=99.48  E-value=4.1e-13  Score=135.08  Aligned_cols=175  Identities=22%  Similarity=0.247  Sum_probs=141.6

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh-----------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEE
Q 026737           22 TGSIISVKVIQANEEMKKLVFSEKDA-----------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL   85 (234)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~-----------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~gl   85 (234)
                      .++.+.+.++.++..++.+.||.+..           .-.+..++++.|+++.|.     +.|+|+.+.     ++++|+
T Consensus      1115 ~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls-----~~v~a~ 1189 (1710)
T KOG1070|consen 1115 KIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALS-----RKVEAF 1189 (1710)
T ss_pred             cccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEEc-----cceEEE
Confidence            67999999999999988899998832           123457889999999999     889999998     589999


Q ss_pred             EEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhh--ccccc-----ccc------ceee
Q 026737           86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLE--KVIPQ-----GLE------PYLK  152 (234)
Q Consensus        86 v~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~--~~~~~-----G~~------G~fV  152 (234)
                      +++++++..+.+.++..|++|+.+.++|++++...+|+.||+|.....--.....  ..+..     |++      |.||
T Consensus      1190 v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi 1269 (1710)
T KOG1070|consen 1190 VPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFI 1269 (1710)
T ss_pred             EEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEE
Confidence            9999999999999999999999999999999999999999999865422111111  11222     332      9999


Q ss_pred             eecCCc--eEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccc
Q 026737          153 SFYKKM--DDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRH  218 (234)
Q Consensus       153 ~l~~gi--~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~  218 (234)
                      ++++++  .|+| +++++.++.                 .+++..+..|++|+|.+++.+.    |+|++|.+
T Consensus      1270 ~l~~tv~~~g~~~~~e~~d~~~-----------------e~it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~s 1325 (1710)
T KOG1070|consen 1270 KLDVTVNMVGLCHISEEADDRG-----------------ENITALYYAGDRVKACVLKEDSEKKRISLGLKSS 1325 (1710)
T ss_pred             EecCcceecccccceeecchhh-----------------hhcccceeccceeeeEeeeccchhhhhhhhhhhh
Confidence            999855  9999 888753321                 3456688999999999999985    99999987

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

Probab=99.48  E-value=1.3e-13  Score=100.04  Aligned_cols=72  Identities=31%  Similarity=0.390  Sum_probs=66.4

Q ss_pred             hhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737           51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (234)
Q Consensus        51 ~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~L  125 (234)
                      ..+.++++|+++.|+     ++|+||+++     ++++||+|+++++++++.++.+.|++||.++|+|+++|.+++++.|
T Consensus         7 ~~~~~~~~G~i~~g~V~~v~~~G~fv~l~-----~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~l   81 (83)
T cd04461           7 TNFSDLKPGMVVHGYVRNITPYGVFVEFL-----GGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLL   81 (83)
T ss_pred             hhHHhCCCCCEEEEEEEEEeeceEEEEcC-----CCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEE
Confidence            345668999999999     999999997     3699999999999999999999999999999999999999999999


Q ss_pred             EE
Q 026737          126 SI  127 (234)
Q Consensus       126 S~  127 (234)
                      |+
T Consensus        82 sl   83 (83)
T cd04461          82 SL   83 (83)
T ss_pred             eC
Confidence            85

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

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

Probab=99.47  E-value=1.5e-13  Score=97.19  Aligned_cols=69  Identities=43%  Similarity=0.731  Sum_probs=64.6

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      ++++|+++.|+     ++|+||+++     .+++||||++++++.+..++...|++||.++|+|+++|.+++++.||+|
T Consensus         1 k~~~G~iv~g~V~~v~~~g~~V~l~-----~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k   74 (74)
T PF00575_consen    1 KLKEGDIVEGKVTSVEDFGVFVDLG-----NGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEES-----TSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEEC-----CcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            47899999999     899999997     3799999999999999999999999999999999999999999999986

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....

>PHA02945 interferon resistance protein; Provisional

Probab=99.45  E-value=4.7e-13  Score=97.03  Aligned_cols=75  Identities=31%  Similarity=0.396  Sum_probs=67.5

Q ss_pred             cCCCCCcEEEEE----EeeEEEEEecCCCcceeEEEEEceec--ccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVSEV--SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        54 ~~~~~G~iv~g~----~~G~fV~l~~~~g~~g~~glv~isel--s~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      .-+++|+++.|+    +||+||.|.+++   |.+||+|+|+.  +..++++ ++++ .||++.|||+++|+.++.|.||+
T Consensus         7 ~~P~~GelvigtV~~~d~ga~v~L~EY~---g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSl   81 (88)
T PHA02945          7 SLPNVGDVLKGKVYENGYALYIDLFDYP---HSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNY   81 (88)
T ss_pred             cCCCCCcEEEEEEEecCceEEEEecccC---CcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEe
Confidence            346899999999    999999998643   69999999955  9999999 9999 99999999999999999999999


Q ss_pred             eecccC
Q 026737          128 KQLEED  133 (234)
Q Consensus       128 K~~~~~  133 (234)
                      |++.++
T Consensus        82 K~V~~~   87 (88)
T PHA02945         82 KRMCRH   87 (88)
T ss_pred             eEcccC
Confidence            998654

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

Probab=99.45  E-value=7e-13  Score=94.18  Aligned_cols=71  Identities=34%  Similarity=0.489  Sum_probs=64.1

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      ++.|+++.|+     ++|+||++.+.   ++.+||+|+++++++++.++.+.|++||.++|+|+++|.+++++.||+|+
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~---~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~   76 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEY---GNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCC---CCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            3679999998     99999999621   14899999999999999999999999999999999999989999999975

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

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

Probab=99.45  E-value=3.6e-13  Score=94.36  Aligned_cols=65  Identities=29%  Similarity=0.396  Sum_probs=60.5

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      |+++.|+     ++|+||++.     ++++||+|+++++++++.++.+.|++||.++++|+++|++++++.||+|
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~-----~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k   70 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFY-----NNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEEC-----CCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            6788888     999999997     3699999999999999999999999999999999999999999999986

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.

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

Probab=99.44  E-value=5.3e-13  Score=94.72  Aligned_cols=67  Identities=33%  Similarity=0.541  Sum_probs=60.0

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      ++.|++++|+     +||+||++.+    .+.+||+|+++++|.++.++.+.|++||+++|+|+++|.++ ++.||+
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~~----~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIPG----CRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEECC----CCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence            3579999998     9999999962    23699999999999999999999999999999999999865 999986

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

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

Probab=99.44  E-value=5.5e-13  Score=94.22  Aligned_cols=68  Identities=26%  Similarity=0.418  Sum_probs=63.0

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      +++|+++.|+     ++|+||+|+     ++++|++|++++++++..++.+.|++||.++++|+++|.+++++.||+|
T Consensus         1 ~~~G~iv~g~V~~v~~~gi~v~l~-----~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~   73 (73)
T cd05706           1 LKVGDILPGRVTKVNDRYVLVQLG-----NKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeC-----CCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            4689999998     999999997     4799999999999998888889999999999999999999999999985

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.

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

Probab=99.42  E-value=8.3e-13  Score=132.89  Aligned_cols=210  Identities=20%  Similarity=0.249  Sum_probs=151.5

Q ss_pred             CCCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCCCEEEEEechhhHh------hhhcCCCCCcEEEEE-----EeeE
Q 026737            1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWN------KYSSRVNVEDIFVGR-----DYGA   69 (234)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~------~~~~~~~~G~iv~g~-----~~G~   69 (234)
                      +++.|+..||........  .+|..+.++|+.++.+.+++.|+++.+..+      .-.++..+|+++.|+     ++||
T Consensus       538 lp~~hlsd~~~~~p~~~f--~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~  615 (1710)
T KOG1070|consen  538 LPKEHLSDHPLQPPLRDF--KVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGA  615 (1710)
T ss_pred             cChHhhhhccccccccee--eeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCe
Confidence            467788888877664332  388888889999999999999999987532      234567899999999     9999


Q ss_pred             EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchh----hhhccccc
Q 026737           70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE----TLEKVIPQ  145 (234)
Q Consensus        70 fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~----~~~~~~~~  145 (234)
                      ||.+.+     |++||.|.++++++++.++++.|.+||++.++|+++|++++||.||+|+...  |..    ..+. +..
T Consensus       616 ~V~F~g-----~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~--~~a~~~~~~e~-~~~  687 (1710)
T KOG1070|consen  616 FVTFTG-----GLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSC--ARACVKRSVEN-FVK  687 (1710)
T ss_pred             EEEecC-----ccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhhh--HHHHHHHHHHH-hhc
Confidence            999983     7999999999999999999999999999999999999999999999997653  321    1222 222


Q ss_pred             c-cc----------ceeeeecC-CceEEE-EccccccccccccccccccccCCCCCccee-eeeeCCCEEEEEEeeecc-
Q 026737          146 G-LE----------PYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFT-LLARAGRQVQEIQLSHSL-  210 (234)
Q Consensus       146 G-~~----------G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~G~~v~~~vl~~d~-  210 (234)
                      | +.          -+.|++.+ |+.|++ +.++....-+.+....-.+.      .+.+ ..+-+|+.+.++|++++. 
T Consensus       688 g~v~s~~~~~~tkd~viVei~~~~~~~v~~~~~L~dg~v~~~~~~~~kl~------~~t~~~~lv~gq~~~~~i~~isl~  761 (1710)
T KOG1070|consen  688 GGVKSLKSIDKTKDSVIVEIVDQGITGVGVFGELVDGSVVVNKVLENKLR------KNTSLLHLVVGQVTVGVILSISLK  761 (1710)
T ss_pred             cccccceeehhccccEEEEccCcceEEEEEEEEEccCceEEccchhhhhh------hcchhheeeecceeEEEEEEeehh
Confidence            3 21          45777765 588877 66654333333322211111      1111 135899999999999996 


Q ss_pred             ---chhhhcccccchhHHH
Q 026737          211 ---IRKASKRHCNEYWNVF  226 (234)
Q Consensus       211 ---i~ls~K~~~~~p~~~~  226 (234)
                         +.+++++-+++-...+
T Consensus       762 k~lv~~s~~~~L~~~~~~l  780 (1710)
T KOG1070|consen  762 KSLVLISLCTDLPNNATKL  780 (1710)
T ss_pred             hhhhhccccccccchHHHH
Confidence               6666666665443333

>PRK07252 hypothetical protein; Provisional

Probab=99.42  E-value=8.5e-13  Score=102.68  Aligned_cols=75  Identities=36%  Similarity=0.657  Sum_probs=68.8

Q ss_pred             CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 026737           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (234)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~  131 (234)
                      ++|+++.|+     ++|+||+|+     ++++||+|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+|++.
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~-----~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~   76 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALE-----NGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE   76 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEEC-----CCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence            579999998     999999997     3699999999999999999999999999999999999999999999999998


Q ss_pred             cCc-ch
Q 026737          132 EDP-LL  136 (234)
Q Consensus       132 ~~p-~~  136 (234)
                      +++ |.
T Consensus        77 ~~~~~~   82 (120)
T PRK07252         77 EEKQHF   82 (120)
T ss_pred             cCcccc
Confidence            754 53

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

Probab=99.41  E-value=8.9e-13  Score=92.29  Aligned_cols=64  Identities=22%  Similarity=0.437  Sum_probs=59.5

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      |++++|+     ++|+||+++     ++++||+|++++++.+..++.+.|++||.++++|+++|++++++.||+
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~-----~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~   69 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLS-----DHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEec-----CCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            6788888     999999997     379999999999999999999999999999999999999999999985

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.

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

Probab=99.41  E-value=7e-13  Score=93.73  Aligned_cols=57  Identities=26%  Similarity=0.402  Sum_probs=53.7

Q ss_pred             EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      +||+||++.     ++++||+|+|++++.+..++.+.|++||.++++|+++|+.++++.||+
T Consensus        15 ~~G~~V~l~-----~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696          15 DLGAVFELK-----DGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CceEEEEeC-----CCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            799999997     379999999999999999999999999999999999999999999985

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.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.40  E-value=4.9e-13  Score=119.29  Aligned_cols=86  Identities=21%  Similarity=0.227  Sum_probs=74.7

Q ss_pred             hC-CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec--CCceEEE-Eccccccccccccccc
Q 026737          103 LN-EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY--KKMDDVR-ITRQGFEKRVVSQDLQ  178 (234)
Q Consensus       103 ~~-vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~--~gi~Gl~-~s~~~~~~~~~~~~~~  178 (234)
                      |. +|+.|.++|.++..                       +      |+||+|.  +|++||+ +|+++|.         
T Consensus        14 ~P~~GdvV~g~V~~I~d-----------------------~------GafV~L~EY~gvEGlIhiSElS~~---------   55 (319)
T PTZ00248         14 FPEEDDLVMVKVVRITE-----------------------M------GAYVSLLEYDDIEGMILMSELSKR---------   55 (319)
T ss_pred             CCCCCCEEEEEEEEEeC-----------------------C------eEEEEecCCCCcEEEEEHHHhccc---------
Confidence            44 89999999999864                       5      9999996  6999999 8998542         


Q ss_pred             cccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcccCC
Q 026737          179 LWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAIVNN  234 (234)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~~~~  234 (234)
                         ..     .+++.++++||+|.|+||++|+    |+||+|++.++||+.+.++|+.|+
T Consensus        56 ---ri-----~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~pw~~~~e~~~~g~  107 (319)
T PTZ00248         56 ---RI-----RSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSPEDIEACEEKFSKSK  107 (319)
T ss_pred             ---cc-----CCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecccchHHHHHHhCcCCC
Confidence               21     4577799999999999999986    999999999999999999999874

>PRK08059 general stress protein 13; Validated

Probab=99.39  E-value=2e-12  Score=100.97  Aligned_cols=76  Identities=46%  Similarity=0.813  Sum_probs=71.4

Q ss_pred             cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      +++++|+++.|+     ++|+||++.     ++++|++|+++++++++.++.+.|++||.|+|+|+++|.+++++.||+|
T Consensus         3 ~~~k~G~iv~G~V~~i~~~G~fV~i~-----~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk   77 (123)
T PRK08059          3 SQYEVGSVVTGKVTGIQPYGAFVALD-----EETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR   77 (123)
T ss_pred             ccCCCCCEEEEEEEEEecceEEEEEC-----CCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEE
Confidence            468999999999     999999997     3699999999999999999999999999999999999999999999999


Q ss_pred             ecccCc
Q 026737          129 QLEEDP  134 (234)
Q Consensus       129 ~~~~~p  134 (234)
                      ++..+|
T Consensus        78 ~~~~~~   83 (123)
T PRK08059         78 ATEEAP   83 (123)
T ss_pred             EcccCc
Confidence            998888

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

Probab=99.39  E-value=2.3e-12  Score=90.64  Aligned_cols=68  Identities=34%  Similarity=0.562  Sum_probs=62.5

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~  131 (234)
                      |+++.|+     ++|+||++.     ++++|++|+++++++++.++.+.|++||.++|+|+++|++++++.||+|+++
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~-----~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~~   73 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLG-----DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE   73 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeC-----CCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence            6778887     999999997     3699999999999999999999999999999999999998899999999763

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.

>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.39  E-value=2.5e-12  Score=91.78  Aligned_cols=68  Identities=16%  Similarity=0.149  Sum_probs=60.7

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      ++++|+++.|+     ++|+||+++ .   .+++||+|.++++|.      +.+++||.+.|+|+++|++++++.||+|+
T Consensus         1 dl~~G~~v~g~V~si~d~G~~v~~g-~---~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~   70 (74)
T cd05694           1 DLVEGMVLSGCVSSVEDHGYILDIG-I---PGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADP   70 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeC-C---CCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            37899999999     999999995 1   169999999999986      66899999999999999999999999998


Q ss_pred             ccc
Q 026737          130 LEE  132 (234)
Q Consensus       130 ~~~  132 (234)
                      +.+
T Consensus        71 ~~~   73 (74)
T cd05694          71 SKV   73 (74)
T ss_pred             ccc
Confidence            764

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

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

Probab=99.36  E-value=1.8e-12  Score=90.46  Aligned_cols=63  Identities=29%  Similarity=0.470  Sum_probs=58.4

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      |+++.|+     ++|+||++.     ++++||+|++++++++..++.+.|++||.++|+|+++|++++++.||
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~-----~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls   68 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLG-----RGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeC-----CCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            6778887     999999997     36999999999999999999999999999999999999999999886

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.

>PRK05807 hypothetical protein; Provisional

Probab=99.36  E-value=2.9e-12  Score=101.77  Aligned_cols=70  Identities=46%  Similarity=0.722  Sum_probs=65.6

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      .+++|++++|+     ++|+||+|+      +..||||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|+
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L~------~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~   74 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEVE------GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQ   74 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence            36889999999     999999995      58999999999999999999999999999999999998 7999999999


Q ss_pred             cc
Q 026737          130 LE  131 (234)
Q Consensus       130 ~~  131 (234)
                      +.
T Consensus        75 ~~   76 (136)
T PRK05807         75 AM   76 (136)
T ss_pred             cc
Confidence            86

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

Probab=99.36  E-value=1e-12  Score=112.80  Aligned_cols=76  Identities=36%  Similarity=0.639  Sum_probs=71.7

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~  130 (234)
                      +.+|++|-|+     +||+||.|..++   |++||+|+||++..+++++++++++||.+-|+|+++|+.++.|.||+|.+
T Consensus         9 PeeGEiVv~tV~~V~~~GAyv~L~EY~---g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV   85 (269)
T COG1093           9 PEEGEIVVGTVKQVADYGAYVELDEYP---GKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRV   85 (269)
T ss_pred             CCCCcEEEEEEEEeeccccEEEeeccC---CeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhC
Confidence            6899999999     999999998654   69999999999999999999999999999999999999999999999999


Q ss_pred             ccCc
Q 026737          131 EEDP  134 (234)
Q Consensus       131 ~~~p  134 (234)
                      .++.
T Consensus        86 ~~~q   89 (269)
T COG1093          86 TEHQ   89 (269)
T ss_pred             CHHH
Confidence            8765

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

Probab=99.36  E-value=5.2e-12  Score=89.60  Aligned_cols=70  Identities=41%  Similarity=0.643  Sum_probs=63.8

Q ss_pred             CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (234)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~  130 (234)
                      ++|+++.|+     ++|+||++.+    .+.+|++|++++++.+..++.+.|++||.++|+|+++|.+++++.||+|+.
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~~----~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~   75 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDIDG----TNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECC----CCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            368999998     9999999972    258999999999999988999999999999999999999999999999975

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.

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

Probab=99.35  E-value=2.9e-12  Score=89.29  Aligned_cols=63  Identities=37%  Similarity=0.748  Sum_probs=56.7

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccc-ccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~-~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      |+++.|+     +||+||+++     ++++||+|+++++| .+..++.+.|++||.|+|+|+++|.+++++.||
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~-----~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLD-----GGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeC-----CCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            6777887     999999997     37999999999997 467889999999999999999999999999875

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.

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

Probab=99.34  E-value=6.9e-12  Score=90.09  Aligned_cols=71  Identities=35%  Similarity=0.663  Sum_probs=61.8

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc-cchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeeccc
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE  132 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~-~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~  132 (234)
                      |+++.|+     +||+||+|++.  .++.+||+|+++++|.++ .++.+.|++||.|+|+|+++|  ++++.||+|++.+
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~--~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~   76 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGL--KGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVDQ   76 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCC--CCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEeccc
Confidence            5677777     99999999721  014899999999999986 899999999999999999999  8999999999876


Q ss_pred             C
Q 026737          133 D  133 (234)
Q Consensus       133 ~  133 (234)
                      +
T Consensus        77 ~   77 (79)
T cd05684          77 D   77 (79)
T ss_pred             C
Confidence            5

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.

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

Probab=99.31  E-value=8.6e-12  Score=87.37  Aligned_cols=65  Identities=32%  Similarity=0.532  Sum_probs=60.2

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      |+++.|+     ++|+||+++     .+.+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~-----~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIG-----YKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeC-----CCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            6788888     889999997     3699999999999999999999999999999999999988899999986

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.

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

Probab=99.31  E-value=1.7e-12  Score=99.75  Aligned_cols=77  Identities=13%  Similarity=0.082  Sum_probs=66.3

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.++++|..+-+                       +      ||||+|++|-.||+ |||.+.          .++
T Consensus         3 ~kvG~~l~GkItgI~~-----------------------y------GAFV~l~~g~tGLVHISEIa~----------~fV   43 (129)
T COG1098           3 MKVGSKLKGKITGITP-----------------------Y------GAFVELEGGKTGLVHISEIAD----------GFV   43 (129)
T ss_pred             ccccceEEEEEEeeEe-----------------------c------ceEEEecCCCcceEEehHhhh----------hhH
Confidence            6789999999998864                       6      99999999999999 999852          233


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcccccchhHH
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRHCNEYWNV  225 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~~~~p~~~  225 (234)
                             .++.+.+++||+|+|+||.+|.   |+||||.+.+.|-..
T Consensus        44 -------kdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e~pe~~   83 (129)
T COG1098          44 -------KDIHDHLKVGQEVKVKVLDIDENGKISLSIRKLEEEPEKQ   83 (129)
T ss_pred             -------HhHHHHhcCCCEEEEEEEeeccCCCcceehHHhhhCcccc
Confidence                   3567799999999999999997   999999999888644

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

Probab=99.30  E-value=1.3e-11  Score=85.17  Aligned_cols=64  Identities=44%  Similarity=0.830  Sum_probs=58.9

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      |+++.|+     ++|+||+++     ++.+||+|.++++++++.++.+.|++||.++++|+++|. ++++.||+|
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~-----~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k   69 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELG-----GGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEEC-----CCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence            6777777     999999997     369999999999999999999999999999999999998 899999986

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

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

Probab=99.29  E-value=1.2e-11  Score=87.06  Aligned_cols=66  Identities=39%  Similarity=0.674  Sum_probs=58.4

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc-cccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~-~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      +++|+++.|+     +||+||++.     ++.+||+|+++++|. +..++.+.|++||.++|+|+++|.+++++.|+
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~-----~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELE-----EGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcC-----CCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence            5789999998     999999997     369999999999976 45577788999999999999999999998874

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.

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

Probab=99.24  E-value=2e-11  Score=92.00  Aligned_cols=71  Identities=30%  Similarity=0.466  Sum_probs=62.5

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc-------------------cchhhhhCCCCEEEE
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDEVRV  111 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~-------------------~~~~~~~~vGd~v~v  111 (234)
                      +++|+++.|+     ++|+||.|+     .+++|++|+++++|.+.                   .++.+.|++||.|+|
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L~-----~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~   75 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISLP-----NGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRC   75 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECC-----CCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEE
Confidence            5789999998     999999997     37999999999999763                   347788999999999


Q ss_pred             EEEEEeCC---CCeEEEEEeecc
Q 026737          112 KVIKIDRE---KSRITLSIKQLE  131 (234)
Q Consensus       112 kVl~id~~---~~ri~LS~K~~~  131 (234)
                      +|+++|++   +++|.||+|...
T Consensus        76 kVi~~d~~~~~~~~i~LSlr~~~   98 (100)
T cd05693          76 KVVSLDKSKSGKKRIELSLEPEL   98 (100)
T ss_pred             EEEEccCCcCCCcEEEEEecHHH
Confidence            99999987   799999998643

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

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

Probab=99.22  E-value=4.3e-11  Score=82.42  Aligned_cols=63  Identities=38%  Similarity=0.670  Sum_probs=57.3

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      |+++.|+     ++|+||+++     ++.+||+|.+++++.++.++.+.|++||.++|+|+++|.+++++.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~-----~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIG-----VKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcC-----CCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            5677777     999999997     36999999999999998899999999999999999999989999876

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.

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

Probab=99.21  E-value=7.8e-11  Score=81.94  Aligned_cols=62  Identities=27%  Similarity=0.545  Sum_probs=55.9

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      |++++|+     ++|+||+++      +++||+|.+++++.+..++...  +||.++|+|+++|.+++++.||+|
T Consensus         1 G~iv~g~V~~v~~~G~~v~l~------g~~gfip~s~~~~~~~~~~~~~--vG~~i~~~i~~vd~~~~~i~lS~k   67 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDIE------GVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHCCCcccCChHHh--CCCEEEEEEEEEeCCCCEEEEEcC
Confidence            6788887     999999995      6999999999999888877763  899999999999999999999985

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.

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

Probab=99.20  E-value=6.9e-11  Score=103.47  Aligned_cols=76  Identities=37%  Similarity=0.629  Sum_probs=69.4

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~  130 (234)
                      +++|+++.|+     ++|+||+|...+   +++||+|+|+++++++.++.+.|++||.+.|+|+++|.++++|.||+|++
T Consensus         6 P~~GdiV~G~V~~I~~~G~fV~L~e~~---gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v   82 (262)
T PRK03987          6 PEEGELVVGTVKEVKDFGAFVTLDEYP---GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRV   82 (262)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCCC---CcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEec
Confidence            6899999998     999999997321   59999999999999999999999999999999999999999999999988


Q ss_pred             ccCc
Q 026737          131 EEDP  134 (234)
Q Consensus       131 ~~~p  134 (234)
                      .++.
T Consensus        83 ~~~e   86 (262)
T PRK03987         83 NEHQ   86 (262)
T ss_pred             ccch
Confidence            7654

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

Probab=99.20  E-value=7.8e-11  Score=81.34  Aligned_cols=63  Identities=44%  Similarity=0.865  Sum_probs=58.1

Q ss_pred             CCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        58 ~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      +|+++.|+     ++|+||+++      +.+|++|.+++++.++.++.+.|++||.++|+|+++|.+++++.||
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~------~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLG------GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC------CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            48888888     999999996      5999999999999889899999999999999999999999999876

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.

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

Probab=99.19  E-value=8.6e-11  Score=85.65  Aligned_cols=70  Identities=23%  Similarity=0.363  Sum_probs=62.0

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccc----ccccchhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW----DLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~----~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~L  125 (234)
                      .+++|++|.|+     ++|++|+++     ++.+|++|++++++    .+..++.+.+++||.++|+|++++++ +++.|
T Consensus         3 ~p~~GdiV~g~V~~i~~~g~~v~i~-----~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~L   76 (86)
T cd05789           3 IPEVGDVVIGRVTEVGFKRWKVDIN-----SPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSL   76 (86)
T ss_pred             cCCCCCEEEEEEEEECCCEEEEECC-----CCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEE
Confidence            36899999999     999999997     37999999999996    45577888899999999999999875 99999


Q ss_pred             EEeec
Q 026737          126 SIKQL  130 (234)
Q Consensus       126 S~K~~  130 (234)
                      |+|+.
T Consensus        77 S~~~~   81 (86)
T cd05789          77 HTRSL   81 (86)
T ss_pred             EeCcc
Confidence            99874

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".

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

Probab=99.18  E-value=1.1e-10  Score=80.63  Aligned_cols=63  Identities=44%  Similarity=0.783  Sum_probs=57.3

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      |+++.|+     ++|+||+++     .+.+||+|+++++++++.++.+.|++||.++|+|+++|+ ++++.||+
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~-----~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~   68 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEIL-----PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeC-----CCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence            5677777     999999997     369999999999999998999999999999999999998 99999985

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.18  E-value=1.1e-10  Score=113.60  Aligned_cols=89  Identities=24%  Similarity=0.506  Sum_probs=73.0

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhhc--CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc---
Q 026737           31 IQANEEMKKLVFSEKDA--------VWNKYSS--RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS---   92 (234)
Q Consensus        31 i~id~~~~~i~lS~k~~--------~~~~~~~--~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels---   92 (234)
                      |++++ .+.+.++....        ..+.+..  .+++|++|+|+     +||+||+|.     +|.+||||+|+++   
T Consensus       611 Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~-----~G~eGLvHISeisdls  684 (719)
T TIGR02696       611 ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLL-----PGKDGLLHISQIRKLA  684 (719)
T ss_pred             EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEec-----CCceEEEEhhhccccc
Confidence            67775 57777765432        1333444  58999999999     999999997     4799999999996   


Q ss_pred             -cccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           93 -WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        93 -~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                       |.++.++.+.|++||.|+|||+++|. ++||+|+
T Consensus       685 ~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~  718 (719)
T TIGR02696       685 GGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV  718 (719)
T ss_pred             cccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence             46899999999999999999999995 8899986

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.

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

Probab=99.17  E-value=7.3e-11  Score=82.22  Aligned_cols=61  Identities=20%  Similarity=0.333  Sum_probs=53.4

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      |++++|+     ++|+||+|.     .+++||+|.++++..+..  .+.|++||.++|+|+++|+++++|.||
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~-----~~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFL-----SSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEc-----CCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            6788888     999999996     269999999999865544  677999999999999999999999886

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=99.15  E-value=1.5e-10  Score=113.71  Aligned_cols=93  Identities=34%  Similarity=0.615  Sum_probs=77.4

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc
Q 026737           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (234)
Q Consensus        31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~   97 (234)
                      +++++ .+.+.++....        ..+.+...+++|+++.|+     +||+||+|.     ++.+||+|+|+++|.++.
T Consensus       587 idi~d-~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~-----~~~~GllhiSels~~~v~  660 (693)
T PRK11824        587 IDIED-DGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEIL-----PGKDGLVHISEIADERVE  660 (693)
T ss_pred             cccCC-CceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEEC-----CCCEEEEEeeeccCcccc
Confidence            44443 46666665321        234455678999999999     999999997     479999999999999999


Q ss_pred             chhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (234)
Q Consensus        98 ~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~  130 (234)
                      ++.+.|++||.|+|+|+++|.+ +++.||+|.+
T Consensus       661 ~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~  692 (693)
T PRK11824        661 KVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV  692 (693)
T ss_pred             CccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence            9999999999999999999986 9999999976

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

Probab=99.12  E-value=4.1e-10  Score=77.60  Aligned_cols=67  Identities=43%  Similarity=0.725  Sum_probs=61.1

Q ss_pred             CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      ++|+++.|+     ++|+||+++     +++.|++|.+++++.+..++...|++||.++++|++++.+++++.||++
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~-----~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLG-----NGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeC-----CCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            368999998     889999997     3699999999999998888888999999999999999998899999975

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

Probab=99.11  E-value=3.6e-10  Score=83.27  Aligned_cols=69  Identities=26%  Similarity=0.411  Sum_probs=59.1

Q ss_pred             CCCCCcEEEEE-----Ee--eEEEEEecCCCcceeEEEEEceeccc---ccccchhhhhCCCCEEEEEEEEEeCCCCeEE
Q 026737           55 RVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSW---DLIQDIRDILNEGDEVRVKVIKIDREKSRIT  124 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~--G~fV~l~~~~g~~g~~glv~isels~---~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~  124 (234)
                      .+++|++|.|+     ++  ||||+|+     ++.+||||+|+++|   .++.++.+.+++||.|.|+|++.....+...
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~-----~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~   78 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIG-----LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPR   78 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeC-----CCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCce
Confidence            57899999999     65  9999997     37999999999999   6788899999999999999999876665555


Q ss_pred             EEEe
Q 026737          125 LSIK  128 (234)
Q Consensus       125 LS~K  128 (234)
                      ||.+
T Consensus        79 lt~~   82 (88)
T cd04453          79 LTTN   82 (88)
T ss_pred             EEEE
Confidence            5554

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

>PRK08582 hypothetical protein; Provisional

Probab=99.09  E-value=3.4e-10  Score=90.27  Aligned_cols=77  Identities=14%  Similarity=0.087  Sum_probs=64.8

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.+.++|..+..                       +      |+||+|.++++||+ +|+++++.          +
T Consensus         3 ~kvG~iv~G~V~~I~~-----------------------f------G~fV~L~~~~~GlVhiSels~~~----------v   43 (139)
T PRK08582          3 IEVGSKLQGKVTGITN-----------------------F------GAFVELPEGKTGLVHISEVADNY----------V   43 (139)
T ss_pred             CcCCCEEEEEEEEEEC-----------------------C------eEEEEECCCCEEEEEeeccCccc----------c
Confidence            6789999999999864                       4      99999999999999 88885321          1


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcccccchhHH
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRHCNEYWNV  225 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~~~~p~~~  225 (234)
                             .++...+++||.|+|+|+++|.   |.||+|++.++||..
T Consensus        44 -------~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~~~~~~   83 (139)
T PRK08582         44 -------KDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRPKRQ   83 (139)
T ss_pred             -------cccccccCCCCEEEEEEEEECCCCcEEEEEEecccCchhh
Confidence                   1234589999999999999984   999999999999964

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=99.07  E-value=2.5e-10  Score=110.90  Aligned_cols=75  Identities=37%  Similarity=0.648  Sum_probs=70.1

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      +.++++|++++|+     +||+||+|+     .+.+|+||+|+++..++.+|.+++++||.|+|+|+++|..+++|.|||
T Consensus       653 i~dLk~Gm~leg~Vrnv~~fgafVdIg-----v~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsm  727 (780)
T COG2183         653 ITDLKPGMILEGTVRNVVDFGAFVDIG-----VHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSM  727 (780)
T ss_pred             HhhccCCCEEEEEEEEeeeccceEEec-----cccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEe
Confidence            3579999999999     999999997     478999999999999999999999999999999999999999999999


Q ss_pred             eeccc
Q 026737          128 KQLEE  132 (234)
Q Consensus       128 K~~~~  132 (234)
                      +....
T Consensus       728 r~~~~  732 (780)
T COG2183         728 RLDEE  732 (780)
T ss_pred             eccCC
Confidence            97654

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

Probab=99.06  E-value=9.6e-10  Score=79.05  Aligned_cols=66  Identities=30%  Similarity=0.610  Sum_probs=55.7

Q ss_pred             CCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc-----------chhhhhCCCCEEEEEEEEEeCCCC
Q 026737           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKS  121 (234)
Q Consensus        58 ~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~-----------~~~~~~~vGd~v~vkVl~id~~~~  121 (234)
                      +|++++|+     ++|+||+++.    ++.+|++|++++++.++.           +....|++||.|+|+|.++|.+++
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~----~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~   76 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDN----LTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRR   76 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecC----CCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccC
Confidence            37888888     9999999972    269999999999876432           345779999999999999999899


Q ss_pred             eEEEEE
Q 026737          122 RITLSI  127 (234)
Q Consensus       122 ri~LS~  127 (234)
                      ++.|++
T Consensus        77 ~i~~~l   82 (83)
T cd04471          77 KIDFEL   82 (83)
T ss_pred             EEEEEE
Confidence            999986

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.04  E-value=7e-11  Score=117.28  Aligned_cols=110  Identities=12%  Similarity=0.056  Sum_probs=81.3

Q ss_pred             EeeEE-EEEecCCCcceeEEEEEceecccccccch-------hhhhCCCCEEE-EEEEEEeCCCCeEEEEEeecccCcch
Q 026737           66 DYGAF-IHLRFPDGLYHLTGLVHVSEVSWDLIQDI-------RDILNEGDEVR-VKVIKIDREKSRITLSIKQLEEDPLL  136 (234)
Q Consensus        66 ~~G~f-V~l~~~~g~~g~~glv~isels~~~~~~~-------~~~~~vGd~v~-vkVl~id~~~~ri~LS~K~~~~~p~~  136 (234)
                      ++|+- +++.       -+|-+++.--+...+...       -...++|+.+. ++|.++-.                  
T Consensus       713 etg~~~Idi~-------ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~------------------  767 (891)
T PLN00207        713 ETGVEAIDTQ-------DDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAP------------------  767 (891)
T ss_pred             HHCCCccCcC-------CCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEec------------------
Confidence            67775 7775       357776664443333222       22356888885 57877743                  


Q ss_pred             hhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---ch
Q 026737          137 ETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IR  212 (234)
Q Consensus       137 ~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~  212 (234)
                           +      |+||+|.+|++||+ +|+++++..                 .++..++++||.|+|+|+++|.   |+
T Consensus       768 -----F------GaFVeL~~g~EGLVHISeLs~~rv-----------------~~~~dv~kvGD~V~VkVi~ID~~grI~  819 (891)
T PLN00207        768 -----Y------GAFVEIAPGREGLCHISELSSNWL-----------------AKPEDAFKVGDRIDVKLIEVNDKGQLR  819 (891)
T ss_pred             -----c------EEEEEeCCCCEEEEEhhhcCCccc-----------------cCHHHhcCCCCEEEEEEEEECCCCcEE
Confidence                 4      99999999999999 899854321                 2344589999999999999995   99


Q ss_pred             hhhcccccchhHHHHh
Q 026737          213 KASKRHCNEYWNVFHE  228 (234)
Q Consensus       213 ls~K~~~~~p~~~~~~  228 (234)
                      ||+|++.++||+.+.+
T Consensus       820 LSlK~l~~~Pw~~~~~  835 (891)
T PLN00207        820 LSRRALLPEANSEKSS  835 (891)
T ss_pred             EEEeccccCchhhhhh
Confidence            9999999999998866

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

Probab=99.03  E-value=5.8e-10  Score=106.96  Aligned_cols=94  Identities=36%  Similarity=0.631  Sum_probs=80.8

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc
Q 026737           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (234)
Q Consensus        31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~   97 (234)
                      ++++ +.+.+.++....        ..+.....+++|++|.|+     +||+||++.     +|-+|+||+|++++.++.
T Consensus       585 Idie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~-----~gkdgl~hiS~~~~~rv~  658 (692)
T COG1185         585 IDIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELL-----PGKDGLVHISQLAKERVE  658 (692)
T ss_pred             EEec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEec-----CCcceeEEehhhhhhhhh
Confidence            6676 566666665432        245667889999999999     999999998     479999999999999999


Q ss_pred             chhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 026737           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (234)
Q Consensus        98 ~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~  131 (234)
                      ...+.+++||.+.||++.+|. .+|+.||+|...
T Consensus       659 kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~~  691 (692)
T COG1185         659 KVEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAVL  691 (692)
T ss_pred             cccceeecCceEEEEEeeecc-cCCccceehhcc
Confidence            999999999999999999996 899999998754

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=99.00  E-value=2.1e-09  Score=89.88  Aligned_cols=100  Identities=23%  Similarity=0.318  Sum_probs=79.9

Q ss_pred             CCEEEEEE---EEEeCCCCEEEEEechhhHhhhhcCCCCCcEEEEE-----EeeEEEEEecCC--C---cceeEEEEEce
Q 026737           23 GSIISVKV---IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPD--G---LYHLTGLVHVS   89 (234)
Q Consensus        23 G~~v~~~V---i~id~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~--g---~~g~~glv~is   89 (234)
                      +..+.+.+   +++|.+++++.+.    +|..+...+++|++|.|+     ++|+||+|...+  +   .++.+|++|.+
T Consensus        30 ~~~i~as~~G~~~id~~~~~Isv~----P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s  105 (189)
T PRK09521         30 NGEVYASVVGKVFIDDINRKISVI----PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHIS  105 (189)
T ss_pred             CCEEEEEeeEEEEEcCCCCEEEEe----cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhh
Confidence            45555544   5668888888775    355555678999999999     999999996221  0   02578999999


Q ss_pred             ecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           90 EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        90 els~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      ++++.+..++.+.|++||.|.|+|++++   +++.||+|+
T Consensus       106 ~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~  142 (189)
T PRK09521        106 QVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKG  142 (189)
T ss_pred             HcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEec
Confidence            9999988899999999999999999998   789999985

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

Probab=98.99  E-value=2.3e-09  Score=77.51  Aligned_cols=68  Identities=22%  Similarity=0.226  Sum_probs=62.6

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      +++|+++.|+     +.|++|+++     .+.+|++|.++++..+..++.+.|++||.+.|+|++++.+ +++.||++.
T Consensus         4 p~~GdiV~G~V~~v~~~~~~V~i~-----~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~   76 (82)
T cd04454           4 PDVGDIVIGIVTEVNSRFWKVDIL-----SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD   76 (82)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEeC-----CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence            5899999999     889999997     3699999999999888888999999999999999999986 899999986

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

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.94  E-value=2.6e-09  Score=104.94  Aligned_cols=88  Identities=34%  Similarity=0.647  Sum_probs=72.2

Q ss_pred             EEEeCCCCEEEEEech-h-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc
Q 026737           31 IQANEEMKKLVFSEKD-A-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (234)
Q Consensus        31 i~id~~~~~i~lS~k~-~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~   97 (234)
                      +++++ .|.+.++... .       ..+.+...+++|++|.|+     +||+||++.     ++.+||+|+|+++|.++.
T Consensus       584 I~i~d-dG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~-----~g~~GllHiSei~~~~v~  657 (684)
T TIGR03591       584 IDIED-DGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEIL-----PGKDGLVHISEIANERVE  657 (684)
T ss_pred             EEEec-CeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEEC-----CCcEEEEEHHHcCCCccc
Confidence            56665 4666666432 1       233455678999999999     999999997     479999999999999999


Q ss_pred             chhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737           98 DIRDILNEGDEVRVKVIKIDREKSRITL  125 (234)
Q Consensus        98 ~~~~~~~vGd~v~vkVl~id~~~~ri~L  125 (234)
                      ++.+.|++||.|+|+|+++|. +++++|
T Consensus       658 ~~~~~~kvGD~V~VkVi~id~-~gki~L  684 (684)
T TIGR03591       658 KVEDVLKEGDEVKVKVLEIDK-QGRIKL  684 (684)
T ss_pred             ChhhccCCCCEEEEEEEEECC-CCCccC
Confidence            999999999999999999997 787764

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).

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

Probab=98.89  E-value=5.1e-09  Score=73.44  Aligned_cols=57  Identities=21%  Similarity=0.256  Sum_probs=50.9

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccc--ccchhhhhCCCCEEEEEEEEEeCCC
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREK  120 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~--~~~~~~~~~vGd~v~vkVl~id~~~  120 (234)
                      |+++.|+     ++|+||+++     ++++|++|++++++++  ..++.+.|++||.++|+|+++|.++
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~-----~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~   64 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLA-----DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK   64 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeC-----CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence            6788887     889999997     4799999999999885  7889999999999999999999754

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

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

Probab=98.88  E-value=4.9e-09  Score=70.77  Aligned_cols=56  Identities=45%  Similarity=0.781  Sum_probs=51.7

Q ss_pred             EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      ++|+||+++     ++.+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||
T Consensus        10 ~~g~~v~l~-----~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164          10 KFGVFVELE-----DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             eeeEEEEec-----CCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            899999997     36999999999999988888999999999999999999988888875

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.

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

Probab=98.87  E-value=1.4e-08  Score=72.65  Aligned_cols=61  Identities=34%  Similarity=0.578  Sum_probs=53.7

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      ..+++.|+++.|+     ++|+||++.     ++.+||+|.+++.        +.|++||.++++|.++ .+++++.+|+
T Consensus        11 ~~~~~~G~~~~g~V~~i~~~G~fV~l~-----~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~   76 (77)
T cd04473          11 MEDLEVGKLYKGKVNGVAKYGVFVDLN-----DHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP   76 (77)
T ss_pred             hhhCCCCCEEEEEEEeEecceEEEEEC-----CCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence            3458999999999     999999997     3699999999864        4489999999999999 7899999986

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.

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

Probab=98.85  E-value=1.3e-08  Score=76.31  Aligned_cols=65  Identities=31%  Similarity=0.567  Sum_probs=56.4

Q ss_pred             EeeEEEEEecCCCcceeEEEEEceecccccccch-----------hhhhCCCCEEEEEEEEEeCCC-----CeEEEEEee
Q 026737           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----------RDILNEGDEVRVKVIKIDREK-----SRITLSIKQ  129 (234)
Q Consensus        66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~-----------~~~~~vGd~v~vkVl~id~~~-----~ri~LS~K~  129 (234)
                      ++|+||++.      +++|++|+++++++++...           ...|++||.++++|.++|.+.     .++.||+|+
T Consensus        12 ~~GifV~l~------~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~   85 (99)
T cd04460          12 DFGAFVRIG------PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMRQ   85 (99)
T ss_pred             eccEEEEEc------CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEec
Confidence            999999996      4999999999998876533           477999999999999999764     589999999


Q ss_pred             cccCcch
Q 026737          130 LEEDPLL  136 (234)
Q Consensus       130 ~~~~p~~  136 (234)
                      ....||+
T Consensus        86 ~~~g~~~   92 (99)
T cd04460          86 PGLGKLE   92 (99)
T ss_pred             CCCCcHH
Confidence            9888875

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.

>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=98.84  E-value=5.9e-09  Score=73.99  Aligned_cols=67  Identities=9%  Similarity=0.018  Sum_probs=53.0

Q ss_pred             CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737          106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA  184 (234)
Q Consensus       106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~  184 (234)
                      |+.|.++|.++..                       +      |+||+|.++++|++ .|+++++..           ..
T Consensus         1 G~~V~g~V~~i~~-----------------------~------g~~V~l~~~i~G~i~~~~ls~~~~-----------~~   40 (73)
T cd05703           1 GQEVTGFVNNVSK-----------------------E------FVWLTISPDVKGRIPLLDLSDDVS-----------VL   40 (73)
T ss_pred             CCEEEEEEEEEeC-----------------------C------EEEEEeCCCcEEEEEHHHcCCccc-----------cc
Confidence            7888888888763                       4      99999999999999 788753310           00


Q ss_pred             CCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737          185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK  216 (234)
Q Consensus       185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K  216 (234)
                          .++...+++||.|+++|+++|+    |.||+|
T Consensus        41 ----~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k   72 (73)
T cd05703          41 ----EHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             ----cCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence                2355689999999999999996    999886

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.

>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=98.84  E-value=8.6e-09  Score=73.40  Aligned_cols=69  Identities=12%  Similarity=0.064  Sum_probs=54.0

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++||.|.++|.++..                       +      |+||+|.+|++|++ ++++++..          .
T Consensus         1 ~k~G~~V~g~V~~i~~-----------------------~------G~fV~l~~~v~G~v~~~~ls~~~----------~   41 (74)
T cd05705           1 IKEGQLLRGYVSSVTK-----------------------Q------GVFFRLSSSIVGRVLFQNVTKYF----------V   41 (74)
T ss_pred             CCCCCEEEEEEEEEeC-----------------------C------cEEEEeCCCCEEEEEHHHccCcc----------c
Confidence            4789999999998853                       4      99999999999999 78885432          1


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhh
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKA  214 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls  214 (234)
                      .  +  ..++...+++||.|+++|+++|.    |.||
T Consensus        42 ~--~--~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS   74 (74)
T cd05705          42 S--D--PSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             c--C--hhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            1  1  12355689999999999999985    6664

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

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

Probab=98.75  E-value=1.9e-08  Score=71.09  Aligned_cols=69  Identities=14%  Similarity=-0.006  Sum_probs=54.8

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.+.++|.++.+                      .+      |+|++|.+|.+|++ +|+++++          |.
T Consensus         1 l~~G~iv~G~V~~i~~----------------------~~------g~~v~l~~~~~Glvhis~~s~~----------~~   42 (72)
T cd05704           1 LEEGAVTLGMVTKVIP----------------------HS------GLTVQLPFGKTGLVSIFHLSDS----------YT   42 (72)
T ss_pred             CCCCCEEEEEEEEeeC----------------------Cc------EEEEECCCCCEEEEEHHHhcCc----------cc
Confidence            3689999999998742                      03      89999999999999 8888532          21


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc--chhhhc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL--IRKASK  216 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~--i~ls~K  216 (234)
                             .++.+.+++||.|+|+|+++|.  |+||+|
T Consensus        43 -------~~~~~~~~~Gd~v~~kV~~~~~~~i~LSl~   72 (72)
T cd05704          43 -------ENPLEGFKPGKIVRCCILSKKDGKYQLSLR   72 (72)
T ss_pred             -------CCHHHhCCCCCEEEEEEEEecCCEEEEEeC
Confidence                   2345688999999999999984  888875

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

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

Probab=98.70  E-value=6.1e-08  Score=68.25  Aligned_cols=68  Identities=19%  Similarity=0.218  Sum_probs=55.7

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.+.++|.++++                       +      |+||+|..|++|++ .++++++..          
T Consensus         2 ~~~G~iv~g~V~~v~~-----------------------~------g~~V~l~~~~~g~ip~~~l~~~~~----------   42 (74)
T PF00575_consen    2 LKEGDIVEGKVTSVED-----------------------F------GVFVDLGNGIEGFIPISELSDDRI----------   42 (74)
T ss_dssp             SSTTSEEEEEEEEEET-----------------------T------EEEEEESTSSEEEEEGGGSSSSEE----------
T ss_pred             CCCCCEEEEEEEEEEC-----------------------C------EEEEEECCcEEEEEEeehhcCccc----------
Confidence            5789999999999974                       3      99999999999999 788743311          


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK  216 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K  216 (234)
                             ..+...+++||.++|+|+++|.    +.||+|
T Consensus        43 -------~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k   74 (74)
T PF00575_consen   43 -------DDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             -------SSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             -------cccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence                   1234588999999999999996    888876

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 ....

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

Probab=98.69  E-value=4.2e-07  Score=78.96  Aligned_cols=158  Identities=14%  Similarity=0.092  Sum_probs=105.8

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechhhHhhhhcCCCCCcEEEEE-EeeEEEEEecCCCcceeEEEEEceecccccccchh
Q 026737           22 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR  100 (234)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~  100 (234)
                      +|++|++. +..|. .+++.++.+....  ....+--++++.-. +-|+|++.+     ..-+-+||++++...+    .
T Consensus        46 vGdev~vF-iY~D~-~~rl~aTt~~p~~--tvg~~g~~~Vv~v~~~lGaFlD~G-----l~KDl~vp~~elp~~~----~  112 (287)
T COG2996          46 VGDEVTVF-IYVDS-EDRLIATTREPKA--TVGEYGWLKVVEVNKDLGAFLDWG-----LPKDLLVPLDELPTLK----S  112 (287)
T ss_pred             cCcEEEEE-EEECC-CCceeheeecceE--eecceeEEEEEEEcCCcceEEecC-----CCcceeeehhhccccc----c
Confidence            99999998 45565 5667777765420  11122333444444 889999996     3479999999987531    0


Q ss_pred             hhhCCCCEEEEEEEEEeCCCCeEEEEEeec-----ccCcchhhhhcccccccc------ceeeeecCCceEEE-Eccccc
Q 026737          101 DILNEGDEVRVKVIKIDREKSRITLSIKQL-----EEDPLLETLEKVIPQGLE------PYLKSFYKKMDDVR-ITRQGF  168 (234)
Q Consensus       101 ~~~~vGd~v~vkVl~id~~~~ri~LS~K~~-----~~~p~~~~~~~~~~~G~~------G~fV~l~~gi~Gl~-~s~~~~  168 (234)
                      --+++||.+-|.+ .+|. ++||.-+++.-     .+.|....+.+....|++      |.||-++++.-|++ .||.. 
T Consensus       113 ~wpq~Gd~l~v~l-~~Dk-k~Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~-  189 (287)
T COG2996         113 LWPQKGDKLLVYL-YVDK-KGRIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERF-  189 (287)
T ss_pred             cCCCCCCEEEEEE-EEcc-CCcEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhc-
Confidence            1167999999988 8887 66998877631     223322222221222433      99999999999999 45531 


Q ss_pred             cccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcccc
Q 026737          169 EKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRHC  219 (234)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~~  219 (234)
                                              ...+.|+++++.|+.+..   |.||++...
T Consensus       190 ------------------------~~prlG~~l~~rVi~~reDg~lnLSl~p~~  219 (287)
T COG2996         190 ------------------------AEPRLGERLTARVIGVREDGKLNLSLRPRA  219 (287)
T ss_pred             ------------------------ccccCCceEEEEEEEEccCCeeeccccccc
Confidence                                    134899999999999965   999888654

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

Probab=98.69  E-value=2.1e-08  Score=94.24  Aligned_cols=77  Identities=29%  Similarity=0.453  Sum_probs=70.1

Q ss_pred             cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      .++..|-+|+|+     ++|+||++.     ++..||+|+|+|+..++.+|.+.+.+||.|.+|.++.|+ .+.+.+|.|
T Consensus       664 ~~l~~g~vy~~tIt~~rd~G~~V~l~-----p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~r  737 (760)
T KOG1067|consen  664 QDLEFGGVYTATITEIRDTGVMVELY-----PMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSSR  737 (760)
T ss_pred             cceEeeeEEEEEEeeecccceEEEec-----CCchhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehhh
Confidence            356777888888     999999998     578999999999999999999999999999999999997 888999999


Q ss_pred             ecccCcch
Q 026737          129 QLEEDPLL  136 (234)
Q Consensus       129 ~~~~~p~~  136 (234)
                      .+.++|-.
T Consensus       738 alLp~p~~  745 (760)
T KOG1067|consen  738 ALLPDPAT  745 (760)
T ss_pred             hhcCCccc
Confidence            99999853

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.69  E-value=2.2e-08  Score=94.28  Aligned_cols=96  Identities=19%  Similarity=0.277  Sum_probs=78.0

Q ss_pred             cCCCCEEEEEEEEEeCCCCEEEEEe-chh--------hHhhhhcCCC--CCcEEEEE-----EeeEEEEEecCCCcceeE
Q 026737           20 GLTGSIISVKVIQANEEMKKLVFSE-KDA--------VWNKYSSRVN--VEDIFVGR-----DYGAFIHLRFPDGLYHLT   83 (234)
Q Consensus        20 ~~vG~~v~~~Vi~id~~~~~i~lS~-k~~--------~~~~~~~~~~--~G~iv~g~-----~~G~fV~l~~~~g~~g~~   83 (234)
                      ..+|+.+.+.|...+  .+++.++. |+.        .++.++..|+  .|+++.|+     ++|+||+++      +++
T Consensus        87 ~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg------gve  158 (470)
T PRK09202         87 AEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG------RAE  158 (470)
T ss_pred             ccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC------CeE
Confidence            459999999988766  44444443 332        2446777787  99999999     889999996      699


Q ss_pred             EEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCC--eEEEEEee
Q 026737           84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ  129 (234)
Q Consensus        84 glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~--ri~LS~K~  129 (234)
                      ||+|.++++      |.+.|++||.++|+|++++++++  +|.||++.
T Consensus       159 a~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~  200 (470)
T PRK09202        159 AILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH  200 (470)
T ss_pred             EEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence            999999986      67889999999999999999877  99999864

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.65  E-value=1.5e-08  Score=99.06  Aligned_cols=100  Identities=15%  Similarity=0.113  Sum_probs=74.3

Q ss_pred             EeeEEEEEecCCCcceeEEEEEceecccccc-------cchhh--hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcch
Q 026737           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------QDIRD--ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL  136 (234)
Q Consensus        66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~-------~~~~~--~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~  136 (234)
                      .+|+-++|.       -+|.|.++..+....       .....  .+++|+.++++|.++..                  
T Consensus       606 ~tg~~Idi~-------d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~d------------------  660 (719)
T TIGR02696       606 ETGAEISIE-------DDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTA------------------  660 (719)
T ss_pred             HHCCEEEEe-------cCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEEC------------------
Confidence            889999997       468888875443322       23333  36799999999999864                  


Q ss_pred             hhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---ch
Q 026737          137 ETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IR  212 (234)
Q Consensus       137 ~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~  212 (234)
                           +      |+||+|.+|++||+ +|+++        ++ +|-..+    .++.+++++||+|+|+|+++|.   |+
T Consensus       661 -----f------GaFVel~~G~eGLvHISeis--------dl-s~~~rv----~~~~dv~kvGd~V~VKVl~ID~~gKI~  716 (719)
T TIGR02696       661 -----F------GAFVSLLPGKDGLLHISQIR--------KL-AGGKRV----ENVEDVLSVGQKIQVEIADIDDRGKLS  716 (719)
T ss_pred             -----c------eEEEEecCCceEEEEhhhcc--------cc-ccccCc----CCHHHcCCCCCEEEEEEEEECCCCCee
Confidence                 5      99999999999999 78874        11 232222    3567799999999999999995   66


Q ss_pred             hh
Q 026737          213 KA  214 (234)
Q Consensus       213 ls  214 (234)
                      |+
T Consensus       717 L~  718 (719)
T TIGR02696       717 LV  718 (719)
T ss_pred             ec
Confidence            64

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=98.65  E-value=7.1e-08  Score=79.99  Aligned_cols=79  Identities=32%  Similarity=0.574  Sum_probs=64.3

Q ss_pred             hhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc-----------chhhhhCCCCEEEEEEE
Q 026737           51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVI  114 (234)
Q Consensus        51 ~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~-----------~~~~~~~vGd~v~vkVl  114 (234)
                      .+.-+...|+++.|+     ++|+||+++      ..+|++|.+++.+++..           +....++.||.|+++|+
T Consensus        74 ~i~f~p~~gEvv~G~V~~v~~~GifV~lg------~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~  147 (179)
T TIGR00448        74 ALVFKPELGEIVEGEVIEIVEFGAFVSLG------PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIV  147 (179)
T ss_pred             EEEEeccCCCEEEEEEEEEEeeEEEEEeC------CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEE
Confidence            334467789999999     999999996      49999999998866542           23467999999999999


Q ss_pred             EEe-----CCCCeEEEEEeecccCcc
Q 026737          115 KID-----REKSRITLSIKQLEEDPL  135 (234)
Q Consensus       115 ~id-----~~~~ri~LS~K~~~~~p~  135 (234)
                      +++     ++..+|.+|+|+..-.|+
T Consensus       148 ~v~~~~~~~~~~~I~lt~k~~~LG~~  173 (179)
T TIGR00448       148 ALSLKDRRPEGSKIGLTMRQPLLGKL  173 (179)
T ss_pred             EEEccCCCCCcceEEEEeccCcCCcc
Confidence            998     567899999998665553

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

>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=98.64  E-value=7.7e-08  Score=67.81  Aligned_cols=50  Identities=12%  Similarity=-0.045  Sum_probs=39.5

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhh
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKAS  215 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~  215 (234)
                      |+||+|.+|++||+ +|+++++..                 .++...+++||.++++|+++|+    |+||+
T Consensus        17 G~~V~l~~gv~G~i~~s~l~~~~~-----------------~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696          17 GAVFELKDGLLGFVHISHLSDDKV-----------------PSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             eEEEEeCCCCEEEEEHHHCCcchh-----------------cCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            99999999999999 788743211                 1234579999999999999996    77764

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.

>PRK05807 hypothetical protein; Provisional

Probab=98.63  E-value=9.4e-08  Score=75.95  Aligned_cols=70  Identities=14%  Similarity=0.124  Sum_probs=57.8

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.+.++|..+.+                       +      |+||+| ++..||+ +|+++.+          |+
T Consensus         3 ~~vG~vv~G~Vt~i~~-----------------------~------GafV~L-~~~~Glvhiseis~~----------~v   42 (136)
T PRK05807          3 LKAGSILEGTVVNITN-----------------------F------GAFVEV-EGKTGLVHISEVADT----------YV   42 (136)
T ss_pred             ccCCCEEEEEEEEEEC-----------------------C------eEEEEE-CCEEEEEEhhhcccc----------cc
Confidence            6789999999999864                       4      999999 7899999 8887532          22


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcccc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRHC  219 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~~  219 (234)
                             .++...+++||.|+|+|+++|.   |+||+|++.
T Consensus        43 -------~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~   76 (136)
T PRK05807         43 -------KDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM   76 (136)
T ss_pred             -------cCccccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence                   2344578999999999999984   999999987

>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=98.62  E-value=1.3e-07  Score=66.45  Aligned_cols=68  Identities=19%  Similarity=0.135  Sum_probs=53.1

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.+.++|.++..                       +      |+||+|+++++|++ +|+++++.          .
T Consensus         1 ~~~G~iv~g~V~~v~~-----------------------~------gi~v~l~~~~~g~v~~s~l~~~~----------~   41 (73)
T cd05706           1 LKVGDILPGRVTKVND-----------------------R------YVLVQLGNKVTGPSFITDALDDY----------S   41 (73)
T ss_pred             CCCCCEEEEEEEEEeC-----------------------C------eEEEEeCCCcEEEEEhhhccCcc----------c
Confidence            3689999999998853                       3      99999999999999 77774321          0


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK  216 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K  216 (234)
                             .++...+++||.++++|+++|.    |.||+|
T Consensus        42 -------~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~   73 (73)
T cd05706          42 -------EALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             -------cccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence                   1234578999999999999984    777754

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.

>PRK07252 hypothetical protein; Provisional

Probab=98.62  E-value=1e-07  Score=74.21  Aligned_cols=75  Identities=9%  Similarity=0.055  Sum_probs=60.1

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~  182 (234)
                      ++|+.+.++|.++..                       +      |+||++.++++||+ +|+++++.          . 
T Consensus         2 kvG~iv~G~V~~V~~-----------------------~------G~fVei~~~~~GllhiseLs~~~----------~-   41 (120)
T PRK07252          2 KIGDKLKGTITGIKP-----------------------Y------GAFVALENGTTGLIHISEIKTGF----------I-   41 (120)
T ss_pred             CCCCEEEEEEEEEeC-----------------------c------EEEEEECCCCEEEEEHHHcCCcc----------c-
Confidence            479999999998864                       4      99999999999999 78875321          1 


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccccc-chhH
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCN-EYWN  224 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~-~p~~  224 (234)
                            .++...+++||.|+|+|+++|.    |.||+|++++ .+|.
T Consensus        42 ------~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~~~~   82 (120)
T PRK07252         42 ------DNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEKQHF   82 (120)
T ss_pred             ------cChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCcccc
Confidence                  1234578999999999999986    9999999977 4453

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.61  E-value=1.2e-07  Score=81.85  Aligned_cols=71  Identities=27%  Similarity=0.355  Sum_probs=62.9

Q ss_pred             cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc----cchhhhhCCCCEEEEEEEEEeCCCCeEE
Q 026737           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRIT  124 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~----~~~~~~~~vGd~v~vkVl~id~~~~ri~  124 (234)
                      ..+++|++|.|+     ++|+||+|+     .+.+|++|++++++.++    .++.+.|++||.|.|+|+++++ .+++.
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~-----~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~-~~~~~  132 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDIN-----SPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR-TRDVV  132 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeC-----CCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC-CCcEE
Confidence            346999999999     889999997     36899999999999987    7899999999999999999996 45699


Q ss_pred             EEEeec
Q 026737          125 LSIKQL  130 (234)
Q Consensus       125 LS~K~~  130 (234)
                      ||+|+.
T Consensus       133 LS~k~~  138 (235)
T PRK04163        133 LTLKGK  138 (235)
T ss_pred             EEEcCC
Confidence            999753

>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=98.59  E-value=1.2e-07  Score=66.14  Aligned_cols=65  Identities=18%  Similarity=0.171  Sum_probs=50.4

Q ss_pred             CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737          106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA  184 (234)
Q Consensus       106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~  184 (234)
                      |+.+.++|.++.+                       +      |+||+|.++++||+ +|+++.+. .            
T Consensus         1 g~~~~g~V~~v~~-----------------------~------G~~V~l~~~~~gli~~s~l~~~~-~------------   38 (70)
T cd05698           1 GLKTHGTIVKVKP-----------------------N------GCIVSFYNNVKGFLPKSELSEAF-I------------   38 (70)
T ss_pred             CCEEEEEEEEEec-----------------------C------cEEEEECCCCEEEEEHHHcChhh-c------------
Confidence            6778888887753                       4      99999999999999 78774321 1            


Q ss_pred             CCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737          185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK  216 (234)
Q Consensus       185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K  216 (234)
                          .++...+++||.++++|+++|+    +.||+|
T Consensus        39 ----~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k   70 (70)
T cd05698          39 ----KDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             ----CCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence                2244579999999999999986    777765

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.

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

Probab=98.58  E-value=3.3e-07  Score=64.25  Aligned_cols=63  Identities=13%  Similarity=0.197  Sum_probs=49.4

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      |++|+.+.++|.++.+                       +      |+||+|.+|++||+ ++++.++..          
T Consensus         1 ~~~g~~~~g~V~~i~~-----------------------~------G~fv~l~~~~~Gl~~~~~l~~~~~----------   41 (72)
T cd05689           1 YPEGTRLFGKVTNLTD-----------------------Y------GCFVELEEGVEGLVHVSEMDWTNK----------   41 (72)
T ss_pred             CcCCCEEEEEEEEEEe-----------------------e------EEEEEcCCCCEEEEEEEeccCccc----------
Confidence            4689999999988864                       4      99999999999999 787743211          


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                       .     .+....++.||+|+|+++++|.
T Consensus        42 -~-----~~~~~~~~~Gd~v~v~v~~id~   64 (72)
T cd05689          42 -N-----IHPSKVVSLGDEVEVMVLDIDE   64 (72)
T ss_pred             -c-----cCcccEeCCCCEEEEEEEEeeC
Confidence             0     1234579999999999999985

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

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

Probab=98.56  E-value=2e-07  Score=66.70  Aligned_cols=57  Identities=16%  Similarity=0.179  Sum_probs=45.4

Q ss_pred             ceeeeec---CCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc--chhhhcccccc
Q 026737          149 PYLKSFY---KKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL--IRKASKRHCNE  221 (234)
Q Consensus       149 G~fV~l~---~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~--i~ls~K~~~~~  221 (234)
                      |+||+|+   ++++||+ +|+++++..            .    .++...++.||.|+|+++++|.  +.||+|++.++
T Consensus        15 G~fv~l~~~~~~~~gll~~s~l~~~~~------------~----~~~~~~~~~Gd~v~v~v~~vd~~~i~~s~k~~~~~   77 (79)
T cd05684          15 GCFVQLEGLKGRKEGLVHISQLSFEGR------------V----ANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQD   77 (79)
T ss_pred             eEEEEEeCCCCCcEEEEEhHhccCCCC------------c----CChhheeCCCCEEEEEEEEEeCCEEEEEEEecccC
Confidence            9999998   4799999 788754321            0    1234589999999999999986  99999998865

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.

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

Probab=98.56  E-value=2.2e-07  Score=64.45  Aligned_cols=50  Identities=14%  Similarity=0.274  Sum_probs=38.2

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhh
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKA  214 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls  214 (234)
                      |+||+|+++++||+ +|+++|..+            .    .++...+++||+|+|+|+++|.    |+||
T Consensus        15 G~fv~l~~~~~Glv~~~~l~~~~~------------~----~~~~~~~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690          15 GIFVGLDGGIDGLVHISDISWTQR------------V----RHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             eEEEEeCCCCEEEEEHHHCCCccc------------c----CChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            99999999999999 777742211            1    2345589999999999999985    5554

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.

>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=98.56  E-value=2e-07  Score=66.38  Aligned_cols=66  Identities=11%  Similarity=0.012  Sum_probs=54.6

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec-CCceEEE-Eccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY-KKMDDVR-ITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~-~gi~Gl~-~s~~~~~~~~~~~~~~~~  180 (234)
                      ++.|+.+.+.|.++..                       +      |+||++. +|++||+ .++++            |
T Consensus         2 l~~G~~v~g~V~si~d-----------------------~------G~~v~~g~~gv~Gfl~~~~~~------------~   40 (74)
T cd05694           2 LVEGMVLSGCVSSVED-----------------------H------GYILDIGIPGTTGFLPKKDAG------------N   40 (74)
T ss_pred             CCCCCEEEEEEEEEeC-----------------------C------EEEEEeCCCCcEEEEEHHHCC------------c
Confidence            5689999999988864                       4      9999996 6999999 56652            2


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccccc
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCN  220 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~  220 (234)
                      .           ..+++||.+.|+|+++|+    +.||+|++.+
T Consensus        41 ~-----------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~   73 (74)
T cd05694          41 F-----------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV   73 (74)
T ss_pred             c-----------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            1           368999999999999986    9999998864

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.

>PRK08059 general stress protein 13; Validated

Probab=98.55  E-value=1.6e-07  Score=73.35  Aligned_cols=74  Identities=16%  Similarity=0.091  Sum_probs=61.3

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.+.++|.++.+                       +      |+||++.++++|++ +|+++.+.          .
T Consensus         5 ~k~G~iv~G~V~~i~~-----------------------~------G~fV~i~~~~~Gli~~sel~~~~----------~   45 (123)
T PRK08059          5 YEVGSVVTGKVTGIQP-----------------------Y------GAFVALDEETQGLVHISEITHGF----------V   45 (123)
T ss_pred             CCCCCEEEEEEEEEec-----------------------c------eEEEEECCCCEEEEEHHHCCccc----------c
Confidence            6789999999999864                       4      99999999999999 77774321          1


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccch
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEY  222 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p  222 (234)
                             .++...+++||.|+|+|+++|.    +.||+|++..+|
T Consensus        46 -------~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~~~   83 (123)
T PRK08059         46 -------KDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEAP   83 (123)
T ss_pred             -------cCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcccCc
Confidence                   2234578999999999999975    999999999888

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

Probab=98.54  E-value=3e-07  Score=65.03  Aligned_cols=66  Identities=8%  Similarity=0.024  Sum_probs=50.5

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC-CceEEE-Ecccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      ..|+.++++|.++.+                       +      |+||++.+ +.+||+ +|+++++ +.         
T Consensus         2 ~~g~~~~g~V~~i~~-----------------------f------G~fv~l~~~~~eGlvh~sel~~~-~~---------   42 (73)
T cd05686           2 ALYQIFKGEVASVTE-----------------------Y------GAFVKIPGCRKQGLVHKSHMSSC-RV---------   42 (73)
T ss_pred             cCCCEEEEEEEEEEe-----------------------e------eEEEEECCCCeEEEEEchhhCCC-cc---------
Confidence            468999999988864                       5      99999943 369999 8888543 11         


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhh
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKAS  215 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~  215 (234)
                             .++...+++||+|+|+|+++|.   |+||+
T Consensus        43 -------~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~   72 (73)
T cd05686          43 -------DDPSEVVDVGEKVWVKVIGREMKDKMKLSL   72 (73)
T ss_pred             -------cCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence                   2445689999999999999986   56654

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.

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

Probab=98.54  E-value=2.4e-07  Score=65.42  Aligned_cols=68  Identities=19%  Similarity=0.249  Sum_probs=53.6

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC--CceEEE-Eccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK--KMDDVR-ITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~--gi~Gl~-~s~~~~~~~~~~~~~~~~  180 (234)
                      +.|+.+.++|.++..                       +      |+||++.+  |++||+ +|+++++..         
T Consensus         2 ~~G~~~~g~V~~v~~-----------------------~------g~~v~l~~~~~~~gll~~s~l~~~~~---------   43 (76)
T cd04452           2 EEGELVVVTVKSIAD-----------------------M------GAYVSLLEYGNIEGMILLSELSRRRI---------   43 (76)
T ss_pred             CCCCEEEEEEEEEEc-----------------------c------EEEEEEcCCCCeEEEEEhHHcCCccc---------
Confidence            478999999988853                       3      99999974  699999 788753221         


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcc
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKR  217 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~  217 (234)
                              .++...++.||.|+|+|+++|.    +.||+|+
T Consensus        44 --------~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~   76 (76)
T cd04452          44 --------RSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             --------CCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence                    2345689999999999999985    8888875

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

>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=98.53  E-value=2e-07  Score=64.92  Aligned_cols=63  Identities=13%  Similarity=0.041  Sum_probs=48.7

Q ss_pred             CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737          106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA  184 (234)
Q Consensus       106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~  184 (234)
                      |+.+.++|.++..                       +      |+||+|.+|++|++ .++++++..             
T Consensus         1 G~~v~g~V~~v~~-----------------------~------Gv~V~l~~~v~g~i~~~~l~~~~~-------------   38 (69)
T cd05697           1 GQVVKGTIRKLRP-----------------------S------GIFVKLSDHIKGLVPPMHLADVRL-------------   38 (69)
T ss_pred             CCEEEEEEEEEec-----------------------c------EEEEEecCCcEEEEEHHHCCCccc-------------
Confidence            6888888888753                       3      99999999999999 677743311             


Q ss_pred             CCCCcceeeeeeCCCEEEEEEeeecc----chhh
Q 026737          185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKA  214 (234)
Q Consensus       185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls  214 (234)
                          .++...++.||.++++|+++|+    |.||
T Consensus        39 ----~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls   68 (69)
T cd05697          39 ----KHPEKKFKPGLKVKCRVLSVEPERKRLVLT   68 (69)
T ss_pred             ----cCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence                1234579999999999999985    5555

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.

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

Probab=98.53  E-value=3.3e-07  Score=63.77  Aligned_cols=59  Identities=17%  Similarity=0.281  Sum_probs=49.1

Q ss_pred             CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCC--CeEEEEE
Q 026737           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLSI  127 (234)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~--~ri~LS~  127 (234)
                      ..|++++|+     ++|+||+++      +.+|++|.++++.      .+.|++||.+++.|++++.++  .+|.||.
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig------~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr   67 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLG------KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcC------CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence            468999998     889999996      4899999999873      356899999999999999643  4677773

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.

>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=98.52  E-value=2.4e-07  Score=66.99  Aligned_cols=67  Identities=15%  Similarity=0.009  Sum_probs=53.9

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.+.++|.++..                       +      |+||+|.+|++|++ +++++++..          
T Consensus        12 ~~~G~i~~g~V~~v~~-----------------------~------G~fv~l~~~~~g~v~~~el~~~~~----------   52 (83)
T cd04461          12 LKPGMVVHGYVRNITP-----------------------Y------GVFVEFLGGLTGLAPKSYISDEFV----------   52 (83)
T ss_pred             CCCCCEEEEEEEEEee-----------------------c------eEEEEcCCCCEEEEEHHHCCcccc----------
Confidence            7899999999998864                       4      99999999999999 677743211          


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhh
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKAS  215 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~  215 (234)
                             .++...+++||.++|+|+++|.    |.||+
T Consensus        53 -------~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461          53 -------TDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             -------cCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence                   2345689999999999999985    66664

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.

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

Probab=98.49  E-value=3.3e-07  Score=64.08  Aligned_cols=54  Identities=9%  Similarity=0.000  Sum_probs=42.9

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccc
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHC  219 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~  219 (234)
                      |+||++.++++|++ +|+++.+.          .       .++...+++||.++++|+++|.    +.||+|+++
T Consensus        15 g~~v~l~~~~~g~i~~~~~~~~~----------~-------~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~~   73 (73)
T cd05691          15 GATVKLGDGVEGFLRAAELSRDR----------V-------EDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE   73 (73)
T ss_pred             eEEEEeCCCCEEEEEHHHCCCcc----------c-------cCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence            99999999999999 67764221          1       2345678999999999999985    899988753

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.

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

Probab=98.48  E-value=3.1e-07  Score=76.51  Aligned_cols=79  Identities=24%  Similarity=0.563  Sum_probs=63.1

Q ss_pred             HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc-----------chhhhhCCCCEEEEE
Q 026737           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVK  112 (234)
Q Consensus        49 ~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~-----------~~~~~~~vGd~v~vk  112 (234)
                      +..+...+..|+++.|+     ++|+||+++      .++|++|.+++.+++..           +....+++||.|+++
T Consensus        72 f~~lvf~P~~GEVv~g~V~~v~~~Gi~V~lg------~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~Vrvr  145 (187)
T PRK08563         72 FDALVFKPELQEVVEGEVVEVVEFGAFVRIG------PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRAR  145 (187)
T ss_pred             EEEEEEeccCCCEEEEEEEEEEccEEEEEEe------CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEE
Confidence            33445568899999999     999999997      49999999999876532           345678999999999


Q ss_pred             EEEEeCCC-----CeEEEEEeecccC
Q 026737          113 VIKIDREK-----SRITLSIKQLEED  133 (234)
Q Consensus       113 Vl~id~~~-----~ri~LS~K~~~~~  133 (234)
                      |++++.+.     .+|.+|+|+..--
T Consensus       146 V~~v~~~~~~~~~~~I~ls~~~~~LG  171 (187)
T PRK08563        146 IVAVSLKERRPRGSKIGLTMRQPGLG  171 (187)
T ss_pred             EEEEEcccCCCCCCEEEEEecCCCCC
Confidence            99999754     3899999975443

>TIGR02063 RNase_R ribonuclease R

Probab=98.44  E-value=6.8e-07  Score=88.50  Aligned_cols=69  Identities=28%  Similarity=0.549  Sum_probs=58.7

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc-----------cchhhhhCCCCEEEEEEEEEeC
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDR  118 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~-----------~~~~~~~~vGd~v~vkVl~id~  118 (234)
                      ..++|++++|+     +||+||+|.+    ++++|+||+++++++++           .+....|++||.|+|+|.++|.
T Consensus       624 ~~~iG~~~~g~V~~v~~fGifV~L~~----~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~  699 (709)
T TIGR02063       624 SEKIGEEFEGVISGVTSFGLFVELEN----NTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADL  699 (709)
T ss_pred             hccCCcEEEEEEEEEEeCCEEEEecC----CceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEec
Confidence            45789999998     9999999972    26999999999987653           2334679999999999999999


Q ss_pred             CCCeEEEEE
Q 026737          119 EKSRITLSI  127 (234)
Q Consensus       119 ~~~ri~LS~  127 (234)
                      .+++|.|++
T Consensus       700 ~~~~I~~~l  708 (709)
T TIGR02063       700 DTGKIDFEL  708 (709)
T ss_pred             ccCeEEEEE
Confidence            999999986

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.

>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=98.43  E-value=7e-07  Score=62.99  Aligned_cols=69  Identities=13%  Similarity=0.121  Sum_probs=54.3

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC-CceEEE-Ecccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      ++|+.+.++|.++.+                       .      |+||++.+ +++|++ +++++++..          
T Consensus         1 ~~g~~v~g~V~~i~~-----------------------~------g~~v~l~~~~~~g~i~~~~l~~~~~----------   41 (77)
T cd05708           1 KVGQKIDGTVRRVED-----------------------Y------GVFIDIDGTNVSGLCHKSEISDNRV----------   41 (77)
T ss_pred             CCCCEEEEEEEEEEc-----------------------c------eEEEEECCCCeEEEEEHHHCCCCcc----------
Confidence            368899999988864                       3      99999985 899999 677743211          


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRH  218 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~  218 (234)
                             .++...+++||.|+|+|+++|.    +.|++|+.
T Consensus        42 -------~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~   75 (77)
T cd05708          42 -------ADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             -------CCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence                   2245689999999999999985    88998875

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.

>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=98.40  E-value=8.1e-07  Score=61.65  Aligned_cols=45  Identities=13%  Similarity=0.139  Sum_probs=36.3

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      |+||+|.++++||+ +|+++++          |.       .++...+++||.++|+|+++|+
T Consensus        15 Gv~V~l~~~~~G~v~~s~l~~~----------~~-------~~~~~~~~~Gd~v~~~v~~~d~   60 (68)
T cd05707          15 GVFVTLGRGVDARVRVSELSDS----------YL-------KDWKKRFKVGQLVKGKIVSIDP   60 (68)
T ss_pred             cEEEEeCCCCEEEEEHHHCCch----------hh-------cCHhhccCCCCEEEEEEEEEeC
Confidence            99999999999999 7777422          11       2345688999999999999996

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.

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

Probab=98.40  E-value=3.7e-07  Score=88.00  Aligned_cols=110  Identities=18%  Similarity=0.184  Sum_probs=84.8

Q ss_pred             CCCcEEEEE--EeeEEEEEecCCCcceeEEEEEceeccc-------ccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           57 NVEDIFVGR--DYGAFIHLRFPDGLYHLTGLVHVSEVSW-------DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        57 ~~G~iv~g~--~~G~fV~l~~~~g~~g~~glv~isels~-------~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      +-|+++.+.  .+|+-++|+       -+|.|.++--+.       .++......+.+|+.+.++|.++..         
T Consensus       569 ~gGk~I~~I~eetg~~Idie-------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~---------  632 (692)
T COG1185         569 PGGKTIKAITEETGVKIDIE-------DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVD---------  632 (692)
T ss_pred             CcccchhhhhhhhCcEEEec-------CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEee---------
Confidence            445666666  999999997       456666653332       2345556668999999999988753         


Q ss_pred             eecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEe
Q 026737          128 KQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQL  206 (234)
Q Consensus       128 K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl  206 (234)
                                    +      |+||+|.+|-+||| +|++++. |+                .+.+++++.||.+.|+++
T Consensus       633 --------------f------GaFv~l~~gkdgl~hiS~~~~~-rv----------------~kv~dvlk~Gd~v~Vkv~  675 (692)
T COG1185         633 --------------F------GAFVELLPGKDGLVHISQLAKE-RV----------------EKVEDVLKEGDEVKVKVI  675 (692)
T ss_pred             --------------c------ceEEEecCCcceeEEehhhhhh-hh----------------hcccceeecCceEEEEEe
Confidence                          5      99999999999999 8998533 21                345569999999999999


Q ss_pred             eecc---chhhhcccc
Q 026737          207 SHSL---IRKASKRHC  219 (234)
Q Consensus       207 ~~d~---i~ls~K~~~  219 (234)
                      ++|+   ++|++|...
T Consensus       676 ~iD~~Gri~ls~~~~~  691 (692)
T COG1185         676 EIDKQGRIRLSIKAVL  691 (692)
T ss_pred             eecccCCccceehhcc
Confidence            9998   999999764

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=98.39  E-value=1.2e-06  Score=63.18  Aligned_cols=69  Identities=25%  Similarity=0.340  Sum_probs=62.7

Q ss_pred             cCCCCCcEEEEE----EeeEEEEEecCCCcceeEEEEE-ceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        54 ~~~~~G~iv~g~----~~G~fV~l~~~~g~~g~~glv~-isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      .-+++|+++.|.    +.|+||.|-+    ++.+|++. .+|++.+++....+.+ +|....|+|+.+|+++|.|.||.
T Consensus        12 ~~P~v~dvv~~Vv~i~d~~~YV~Lle----Y~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         12 VFPNINEVTKGIVFVKDNIFYVKLID----YGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             ecCCCCeEEEEEEEEeccEEEEEEec----CccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence            447899999987    9999999984    56899988 9999999999999999 99999999999999999999984

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

Probab=98.35  E-value=8.9e-07  Score=64.31  Aligned_cols=74  Identities=11%  Similarity=0.033  Sum_probs=56.5

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++||.|.++|+++..                       .      |+||++.++++|++ +|++++++..      .+ 
T Consensus         4 p~~GdiV~g~V~~i~~-----------------------~------g~~v~i~~~~~G~l~~se~~~~~~~------~~-   47 (86)
T cd05789           4 PEVGDVVIGRVTEVGF-----------------------K------RWKVDINSPYDAVLPLSEVNLPRTD------ED-   47 (86)
T ss_pred             CCCCCEEEEEEEEECC-----------------------C------EEEEECCCCeEEEEEHHHccCCCCc------cc-
Confidence            4689999999999864                       3      88999999999999 7777432100      01 


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhccc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRH  218 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~  218 (234)
                            ..++...+++||.++++|++++.   +.||+|+.
T Consensus        48 ------~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~   81 (86)
T cd05789          48 ------ELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL   81 (86)
T ss_pred             ------hHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence                  12345578999999999999984   89998874

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".

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.34  E-value=2.6e-07  Score=91.08  Aligned_cols=101  Identities=20%  Similarity=0.204  Sum_probs=75.7

Q ss_pred             EeeEEEEEecCCCcceeEEEEEceecccccc-------cchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhh
Q 026737           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET  138 (234)
Q Consensus        66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~-------~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~  138 (234)
                      .+|+-+++.       -+|.+++.-.....+       ......+++|+.+.++|.++..                    
T Consensus       582 ~~~~~idi~-------d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~--------------------  634 (693)
T PRK11824        582 ETGAKIDIE-------DDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVD--------------------  634 (693)
T ss_pred             HHCCccccC-------CCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEEC--------------------
Confidence            778877765       467777764443322       2223347899999999998864                    


Q ss_pred             hhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---chhh
Q 026737          139 LEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKA  214 (234)
Q Consensus       139 ~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls  214 (234)
                         +      |+||+|.+|++||+ +|+++++.          +       .++...+++||.|+|+|+++|.   |+||
T Consensus       635 ---f------GafVei~~~~~GllhiSels~~~----------v-------~~~~~v~kvGD~V~VkV~~iD~~grI~LS  688 (693)
T PRK11824        635 ---F------GAFVEILPGKDGLVHISEIADER----------V-------EKVEDVLKEGDEVKVKVLEIDKRGRIRLS  688 (693)
T ss_pred             ---C------eEEEEECCCCEEEEEeeeccCcc----------c-------cCccceeCCCCEEEEEEEEECCCCcEEEE
Confidence               4      99999999999999 89885332          1       2345689999999999999984   9999


Q ss_pred             hcccc
Q 026737          215 SKRHC  219 (234)
Q Consensus       215 ~K~~~  219 (234)
                      +|++.
T Consensus       689 ~k~~~  693 (693)
T PRK11824        689 RKAVL  693 (693)
T ss_pred             EEecC
Confidence            99763

>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=98.33  E-value=6.7e-07  Score=67.37  Aligned_cols=80  Identities=19%  Similarity=0.084  Sum_probs=58.8

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.|.++|.++..                       .      |+||+|.+|++|++ +++++++..       .|.
T Consensus         1 L~~G~vV~G~V~~v~~-----------------------~------gl~v~L~~g~~G~v~~seis~~~~-------~~~   44 (100)
T cd05693           1 LSEGMLVLGQVKEITK-----------------------L------DLVISLPNGLTGYVPITNISDAYT-------ERL   44 (100)
T ss_pred             CCCCCEEEEEEEEEcC-----------------------C------CEEEECCCCcEEEEEHHHhhHHHH-------HHH
Confidence            4689999999998853                       3      89999999999999 888864321       121


Q ss_pred             cc---------CCCCCcceeeeeeCCCEEEEEEeeecc-------chhhhccc
Q 026737          182 SN---------APPSGKKFTLLARAGRQVQEIQLSHSL-------IRKASKRH  218 (234)
Q Consensus       182 ~~---------~~~~~~~~~~~~~~G~~v~~~vl~~d~-------i~ls~K~~  218 (234)
                      ..         .+....++...+++||.|+|+|+++|.       |.||+|..
T Consensus        45 ~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          45 EELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDKSKSGKKRIELSLEPE   97 (100)
T ss_pred             HHhhhhccccccccccCCHHHhccCCCEEEEEEEEccCCcCCCcEEEEEecHH
Confidence            11         111123467789999999999999983       78888753

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.

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

Probab=98.32  E-value=1.9e-06  Score=71.03  Aligned_cols=82  Identities=27%  Similarity=0.513  Sum_probs=65.0

Q ss_pred             HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc----------c-hhhhhCCCCEEEEE
Q 026737           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----------D-IRDILNEGDEVRVK  112 (234)
Q Consensus        49 ~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~----------~-~~~~~~vGd~v~vk  112 (234)
                      +..+...+..|++|.|.     +||+||.++      ..+||+|.+++.++++.          . ....+++|+.|+++
T Consensus        72 f~al~fkP~~gEVV~GeVv~~~~~G~fV~ig------p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~R  145 (183)
T COG1095          72 FRALVFKPFRGEVVEGEVVEVVEFGAFVRIG------PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRAR  145 (183)
T ss_pred             EEEEEEEeccccEEEEEEEEEeecceEEEec------cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEE
Confidence            44455678889999998     999999997      59999999999988431          1 23468999999999


Q ss_pred             EEEEeCCC-----CeEEEEEeeccc--Ccch
Q 026737          113 VIKIDREK-----SRITLSIKQLEE--DPLL  136 (234)
Q Consensus       113 Vl~id~~~-----~ri~LS~K~~~~--~p~~  136 (234)
                      |+.+....     .+|.+|||+.-.  -+|.
T Consensus       146 Iv~~s~~~~~~~~~~I~lTmrq~~LGklew~  176 (183)
T COG1095         146 IVGVSLKSRRPRESKIGLTMRQPGLGKLEWI  176 (183)
T ss_pred             EEEEecccCccccceEEEEeccccCCcchhh
Confidence            99998755     578999998644  3464

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

Probab=98.32  E-value=1.1e-06  Score=77.08  Aligned_cols=75  Identities=16%  Similarity=0.174  Sum_probs=60.3

Q ss_pred             hhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC--CceEEE-Ecccccccccccccc
Q 026737          101 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK--KMDDVR-ITRQGFEKRVVSQDL  177 (234)
Q Consensus       101 ~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~--gi~Gl~-~s~~~~~~~~~~~~~  177 (234)
                      .+.++|+.+.++|.++..                       +      |+||+|.+  |++||+ +|+++++        
T Consensus         4 ~~P~~GdiV~G~V~~I~~-----------------------~------G~fV~L~e~~gieGlI~iSEls~~--------   46 (262)
T PRK03987          4 EWPEEGELVVGTVKEVKD-----------------------F------GAFVTLDEYPGKEGFIHISEVASG--------   46 (262)
T ss_pred             CCCCCCCEEEEEEEEEEC-----------------------C------EEEEEECCCCCcEEEEEHHHcCcc--------
Confidence            345789999999998864                       4      99999975  899999 7887532        


Q ss_pred             ccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccc
Q 026737          178 QLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNE  221 (234)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~  221 (234)
                        |.       .++...+++||.|.|+|+++|.    |.||+|++.++
T Consensus        47 --~i-------~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~~   85 (262)
T PRK03987         47 --WV-------KNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNEH   85 (262)
T ss_pred             --cc-------cCHHHhCCCCCEEEEEEEEEecccCeEEEEEEecccc
Confidence              22       2345589999999999999995    99999988764

>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=98.29  E-value=2.7e-06  Score=59.03  Aligned_cols=61  Identities=15%  Similarity=0.096  Sum_probs=46.2

Q ss_pred             CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737          106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA  184 (234)
Q Consensus       106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~  184 (234)
                      |+.|.++|.++..                       +      |+||+|.++++|++ .|+++.+          +    
T Consensus         1 G~~V~g~V~~i~~-----------------------~------G~~v~l~~~v~g~v~~~~l~~~----------~----   37 (66)
T cd05695           1 GMLVNARVKKVLS-----------------------N------GLILDFLSSFTGTVDFLHLDPE----------K----   37 (66)
T ss_pred             CCEEEEEEEEEeC-----------------------C------cEEEEEcCCceEEEEHHHcCCc----------c----
Confidence            6788888888753                       3      99999988999999 6765211          0    


Q ss_pred             CCCCcceeeeeeCCCEEEEEEeeecc----chhh
Q 026737          185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKA  214 (234)
Q Consensus       185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls  214 (234)
                          .. ...+++||+++|+|+.+|+    |.||
T Consensus        38 ----~~-~~~~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695          38 ----SS-KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             ----Cc-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence                01 3368999999999999995    6554

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.

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

Probab=98.26  E-value=2.3e-06  Score=59.54  Aligned_cols=65  Identities=17%  Similarity=0.132  Sum_probs=50.1

Q ss_pred             CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737          106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA  184 (234)
Q Consensus       106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~  184 (234)
                      |+.|.++|.++..                       .      |+||+|..+.+|++ ++++++..            . 
T Consensus         1 G~iv~g~V~~i~~-----------------------~------~~~v~l~~~~~g~l~~~e~~~~~------------~-   38 (70)
T cd05687           1 GDIVKGTVVSVDD-----------------------D------EVLVDIGYKSEGIIPISEFSDDP------------I-   38 (70)
T ss_pred             CCEEEEEEEEEeC-----------------------C------EEEEEeCCCceEEEEHHHhCccc------------c-
Confidence            6788888888763                       3      89999988999999 67764221            1 


Q ss_pred             CCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737          185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK  216 (234)
Q Consensus       185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K  216 (234)
                          .++...+++||.++++|+++|+    |.||+|
T Consensus        39 ----~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687          39 ----ENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             ----CCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence                2355689999999999999984    777765

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.

>PRK11642 exoribonuclease R; Provisional

Probab=98.25  E-value=3.3e-06  Score=84.65  Aligned_cols=70  Identities=30%  Similarity=0.544  Sum_probs=59.5

Q ss_pred             CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc-----------chhhhhCCCCEEEEEEEEEeCCC
Q 026737           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK  120 (234)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~-----------~~~~~~~vGd~v~vkVl~id~~~  120 (234)
                      ++|+++.|+     +||+||+|+  +  .+++||||++++.++++.           +....|++||.|+|+|.++|.++
T Consensus       642 ~iGe~f~G~Is~V~~fGifVeL~--~--~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~  717 (813)
T PRK11642        642 QVGNVFKGVISSVTGFGFFVRLD--D--LFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDE  717 (813)
T ss_pred             cCCcEEEEEEEEeecCceEEEEC--C--CCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCC
Confidence            789999998     999999997  2  259999999999987432           22467999999999999999999


Q ss_pred             CeEEEEEeec
Q 026737          121 SRITLSIKQL  130 (234)
Q Consensus       121 ~ri~LS~K~~  130 (234)
                      ++|.|++-..
T Consensus       718 rkI~f~l~~~  727 (813)
T PRK11642        718 RKIDFSLISS  727 (813)
T ss_pred             CeEEEEEecc
Confidence            9999998543

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

Probab=98.25  E-value=7.8e-07  Score=76.88  Aligned_cols=74  Identities=16%  Similarity=0.151  Sum_probs=60.5

Q ss_pred             hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC--CceEEE-Eccccccccccccccc
Q 026737          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK--KMDDVR-ITRQGFEKRVVSQDLQ  178 (234)
Q Consensus       102 ~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~--gi~Gl~-~s~~~~~~~~~~~~~~  178 (234)
                      +...|+.|-++|.++-.                       +      |+||.|++  |++||+ +||++.          
T Consensus         8 ~PeeGEiVv~tV~~V~~-----------------------~------GAyv~L~EY~g~Eg~ihiSEvas----------   48 (269)
T COG1093           8 YPEEGEIVVGTVKQVAD-----------------------Y------GAYVELDEYPGKEGFIHISEVAS----------   48 (269)
T ss_pred             CCCCCcEEEEEEEEeec-----------------------c------ccEEEeeccCCeeeeEEHHHHHH----------
Confidence            34578888888877642                       4      99999975  999999 899852          


Q ss_pred             cccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccc
Q 026737          179 LWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNE  221 (234)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~  221 (234)
                      .|++       ++.+++|+||+|-|+||.+|+    |-||||++.++
T Consensus        49 ~wVk-------nIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~~   88 (269)
T COG1093          49 GWVK-------NIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTEH   88 (269)
T ss_pred             HHHH-------HHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCHH
Confidence            6875       456699999999999999998    99999999654

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

Probab=98.22  E-value=4.9e-06  Score=61.73  Aligned_cols=73  Identities=22%  Similarity=0.276  Sum_probs=56.5

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCC---cceeEEEEEceeccccccc--chhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRITL  125 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g---~~g~~glv~isels~~~~~--~~~~~~~vGd~v~vkVl~id~~~~ri~L  125 (234)
                      +++|++|.|+     ...++|+|...++   .....|++|++++...+..  ++.+.|++||.|+|||++++. ...+.|
T Consensus         4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~~~L   82 (92)
T cd05791           4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASSYYL   82 (92)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCCcEE
Confidence            5789998888     5568888821100   0257899999999877665  788999999999999999975 567889


Q ss_pred             EEee
Q 026737          126 SIKQ  129 (234)
Q Consensus       126 S~K~  129 (234)
                      |++.
T Consensus        83 st~~   86 (92)
T cd05791          83 STAE   86 (92)
T ss_pred             EecC
Confidence            8875

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".

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

Probab=98.22  E-value=4.4e-06  Score=82.06  Aligned_cols=68  Identities=26%  Similarity=0.485  Sum_probs=58.0

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc-----------cchhhhhCCCCEEEEEEEEEeCC
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDRE  119 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~-----------~~~~~~~~vGd~v~vkVl~id~~  119 (234)
                      -++|+++.|+     +||+||+|++    ++++||||++++.+++.           .+....|++||.|+|+|.++|.+
T Consensus       570 ~~iG~~~~g~I~~v~~~GifV~L~~----~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~  645 (654)
T TIGR00358       570 DKVGTEFSGEISSVTRFGMFVRLDD----NGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNME  645 (654)
T ss_pred             hCCCcEEEEEEEeEEcCcEEEEecC----CceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecc
Confidence            3679999998     9999999972    47999999999998752           22346799999999999999999


Q ss_pred             CCeEEEEE
Q 026737          120 KSRITLSI  127 (234)
Q Consensus       120 ~~ri~LS~  127 (234)
                      +++|.+++
T Consensus       646 ~~~I~f~l  653 (654)
T TIGR00358       646 TRSIIFEL  653 (654)
T ss_pred             cCeEEEEE
Confidence            99999985

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.

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

Probab=98.22  E-value=3.6e-06  Score=57.60  Aligned_cols=51  Identities=16%  Similarity=0.137  Sum_probs=39.2

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhc
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASK  216 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K  216 (234)
                      |+||++.++++||+ +++++++..                 .++...++.||.++++|+++|.   +.||+|
T Consensus        15 g~~v~i~~~~~g~l~~~~l~~~~~-----------------~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~k   69 (69)
T cd05692          15 GAFVELGGGISGLVHISQIAHKRV-----------------KDVKDVLKEGDKVKVKVLSIDARGRISLSIK   69 (69)
T ss_pred             eEEEEECCCCEEEEEhHHcCCccc-----------------CCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence            99999999999999 777743211                 2234578999999999999984   666654

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=98.22  E-value=2.2e-06  Score=77.81  Aligned_cols=97  Identities=15%  Similarity=0.265  Sum_probs=72.1

Q ss_pred             ccCCCCEEEEEEEEEeCCCCEEEEEe-ch--------hhHhhhhcCC--CCCcEEEEE-----Eee-EEEEEecCCCcce
Q 026737           19 KGLTGSIISVKVIQANEEMKKLVFSE-KD--------AVWNKYSSRV--NVEDIFVGR-----DYG-AFIHLRFPDGLYH   81 (234)
Q Consensus        19 ~~~vG~~v~~~Vi~id~~~~~i~lS~-k~--------~~~~~~~~~~--~~G~iv~g~-----~~G-~fV~l~~~~g~~g   81 (234)
                      +..+|+.+.+.+..-  +-++..++. ++        +.++.++..|  +.|++++|+     +.| +||+++      +
T Consensus        83 ~~~vGD~I~~~I~~~--~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG------~  154 (341)
T TIGR01953        83 DVQIGDEVKKEIPPE--NFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG------K  154 (341)
T ss_pred             ccccCCEEEEEeccc--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC------C
Confidence            345999999887542  234444443 33        1255666677  599999999     546 699996      6


Q ss_pred             eEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCC--CCeEEEEEee
Q 026737           82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE--KSRITLSIKQ  129 (234)
Q Consensus        82 ~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~--~~ri~LS~K~  129 (234)
                      .+|++|.+++.      |.+.|++||.+++.|++++..  ..+|.||++.
T Consensus       155 ~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~  198 (341)
T TIGR01953       155 TEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH  198 (341)
T ss_pred             eEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence            99999999887      345599999999999999954  3689999975

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.

>PHA02945 interferon resistance protein; Provisional

Probab=98.21  E-value=5e-06  Score=60.54  Aligned_cols=54  Identities=13%  Similarity=0.181  Sum_probs=44.5

Q ss_pred             ceeeeecC--CceEEE-Eccc--cccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccc
Q 026737          149 PYLKSFYK--KMDDVR-ITRQ--GFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHC  219 (234)
Q Consensus       149 G~fV~l~~--gi~Gl~-~s~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~  219 (234)
                      |+||.|++  |.+||+ +|+.  +          ..|++.        .+.+ +||++-|+||.+|+    |-||+|+..
T Consensus        25 ga~v~L~EY~g~eg~i~~seveva----------~~wvK~--------rd~l-~GqkvV~KVirVd~~kg~IDlSlK~V~   85 (88)
T PHA02945         25 ALYIDLFDYPHSEAILAESVQMHM----------NRYFKY--------RDKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC   85 (88)
T ss_pred             eEEEEecccCCcEEEEEeehhhhc----------cceEee--------eeEe-cCCEEEEEEEEECCCCCEEEeEeeEcc
Confidence            99999975  999999 8854  3          257753        3477 99999999999997    999999986


Q ss_pred             cc
Q 026737          220 NE  221 (234)
Q Consensus       220 ~~  221 (234)
                      ++
T Consensus        86 ~~   87 (88)
T PHA02945         86 RH   87 (88)
T ss_pred             cC
Confidence            53

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.12  E-value=1.9e-06  Score=84.99  Aligned_cols=92  Identities=21%  Similarity=0.233  Sum_probs=69.7

Q ss_pred             EeeEEEEEecCCCcceeEEEEEceecccc-------cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhh
Q 026737           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-------LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET  138 (234)
Q Consensus        66 ~~G~fV~l~~~~g~~g~~glv~isels~~-------~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~  138 (234)
                      .+|+-+++.       .+|.|.+.-....       .+......+++|+.+.++|.++..                    
T Consensus       579 ~tg~~I~i~-------ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~--------------------  631 (684)
T TIGR03591       579 ETGAKIDIE-------DDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMD--------------------  631 (684)
T ss_pred             HHCCEEEEe-------cCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeC--------------------
Confidence            889999997       4677777643322       233334447889999999998853                    


Q ss_pred             hhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          139 LEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       139 ~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                         +      |+||++.+|++||+ +|+++++ +         +       .++...+++||.|+|+|+++|.
T Consensus       632 ---~------GafVei~~g~~GllHiSei~~~-~---------v-------~~~~~~~kvGD~V~VkVi~id~  678 (684)
T TIGR03591       632 ---F------GAFVEILPGKDGLVHISEIANE-R---------V-------EKVEDVLKEGDEVKVKVLEIDK  678 (684)
T ss_pred             ---C------EEEEEECCCcEEEEEHHHcCCC-c---------c-------cChhhccCCCCEEEEEEEEECC
Confidence               4      99999999999999 8988432 1         1       2455689999999999999985

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).

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

Probab=98.11  E-value=8.1e-06  Score=60.02  Aligned_cols=67  Identities=13%  Similarity=-0.014  Sum_probs=50.8

Q ss_pred             hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccc
Q 026737          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       102 ~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~  180 (234)
                      .+++|+.+.++|.++.+                   ++  .      ||||+|.+|.+||+ +|+++|..+         
T Consensus         4 ~~~~G~iy~g~V~~i~~-------------------~~--~------GaFV~l~~g~~Gllh~seis~~~~---------   47 (88)
T cd04453           4 EPIVGNIYLGRVKKIVP-------------------GL--Q------AAFVDIGLGKNGFLHLSDILPAYF---------   47 (88)
T ss_pred             cCCCCCEEEEEEEEecc-------------------CC--c------EEEEEeCCCCEEEEEhHHcCchhc---------
Confidence            36789999999999864                   11  2      99999999999999 788854221         


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeec
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHS  209 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d  209 (234)
                      . ..    .++...+++||.|.|+|++..
T Consensus        48 ~-~v----~~~~~~~~~Gd~v~VqV~~~~   71 (88)
T cd04453          48 K-KH----KKIAKLLKEGQEILVQVVKEP   71 (88)
T ss_pred             c-cc----CCHHHcCCCCCEEEEEEEEec
Confidence            0 01    344568999999999999975

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

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

Probab=98.09  E-value=1.2e-05  Score=56.15  Aligned_cols=61  Identities=15%  Similarity=0.158  Sum_probs=46.6

Q ss_pred             CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737          106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA  184 (234)
Q Consensus       106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~  184 (234)
                      |+.|.++|++++.                       .      |+||++.+|++|++ +++++++          |... 
T Consensus         1 G~iV~g~V~~i~~-----------------------~------gi~v~l~~~i~g~i~~~~i~~~----------~~~~-   40 (70)
T cd05702           1 GDLVKAKVKSVKP-----------------------T------QLNVQLADNVHGRIHVSEVFDE----------WPDG-   40 (70)
T ss_pred             CCEEEEEEEEEEC-----------------------C------cEEEEeCCCcEEEEEHHHhccc----------cccc-
Confidence            7888889988864                       3      88999999999999 7777422          1011 


Q ss_pred             CCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          185 PPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       185 ~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                          .++...+++||.|+|+|+++|.
T Consensus        41 ----~~~~~~~~~Gd~i~~kVl~~d~   62 (70)
T cd05702          41 ----KNPLSKFKIGQKIKARVIGGHD   62 (70)
T ss_pred             ----cChhHhCCCCCEEEEEEEEEeC
Confidence                2345578999999999999985

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.

>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=98.08  E-value=1e-05  Score=55.26  Aligned_cols=45  Identities=13%  Similarity=0.014  Sum_probs=35.1

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      |+||++.++.+|++ .++++.+.          .       .++...+++||.++|+|+++|.
T Consensus        15 G~fv~l~~~~~g~~~~~~l~~~~----------~-------~~~~~~~~~Gd~v~v~i~~vd~   60 (68)
T cd05685          15 GAFVDIGVKQDGLIHISKMADRF----------V-------SHPSDVVSVGDIVEVKVISIDE   60 (68)
T ss_pred             cEEEEcCCCCEEEEEHHHCCCcc----------c-------cCHHHhcCCCCEEEEEEEEEEC
Confidence            99999999999999 67664221          1       1234578999999999999985

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.07  E-value=9.5e-06  Score=74.24  Aligned_cols=97  Identities=16%  Similarity=0.243  Sum_probs=69.9

Q ss_pred             ccCCCCEEEEEEEEEeCCCCEEEEEechh--------hHhhhhcCC--CCCcEEEEE-----EeeEEEEEecCCCcceeE
Q 026737           19 KGLTGSIISVKVIQANEEMKKLVFSEKDA--------VWNKYSSRV--NVEDIFVGR-----DYGAFIHLRFPDGLYHLT   83 (234)
Q Consensus        19 ~~~vG~~v~~~Vi~id~~~~~i~lS~k~~--------~~~~~~~~~--~~G~iv~g~-----~~G~fV~l~~~~g~~g~~   83 (234)
                      +..+|+.+.+.+...+- ++....+.++.        ..+..+..|  +.|++++|+     ++|+||+++      +++
T Consensus        86 ~~~vGD~i~~~I~~~~f-gR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg------~vE  158 (362)
T PRK12327         86 AYELGDVIEIEVTPKDF-GRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG------KIE  158 (362)
T ss_pred             cccCCCEEEEecCcCCC-ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC------CeE
Confidence            34589999988655332 12222222221        244566677  999999999     889999997      699


Q ss_pred             EEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCC--eEEEEEe
Q 026737           84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIK  128 (234)
Q Consensus        84 glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~--ri~LS~K  128 (234)
                      |++|.+++.      |.+.|++||.++|.|++++.+++  +|.||+.
T Consensus       159 a~LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt  199 (362)
T PRK12327        159 AVLPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT  199 (362)
T ss_pred             EEecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence            999988775      35679999999999999996554  5777764

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

Probab=98.06  E-value=4.4e-05  Score=66.56  Aligned_cols=96  Identities=14%  Similarity=0.211  Sum_probs=74.4

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh-hHhhhhcCCCC---CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc
Q 026737           22 TGSIISVKVIQANEEMKKLVFSEKDA-VWNKYSSRVNV---EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (234)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~-~~~~~~~~~~~---G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels   92 (234)
                      +|+++-|. +.+|+++ |+....+.. ..+........   ++.+.|+     ..|.||-++     .++-||||-||..
T Consensus       117 ~Gd~l~v~-l~~Dkk~-Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e-----~~~~GfIh~sEr~  189 (287)
T COG2996         117 KGDKLLVY-LYVDKKG-RIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITE-----NGYLGFIHKSERF  189 (287)
T ss_pred             CCCEEEEE-EEEccCC-cEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEc-----CCeEEEEcchhhc
Confidence            89999999 6778755 777776654 34444444444   8888888     889999997     3799999988754


Q ss_pred             cccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccC
Q 026737           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED  133 (234)
Q Consensus        93 ~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~  133 (234)
                      -        .++.|+.+.++|+.+.+ .++|.||++....+
T Consensus       190 ~--------~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E  221 (287)
T COG2996         190 A--------EPRLGERLTARVIGVRE-DGKLNLSLRPRAHE  221 (287)
T ss_pred             c--------cccCCceEEEEEEEEcc-CCeeecccccccHH
Confidence            2        26789999999999986 99999999876443

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

Probab=98.04  E-value=1.3e-05  Score=55.44  Aligned_cols=62  Identities=10%  Similarity=0.089  Sum_probs=45.4

Q ss_pred             CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737          106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA  184 (234)
Q Consensus       106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~  184 (234)
                      |+.+.++|.++..                       .      |+||++ +|++||+ .|++++..            ..
T Consensus         1 G~iv~g~V~~v~~-----------------------~------G~~v~l-~g~~gfip~s~~~~~~------------~~   38 (67)
T cd04465           1 GEIVEGKVTEKVK-----------------------G------GLIVDI-EGVRAFLPASQVDLRP------------VE   38 (67)
T ss_pred             CCEEEEEEEEEEC-----------------------C------eEEEEE-CCEEEEEEHHHCCCcc------------cC
Confidence            6778888887753                       3      999999 8999999 67773211            11


Q ss_pred             CCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737          185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK  216 (234)
Q Consensus       185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K  216 (234)
                           ++..  .+||.++++|+++|+    |.||+|
T Consensus        39 -----~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k   67 (67)
T cd04465          39 -----DLDE--YVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             -----ChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence                 1111  489999999999995    777765

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.

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

Probab=98.00  E-value=3e-05  Score=55.35  Aligned_cols=56  Identities=9%  Similarity=0.042  Sum_probs=37.5

Q ss_pred             ceeeeecC-CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      |+||++.+ |++|++ .|++.++... -++- .|....    .+....+++||.|+|+|+++|.
T Consensus        16 G~fv~l~~~~~~G~v~~~~l~~~~~~-~d~~-~~~~~~----~~~~~~~~~gd~v~v~v~~vd~   73 (83)
T cd04471          16 GLFVELDNLTVEGLVHVSTLGDDYYE-FDEE-NHALVG----ERTGKVFRLGDKVKVRVVRVDL   73 (83)
T ss_pred             eEEEEecCCCEEEEEEEEecCCCcEE-Eccc-ceEEEe----ccCCCEEcCCCEEEEEEEEecc
Confidence            99999998 999999 7877543321 1111 111111    1234589999999999999985

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=97.96  E-value=2.6e-05  Score=53.38  Aligned_cols=45  Identities=13%  Similarity=0.122  Sum_probs=35.4

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      |+||++.++++|++ +++++++.          .       .++...++.||.++|+|+++|.
T Consensus        15 G~~v~l~~~~~g~l~~~~l~~~~----------~-------~~~~~~~~~Gd~v~v~v~~~d~   60 (68)
T cd04472          15 GAFVEILPGKDGLVHISELSDER----------V-------EKVEDVLKVGDEVKVKVIEVDD   60 (68)
T ss_pred             EEEEEeCCCCEEEEEhHHcCCcc----------c-------cCHHHccCCCCEEEEEEEEECC
Confidence            99999998999999 77774321          1       1234578999999999999985

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.

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

Probab=97.96  E-value=7.1e-06  Score=70.96  Aligned_cols=79  Identities=27%  Similarity=0.464  Sum_probs=71.0

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~  130 (234)
                      +.++++|-+.     +-|+||.|-.++   +++|+|-+||||.+++....+..++|..=-|.|+.+|+++|.|.||.+.+
T Consensus        14 Pev~e~VmvnV~sIaemGayv~LlEYn---niEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrV   90 (304)
T KOG2916|consen   14 PEVEEIVMVNVRSIAEMGAYVKLLEYN---NIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRV   90 (304)
T ss_pred             CCcccEEEEEeeEehhccceEeeeecC---CcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccC
Confidence            5788888877     889999998655   59999999999999999999999999999999999999999999999999


Q ss_pred             ccCcchh
Q 026737          131 EEDPLLE  137 (234)
Q Consensus       131 ~~~p~~~  137 (234)
                      .++....
T Consensus        91 s~ed~~k   97 (304)
T KOG2916|consen   91 SPEDKEK   97 (304)
T ss_pred             CHHHHHH
Confidence            8766433

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

Probab=97.92  E-value=3.5e-05  Score=52.54  Aligned_cols=66  Identities=18%  Similarity=0.122  Sum_probs=50.2

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~  182 (234)
                      ++|+.+.++|.++..                       .      |+|+++.+++.|++ .+++....            
T Consensus         1 ~~G~~v~g~V~~v~~-----------------------~------g~~v~i~~~~~g~l~~~~~~~~~------------   39 (72)
T smart00316        1 EVGDVVEGTVTEITP-----------------------F------GAFVDLGNGVEGLIPISELSDKR------------   39 (72)
T ss_pred             CCCCEEEEEEEEEEc-----------------------c------EEEEEeCCCCEEEEEHHHCCccc------------
Confidence            369999999998864                       3      89999998999999 67663211            


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc----chhhh
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKAS  215 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~  215 (234)
                           ..++...++.||.++++|++++.    +.|++
T Consensus        40 -----~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~   71 (72)
T smart00316       40 -----VKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL   71 (72)
T ss_pred             -----cCCHHHeecCCCEEEEEEEEEeCCCCEEEEEe
Confidence                 02344578999999999999985    55554

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

Probab=97.88  E-value=5.2e-05  Score=51.79  Aligned_cols=59  Identities=20%  Similarity=0.186  Sum_probs=44.8

Q ss_pred             CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccccc
Q 026737          105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSN  183 (234)
Q Consensus       105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~  183 (234)
                      +|+.+.++|.++..                       .      |+||++. +++|++ .+++++.            ..
T Consensus         1 ~g~~~~g~V~~v~~-----------------------~------g~~v~l~-~~~g~l~~~e~~~~------------~~   38 (68)
T cd05688           1 EGDVVEGTVKSITD-----------------------F------GAFVDLG-GVDGLLHISDMSWG------------RV   38 (68)
T ss_pred             CCCEEEEEEEEEEe-----------------------e------eEEEEEC-CeEEEEEhHHCCCc------------cc
Confidence            47888888888863                       3      8999996 799999 6766321            11


Q ss_pred             CCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          184 APPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       184 ~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                           .++...++.||.|+|+|+++|.
T Consensus        39 -----~~~~~~~~~Gd~v~v~i~~vd~   60 (68)
T cd05688          39 -----KHPSEVVNVGDEVEVKVLKIDK   60 (68)
T ss_pred             -----cCHhHEECCCCEEEEEEEEEEC
Confidence                 2345579999999999999985

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.

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

Probab=97.83  E-value=0.0001  Score=54.97  Aligned_cols=74  Identities=9%  Similarity=-0.010  Sum_probs=51.4

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeec---------cchhhhccc
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHS---------LIRKASKRH  218 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d---------~i~ls~K~~  218 (234)
                      |+||++. +++|++ +++++.+.....+.-..|..      .+....++.||.|+++|+++|         .+.||+|+-
T Consensus        14 GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~------~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~~   86 (99)
T cd04460          14 GAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIG------EETKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMRQP   86 (99)
T ss_pred             cEEEEEc-CeEEEEEEEEccCCceEechhheeecc------cCcCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEecC
Confidence            9999997 599999 77775433210000001111      123457899999999999997         399999999


Q ss_pred             ccchhHHHHhh
Q 026737          219 CNEYWNVFHET  229 (234)
Q Consensus       219 ~~~p~~~~~~~  229 (234)
                      ..-||+-+.+.
T Consensus        87 ~~g~~~~~~~~   97 (99)
T cd04460          87 GLGKLEWIEEE   97 (99)
T ss_pred             CCCcHHHhhhh
Confidence            99999776653

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.

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

Probab=97.72  E-value=9.9e-05  Score=53.04  Aligned_cols=68  Identities=10%  Similarity=0.008  Sum_probs=53.9

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~  182 (234)
                      ++||.|.++|++++.                       .      +++|++..+.+|++ .|+++.+.            
T Consensus         5 ~~GdiV~G~V~~v~~-----------------------~------~~~V~i~~~~~g~l~~~~~~~~~------------   43 (82)
T cd04454           5 DVGDIVIGIVTEVNS-----------------------R------FWKVDILSRGTARLEDSSATEKD------------   43 (82)
T ss_pred             CCCCEEEEEEEEEcC-----------------------C------EEEEEeCCCceEEeechhccCcc------------
Confidence            689999999999864                       2      78999988999999 77763221            


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcc
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKR  217 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~  217 (234)
                           ..++...+++||.+.|+|+++|.   +.||++.
T Consensus        44 -----~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~   76 (82)
T cd04454          44 -----KKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD   76 (82)
T ss_pred             -----hHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence                 12345578999999999999985   8888775

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".

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

Probab=97.61  E-value=0.00024  Score=50.60  Aligned_cols=52  Identities=12%  Similarity=0.022  Sum_probs=43.9

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.+.++|.++..                       +      |+||+++++++||+ .|++               
T Consensus        14 ~~~G~~~~g~V~~i~~-----------------------~------G~fV~l~~~~~Glv~~se~---------------   49 (77)
T cd04473          14 LEVGKLYKGKVNGVAK-----------------------Y------GVFVDLNDHVRGLIHRSNL---------------   49 (77)
T ss_pred             CCCCCEEEEEEEeEec-----------------------c------eEEEEECCCcEEEEEchhc---------------
Confidence            6789999999988753                       4      99999999999999 5553               


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeee
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSH  208 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~  208 (234)
                                ...++.||.++++|.++
T Consensus        50 ----------~~~~~iGd~v~v~I~~i   66 (77)
T cd04473          50 ----------LRDYEVGDEVIVQVTDI   66 (77)
T ss_pred             ----------cCcCCCCCEEEEEEEEE
Confidence                      12579999999999998

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=97.57  E-value=0.0002  Score=59.85  Aligned_cols=52  Identities=13%  Similarity=-0.001  Sum_probs=37.8

Q ss_pred             ceeeeec----------CCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc-chhhhc
Q 026737          149 PYLKSFY----------KKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL-IRKASK  216 (234)
Q Consensus       149 G~fV~l~----------~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~-i~ls~K  216 (234)
                      |+||+|.          ++++|++ .|++++..            .     .++...+++||.|+|+|++++. +.||+|
T Consensus        79 g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~------------~-----~~~~~~~~~GD~V~akV~~i~~~i~LS~k  141 (189)
T PRK09521         79 RALVRIVSIEGSERELATSKLAYIHISQVSDGY------------V-----ESLTDAFKIGDIVRAKVISYTDPLQLSTK  141 (189)
T ss_pred             eEEEEEEEecccccccCCCceeeEEhhHcChhh------------h-----hhHHhccCCCCEEEEEEEecCCcEEEEEe
Confidence            6667663          4789999 67663211            0     2345578999999999999976 888888


Q ss_pred             c
Q 026737          217 R  217 (234)
Q Consensus       217 ~  217 (234)
                      +
T Consensus       142 ~  142 (189)
T PRK09521        142 G  142 (189)
T ss_pred             c
Confidence            6

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

Probab=97.50  E-value=0.00046  Score=59.35  Aligned_cols=71  Identities=27%  Similarity=0.432  Sum_probs=61.2

Q ss_pred             cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc----cchhhhhCCCCEEEEEEEEEeCCCCeEE
Q 026737           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRIT  124 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~----~~~~~~~~vGd~v~vkVl~id~~~~ri~  124 (234)
                      ..++.||+|-|.     ..+..|+|+     ..+.|++|+|++.++.+    .+++.+|++||-|.|+|..+|+ .+...
T Consensus        60 YiP~~gD~VIG~I~~v~~~~W~VDI~-----sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~  133 (239)
T COG1097          60 YIPEVGDVVIGKIIEVGPSGWKVDIG-----SPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVE  133 (239)
T ss_pred             ccCCCCCEEEEEEEEEcccceEEEcC-----CccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceE
Confidence            357899999999     788999997     36999999999976653    4778899999999999999997 88999


Q ss_pred             EEEeec
Q 026737          125 LSIKQL  130 (234)
Q Consensus       125 LS~K~~  130 (234)
                      |++|..
T Consensus       134 L~~k~~  139 (239)
T COG1097         134 LTLKDE  139 (239)
T ss_pred             EEeecC
Confidence            999654

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.41  E-value=0.0006  Score=63.63  Aligned_cols=58  Identities=29%  Similarity=0.477  Sum_probs=47.7

Q ss_pred             cCCCCCcEEEEE-----Ee--eEEEEEecCCCcceeEEEEEceecccc------------cccchhhhhCCCCEEEEEEE
Q 026737           54 SRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI  114 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~--G~fV~l~~~~g~~g~~glv~isels~~------------~~~~~~~~~~vGd~v~vkVl  114 (234)
                      ....+|.+|.|+     ++  ||||+|+     .+..||+|++++.+.            +..++.+.+++||.|.|+|.
T Consensus        21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG-----~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~   95 (414)
T TIGR00757        21 SRQLKGNIYKGRVTRILPSLQAAFVDIG-----LEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVV   95 (414)
T ss_pred             CcCCCCCEEEEEEeeecCCCceEEEEcC-----CCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEe
Confidence            346789999999     66  8999997     368999999998763            23456778999999999998


Q ss_pred             EE
Q 026737          115 KI  116 (234)
Q Consensus       115 ~i  116 (234)
                      +-
T Consensus        96 Ke   97 (414)
T TIGR00757        96 KE   97 (414)
T ss_pred             eC
Confidence            83

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.

>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.39  E-value=0.00075  Score=47.69  Aligned_cols=64  Identities=19%  Similarity=0.222  Sum_probs=50.1

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccc--hhhhhCCCCEE-EEEEEEEeCCCCeEEEEEe
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD--IRDILNEGDEV-RVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~--~~~~~~vGd~v-~vkVl~id~~~~ri~LS~K  128 (234)
                      |+++.|+     +-+++|++.+    .++.|++|..++|+..-++  .-..+++||++ ++.|+  +...+.|.||.|
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~----~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K   72 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILP----EEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecC----CCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence            6777787     6679999983    3799999999999943332  34558999999 99999  777888888865

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

>PRK05054 exoribonuclease II; Provisional

Probab=97.36  E-value=0.0006  Score=67.03  Aligned_cols=65  Identities=15%  Similarity=0.148  Sum_probs=51.8

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc---ccc--c-------hhhhhCCCCEEEEEEEEEeCCCC
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD---LIQ--D-------IRDILNEGDEVRVKVIKIDREKS  121 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~---~~~--~-------~~~~~~vGd~v~vkVl~id~~~~  121 (234)
                      |+.+.|.     +||+||+|..    .+++||||++.+...   +.-  +       -...|++||.|+|+|.++|..++
T Consensus       562 ~~~f~g~I~~v~~~G~fV~l~~----~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~  637 (644)
T PRK05054        562 DTRFAAEIIDISRGGMRVRLLE----NGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR  637 (644)
T ss_pred             CeEEEEEEEeeecCcEEEEEeC----CceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence            4488887     9999999973    479999999998653   110  1       12469999999999999999999


Q ss_pred             eEEEEE
Q 026737          122 RITLSI  127 (234)
Q Consensus       122 ri~LS~  127 (234)
                      +|.+++
T Consensus       638 ~i~~~~  643 (644)
T PRK05054        638 SIIARP  643 (644)
T ss_pred             eEEEEE
Confidence            998865

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=97.31  E-value=0.0011  Score=57.24  Aligned_cols=74  Identities=11%  Similarity=-0.002  Sum_probs=55.5

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      .++||.|.++|.++..                       .      |+||++..+++|++ +|++++..          .
T Consensus        61 P~vGDiViG~V~~i~~-----------------------~------~~~vdI~~~~~g~L~~s~i~~~~----------~  101 (235)
T PRK04163         61 PKVGDLVIGKVTDVTF-----------------------S------GWEVDINSPYKAYLPVSEVLGRP----------V  101 (235)
T ss_pred             CCCCCEEEEEEEEEeC-----------------------c------eEEEEeCCCceeEEEHHHcCCCc----------c
Confidence            4789999999998864                       2      67999988999999 77764221          1


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhccc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRH  218 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~  218 (234)
                      .   ....++...+++||.|.|+|+++++   +.||+|+-
T Consensus       102 ~---~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~  138 (235)
T PRK04163        102 N---VEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGK  138 (235)
T ss_pred             c---cchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCC
Confidence            0   0113456689999999999999976   77888753

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

Probab=97.24  E-value=0.00031  Score=66.80  Aligned_cols=61  Identities=11%  Similarity=0.015  Sum_probs=52.0

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcccccchhH
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRHCNEYWN  224 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~~~~p~~  224 (234)
                      |+||+|.++..||| .|++..          -|+       .++++++.+||+++++-++.|.   +.|+.|.++++|..
T Consensus       683 G~~V~l~p~~~~Llh~sqL~~----------e~i-------akpsd~levGq~I~vk~ie~d~~g~~~ls~ralLp~p~~  745 (760)
T KOG1067|consen  683 GVMVELYPMQQGLLHNSQLDQ----------EKI-------AKPSDLLEVGQEIQVKYIERDPRGGIMLSSRALLPDPAT  745 (760)
T ss_pred             ceEEEecCCchhhccchhccc----------ccc-------cChHHHHhhcceeEEEEEeecCccceeehhhhhcCCccc
Confidence            99999999999999 898842          243       4567789999999999999997   99999999999975


Q ss_pred             HH
Q 026737          225 VF  226 (234)
Q Consensus       225 ~~  226 (234)
                      ..
T Consensus       746 ~~  747 (760)
T KOG1067|consen  746 KE  747 (760)
T ss_pred             CC
Confidence            43

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

Probab=97.22  E-value=0.0017  Score=47.68  Aligned_cols=59  Identities=17%  Similarity=0.230  Sum_probs=45.5

Q ss_pred             CCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccch-----------hhhhCCCCEEEEEEEEEeCCCC
Q 026737           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----------RDILNEGDEVRVKVIKIDREKS  121 (234)
Q Consensus        58 ~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~-----------~~~~~vGd~v~vkVl~id~~~~  121 (234)
                      .|+++.|+     ++|+||.++      ++++|+|.+.+......++           ...++.|+.|++||+.+..+.+
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G------pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~   74 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG------PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT   74 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc------CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence            47889998     999999997      5999999987765533222           3447899999999999876544


Q ss_pred             e
Q 026737          122 R  122 (234)
Q Consensus       122 r  122 (234)
                      .
T Consensus        75 ~   75 (88)
T cd04462          75 D   75 (88)
T ss_pred             c
Confidence            3

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.

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

Probab=97.22  E-value=0.0028  Score=52.54  Aligned_cols=74  Identities=28%  Similarity=0.344  Sum_probs=57.2

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCc-----ceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCe
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGL-----YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR  122 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~-----~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~r  122 (234)
                      ...++.|++|-|.     ...+.|++-+.++.     +...|-+|+|+....++++..+.|++||.|+|+|++.-   ..
T Consensus        59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~~  135 (188)
T COG1096          59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---DP  135 (188)
T ss_pred             CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC---CC
Confidence            3457899999998     55677777543320     12467899999999999999999999999999999974   45


Q ss_pred             EEEEEee
Q 026737          123 ITLSIKQ  129 (234)
Q Consensus       123 i~LS~K~  129 (234)
                      +.||++.
T Consensus       136 ~~Lst~~  142 (188)
T COG1096         136 IQLSTKG  142 (188)
T ss_pred             eEEEecC
Confidence            6676653

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

Probab=97.20  E-value=0.00052  Score=45.67  Aligned_cols=45  Identities=11%  Similarity=0.040  Sum_probs=34.7

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      |+||++.++++|++ .++++...         +        .++...+++||.|+++|+++|.
T Consensus        12 g~~v~l~~~~~g~~~~~~~~~~~---------~--------~~~~~~~~~G~~v~~~v~~~d~   57 (65)
T cd00164          12 GVFVELEDGVEGLVHISELSDKF---------V--------KDPSEVFKVGDEVEVKVLEVDP   57 (65)
T ss_pred             eEEEEecCCCEEEEEHHHCCCcc---------c--------cCHhhEeCCCCEEEEEEEEEcC
Confidence            89999999999999 67663211         0        1234578999999999999984

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.

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

Probab=97.09  E-value=0.0017  Score=44.93  Aligned_cols=54  Identities=20%  Similarity=0.168  Sum_probs=42.0

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~  182 (234)
                      +.|+.|+++|++++.                       .      |+||++. +++|++ .+++.               
T Consensus         2 ~~g~iV~G~V~~~~~-----------------------~------~~~vdig-~~eg~lp~~e~~---------------   36 (67)
T cd04455           2 REGEIVTGIVKRVDR-----------------------G------NVIVDLG-KVEAILPKKEQI---------------   36 (67)
T ss_pred             CCCCEEEEEEEEEcC-----------------------C------CEEEEcC-CeEEEeeHHHCC---------------
Confidence            369999999998874                       2      7899995 599999 55541               


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                              +.+.+++||++++.|.+++.
T Consensus        37 --------~~~~~~~Gd~v~v~v~~v~~   56 (67)
T cd04455          37 --------PGESYRPGDRIKAYVLEVRK   56 (67)
T ss_pred             --------CCCcCCCCCEEEEEEEEEec
Confidence                    11256999999999999973

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.

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

Probab=96.95  E-value=0.0028  Score=52.45  Aligned_cols=84  Identities=13%  Similarity=0.062  Sum_probs=57.2

Q ss_pred             CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccccc
Q 026737          105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSN  183 (234)
Q Consensus       105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~  183 (234)
                      +|+.+.++|.+++.                       .      |+||++. .++|++ ++++..+...-..+-..|.-.
T Consensus        81 ~gEvv~G~V~~v~~-----------------------~------GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~  130 (179)
T TIGR00448        81 LGEIVEGEVIEIVE-----------------------F------GAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGK  130 (179)
T ss_pred             CCCEEEEEEEEEEe-----------------------e------EEEEEeC-CceEEEEcHHhCCCceEEccccceEEEc
Confidence            68888888888864                       3      9999995 599999 666643321111111133321


Q ss_pred             CCCCCcceeeeeeCCCEEEEEEeeec---------cchhhhcccccchhH
Q 026737          184 APPSGKKFTLLARAGRQVQEIQLSHS---------LIRKASKRHCNEYWN  224 (234)
Q Consensus       184 ~~~~~~~~~~~~~~G~~v~~~vl~~d---------~i~ls~K~~~~~p~~  224 (234)
                            +....++.||.|+++|+++|         +|.|+||+-.--|++
T Consensus       131 ------~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~~I~lt~k~~~LG~~~  174 (179)
T TIGR00448       131 ------ETKKVLDEGDKVRARIVALSLKDRRPEGSKIGLTMRQPLLGKLE  174 (179)
T ss_pred             ------cCCeEEcCCCEEEEEEEEEEccCCCCCcceEEEEeccCcCCccc
Confidence                  12358999999999999997         299999986555554

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

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

Probab=96.85  E-value=0.0043  Score=51.39  Aligned_cols=74  Identities=16%  Similarity=0.208  Sum_probs=54.7

Q ss_pred             hhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc------------cchhhhhCCCCEEEEE
Q 026737           50 NKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVK  112 (234)
Q Consensus        50 ~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~------------~~~~~~~~vGd~v~vk  112 (234)
                      ....-++-.|+++.|.     ++|+||.++      ..++|||.+++.....            .+-+..++.|+.|++|
T Consensus        73 raivFrPf~gEVv~g~V~~v~~~G~~v~~G------p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~r  146 (176)
T PTZ00162         73 QAIVFKPFKDEVLDAIVTDVNKLGFFAQAG------PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLR  146 (176)
T ss_pred             EEEEEecCCCCEEEEEEEEEecceEEEEee------CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEE
Confidence            3445678899999999     999999997      4789999998864321            1224568999999999


Q ss_pred             EEEEeCCCC--eEEEEEee
Q 026737          113 VIKIDREKS--RITLSIKQ  129 (234)
Q Consensus       113 Vl~id~~~~--ri~LS~K~  129 (234)
                      |+.+..+.+  ++..|+|+
T Consensus       147 V~~v~~~~~~~~~i~T~~~  165 (176)
T PTZ00162        147 LQGVRYDASNLFAIATINS  165 (176)
T ss_pred             EEEEEecCCCcEEEEEecC
Confidence            988875433  34556654

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=96.82  E-value=0.003  Score=62.83  Aligned_cols=71  Identities=31%  Similarity=0.515  Sum_probs=57.5

Q ss_pred             cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc-----------chhhhhCCCCEEEEEEEEEe
Q 026737           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKID  117 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~-----------~~~~~~~vGd~v~vkVl~id  117 (234)
                      -+-.+|+++.|+     .||+||.|.+    .+++|+||++.+..+++.           .....++.||.|++++.+++
T Consensus       618 m~~~vg~~f~g~V~~v~~~g~~V~l~~----~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~  693 (706)
T COG0557         618 MKKRVGEEFDGVVTGVTSFGFFVELPE----LGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVD  693 (706)
T ss_pred             HHHhcCCEEEEEEEEEEeccEEEEecc----cccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEc
Confidence            345788998888     8999999973    468999999999965432           22335899999999999999


Q ss_pred             CCCCeEEEEEe
Q 026737          118 REKSRITLSIK  128 (234)
Q Consensus       118 ~~~~ri~LS~K  128 (234)
                      ...+++.+++-
T Consensus       694 ~~~~~i~~~~v  704 (706)
T COG0557         694 LDERKIDFELV  704 (706)
T ss_pred             ccccceEEEec
Confidence            99999988763

>TIGR02063 RNase_R ribonuclease R

Probab=96.78  E-value=0.0036  Score=62.25  Aligned_cols=71  Identities=11%  Similarity=0.149  Sum_probs=48.6

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC-CceEEE-Ecccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      ++|+.+.++|.++..                       +      |+||+|.+ |++||+ +|++..+..       .|.
T Consensus       626 ~iG~~~~g~V~~v~~-----------------------f------GifV~L~~~~~eGlvhis~l~~d~~-------~~d  669 (709)
T TIGR02063       626 KIGEEFEGVISGVTS-----------------------F------GLFVELENNTIEGLVHISTLKDDYY-------VFD  669 (709)
T ss_pred             cCCcEEEEEEEEEEe-----------------------C------CEEEEecCCceEEEEEeeecCCCcE-------EEc
Confidence            578888888888753                       4      99999988 899999 888853321       111


Q ss_pred             ccCCC-CCcceeeeeeCCCEEEEEEeeecc
Q 026737          182 SNAPP-SGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       182 ~~~~~-~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      ..... ...+....++.||+|+|+|.++|.
T Consensus       670 ~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~  699 (709)
T TIGR02063       670 EKGLALVGERTGKVFRLGDRVKVRVVKADL  699 (709)
T ss_pred             ccceEEEeccCCcEECCCCEEEEEEEEEec
Confidence            00000 001123478999999999999985

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

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

Probab=96.78  E-value=0.0058  Score=44.75  Aligned_cols=68  Identities=19%  Similarity=0.079  Sum_probs=53.9

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      .+++|+.|-|+     ....+|+|+     ....|++|.+++... .+..+..+++||-|.|+|.++++ .....||...
T Consensus         3 ~P~~gD~VIG~V~~~~~~~~~VdI~-----s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~-~~~~eLtc~~   75 (86)
T cd05790           3 VPAKGDHVIGIVVAKAGDFFKVDIG-----GSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANR-DMEPELSCVD   75 (86)
T ss_pred             cCCCCCEEEEEEEEEcCCeEEEEcC-----CCcceEechHHcccc-cccccccCCCCCEEEEEEEecCC-CCCeEEEEeC
Confidence            36889999998     456899997     357899999876543 34456779999999999999997 4567888765

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".

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=96.77  E-value=0.0018  Score=63.94  Aligned_cols=54  Identities=11%  Similarity=0.019  Sum_probs=44.3

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccc
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHC  219 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~  219 (234)
                      |+||.+.=..+||+ +|+++...          +       .++..++++||.|+|+|+++|-    |+|||+.-.
T Consensus       673 gafVdIgv~qDglvHis~ls~~f----------v-------~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~  731 (780)
T COG2183         673 GAFVDIGVHQDGLVHISQLSDKF----------V-------KDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDE  731 (780)
T ss_pred             cceEEeccccceeeeHHHhhhhh----------c-------CChHHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence            99999988999999 89885221          1       3356799999999999999995    999998654

>TIGR02062 RNase_B exoribonuclease II

Probab=96.69  E-value=0.0048  Score=60.73  Aligned_cols=64  Identities=16%  Similarity=0.200  Sum_probs=49.8

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccc--ccc---cc-----h--hhhhCCCCEEEEEEEEEeCCCC
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI---QD-----I--RDILNEGDEVRVKVIKIDREKS  121 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~--~~~---~~-----~--~~~~~vGd~v~vkVl~id~~~~  121 (234)
                      |+.+.|.     .+|+||+|..    .+++||||++.+..  ++.   .+     .  ...|+.||.|+|+|.++|.+++
T Consensus       558 ~~~f~g~I~~v~~~g~~v~l~~----~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~  633 (639)
T TIGR02062       558 NTRFAAEIVDISRGGMRVRLLE----NGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETR  633 (639)
T ss_pred             CcEEEEEEEeeeCCcEEEEEec----CceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccC
Confidence            4478887     8999999972    47999999999865  221   10     1  1259999999999999999999


Q ss_pred             eEEEE
Q 026737          122 RITLS  126 (234)
Q Consensus       122 ri~LS  126 (234)
                      +|.+.
T Consensus       634 ~i~~~  638 (639)
T TIGR02062       634 SIIAR  638 (639)
T ss_pred             cEeee
Confidence            98764

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.

>PRK11642 exoribonuclease R; Provisional

Probab=96.48  E-value=0.0082  Score=60.61  Aligned_cols=77  Identities=10%  Similarity=0.054  Sum_probs=51.6

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC-CceEEE-Ecccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      ++|+.+.++|.++..                       +      |+||+|++ +++||+ +|++.++-...... ...+
T Consensus       642 ~iGe~f~G~Is~V~~-----------------------f------GifVeL~~~~vEGlV~vs~L~~d~y~~d~~-~~~L  691 (813)
T PRK11642        642 QVGNVFKGVISSVTG-----------------------F------GFFVRLDDLFIDGLVHVSSLDNDYYRFDQV-GQRL  691 (813)
T ss_pred             cCCcEEEEEEEEeec-----------------------C------ceEEEECCCCeeeeEEEeecCCcceEecch-heEE
Confidence            589999999988753                       4      99999987 599999 88875432110000 0001


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhh
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKAS  215 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~  215 (234)
                      . .    .+....++.||.|+|+|+++|.    |.|++
T Consensus       692 ~-g----~~~~~~~~lGD~V~VkV~~vD~~~rkI~f~l  724 (813)
T PRK11642        692 I-G----ESSGQTYRLGDRVEVRVEAVNMDERKIDFSL  724 (813)
T ss_pred             e-c----ccCCcEECCCCEEEEEEEEeecCCCeEEEEE
Confidence            1 0    1223478999999999999985    66655

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=96.47  E-value=0.011  Score=40.31  Aligned_cols=48  Identities=33%  Similarity=0.422  Sum_probs=31.4

Q ss_pred             EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      ++|+|++-+     .+-+-++|.++....        +++||+|.|-| ..|. .+|+..|+|
T Consensus        14 ~~g~fL~~~-----~~~~vlLp~~e~~~~--------~~~Gd~v~VFv-Y~D~-~~rl~AT~k   61 (61)
T PF13509_consen   14 EFGYFLDDG-----EGKEVLLPKSEVPEP--------LKVGDEVEVFV-YLDK-EGRLVATTK   61 (61)
T ss_dssp             SSEEEEEET-----T-EEEEEEGGG--------------TTSEEEEEE-EE-T-TS-EEEE--
T ss_pred             CCEEEEECC-----CCCEEEechHHcCCC--------CCCCCEEEEEE-EECC-CCCEEEecC
Confidence            899999975     258999999987633        78999999877 6776 678888775

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

Probab=96.39  E-value=0.0096  Score=58.77  Aligned_cols=72  Identities=15%  Similarity=0.141  Sum_probs=48.8

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec-CCceEEE-Ecccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY-KKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~-~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      ++|+++.++|.++..                       +      |+||+|+ .|++||+ +|++.++..... +-...+
T Consensus       571 ~iG~~~~g~I~~v~~-----------------------~------GifV~L~~~~veGlV~~s~l~~d~y~~d-~~~~~l  620 (654)
T TIGR00358       571 KVGTEFSGEISSVTR-----------------------F------GMFVRLDDNGIDGLIHISTLHNDYYVFD-QEKMAL  620 (654)
T ss_pred             CCCcEEEEEEEeEEc-----------------------C------cEEEEecCCceEEEEEeEeCCCcceEEe-ccccEE
Confidence            578888888888753                       3      9999997 6999999 888865432100 000001


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      . .    .+....++.||+|+|+|+++|.
T Consensus       621 ~-g----~~~~~~~~lGD~V~Vki~~vd~  644 (654)
T TIGR00358       621 I-G----KGTGKVYRIGDRVTVKLTEVNM  644 (654)
T ss_pred             E-e----ccCCcEECCCCEEEEEEEEEec
Confidence            0 0    1123478999999999999985

This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.

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

Probab=96.38  E-value=0.014  Score=48.43  Aligned_cols=79  Identities=11%  Similarity=0.058  Sum_probs=52.6

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~  182 (234)
                      .+|+.+.++|.+++.                       .      |+||++. .++|++ .+++..+...-..+=..|..
T Consensus        80 ~~GEVv~g~V~~v~~-----------------------~------Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~  129 (187)
T PRK08563         80 ELQEVVEGEVVEVVE-----------------------F------GAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIG  129 (187)
T ss_pred             cCCCEEEEEEEEEEc-----------------------c------EEEEEEe-CceEEEEcHHcCCCceEEccccceEEE
Confidence            468888888888864                       3      9999996 499999 66664332110011113432


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc---------chhhhccc
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL---------IRKASKRH  218 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~---------i~ls~K~~  218 (234)
                      .      +....++.||.|+++|++++.         |.||+|+-
T Consensus       130 ~------~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~~I~ls~~~~  168 (187)
T PRK08563        130 K------ESKRVLKVGDVVRARIVAVSLKERRPRGSKIGLTMRQP  168 (187)
T ss_pred             c------cCCeEEcCCCEEEEEEEEEEcccCCCCCCEEEEEecCC
Confidence            1      124578999999999999972         77788774

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.20  E-value=0.012  Score=53.99  Aligned_cols=61  Identities=21%  Similarity=0.345  Sum_probs=50.7

Q ss_pred             CCCCcEEEEE----E--eeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCC---eEEEE
Q 026737           56 VNVEDIFVGR----D--YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS---RITLS  126 (234)
Q Consensus        56 ~~~G~iv~g~----~--~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~---ri~LS  126 (234)
                      -+.|+++.|+    +  .++||+|+      +.+|++|.++..      |.+.|++||.++|.|.+++...+   +|.||
T Consensus       136 ~~~Geiv~g~V~r~~~~~~i~vdlg------~~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilS  203 (374)
T PRK12328        136 KKVGKIVFGTVVRVDNEENTFIEID------EIRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELS  203 (374)
T ss_pred             HhcCcEEEEEEEEEecCCCEEEEcC------CeEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEE
Confidence            4799999999    3  34999996      699999988755      55779999999999999998655   78888


Q ss_pred             Ee
Q 026737          127 IK  128 (234)
Q Consensus       127 ~K  128 (234)
                      +.
T Consensus       204 Rt  205 (374)
T PRK12328        204 RT  205 (374)
T ss_pred             cC
Confidence            74

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

Probab=96.16  E-value=0.033  Score=40.37  Aligned_cols=79  Identities=14%  Similarity=0.064  Sum_probs=39.4

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~  182 (234)
                      ++|+.|.++|.++.  ..+..+.+-.++..++...-         +--..+.....|++ .+..+...            
T Consensus         3 ~vGdiV~~rVtrv~--~~~a~v~Il~v~~~~~~~~~---------~~~~~l~~~f~GiIR~~DVR~te------------   59 (82)
T PF10447_consen    3 KVGDIVIARVTRVN--PRQAKVEILCVEGKGNDSIN---------AGDRPLKEPFQGIIRKQDVRATE------------   59 (82)
T ss_dssp             -TT-EEEEEEEEE---SSEEEEEEEES-------------------SSS----SS-S-EEEEGGGT-S------------
T ss_pred             CCCCEEEEEEEEEe--ccEEEEEEEEEEeccccccc---------cCCcccccccEEEEEeeeecccc------------
Confidence            68999999999997  57777777766555542111         11235566888888 44443211            


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeee
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSH  208 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~  208 (234)
                       .|  .-++.+.|++||-|+|+|+++
T Consensus        60 -~D--kv~~~~~FrpGDIVrA~ViSl   82 (82)
T PF10447_consen   60 -KD--KVKMYDCFRPGDIVRARVISL   82 (82)
T ss_dssp             -S------GGGT--SSSEEEEEEEEE
T ss_pred             -cc--hhhHHhccCCCCEEEEEEeeC
Confidence             11  123566899999999999974

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.

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

Probab=96.11  E-value=0.0051  Score=62.73  Aligned_cols=72  Identities=24%  Similarity=0.275  Sum_probs=59.2

Q ss_pred             cCCCCCcEEEEE------EeeE--EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737           54 SRVNVEDIFVGR------DYGA--FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (234)
Q Consensus        54 ~~~~~G~iv~g~------~~G~--fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~L  125 (234)
                      +.+..|.+|.++      ..|.  -|.+.     +|+.|+|+.+++|.+.+.+|...+++||.|.+||+++|.++=-+.|
T Consensus       981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld-----~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~L 1055 (1299)
T KOG1856|consen  981 ETFYEGAIVPVTVTKVTHRRGICVRVRLD-----CGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVEL 1055 (1299)
T ss_pred             hHhccCceEEEeeeEEEecccceeEEEec-----CCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhh
Confidence            357788888866      3333  34554     5799999999999999999999999999999999999988877888


Q ss_pred             EEeec
Q 026737          126 SIKQL  130 (234)
Q Consensus       126 S~K~~  130 (234)
                      |.|..
T Consensus      1056 s~r~s 1060 (1299)
T KOG1856|consen 1056 SCRTS 1060 (1299)
T ss_pred             hhhhH
Confidence            88743

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.04  E-value=0.0017  Score=61.53  Aligned_cols=87  Identities=16%  Similarity=0.149  Sum_probs=58.0

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEE-EEEeecccCcch-----hhhhcccc--cc-----cc------ceeeeecCCceEEE-
Q 026737          103 LNEGDEVRVKVIKIDREKSRIT-LSIKQLEEDPLL-----ETLEKVIP--QG-----LE------PYLKSFYKKMDDVR-  162 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~-LS~K~~~~~p~~-----~~~~~~~~--~G-----~~------G~fV~l~~gi~Gl~-  162 (234)
                      +++||.+++.|...+.  +|+. .+.|+....-|.     ..++. |.  .|     ++      |+||+| +|++|++ 
T Consensus        87 ~~vGD~ie~~I~~~~f--gRia~q~aKq~i~Qkire~ere~i~~e-yk~~~GeIV~G~V~ri~~~giiVDL-ggvea~LP  162 (470)
T PRK09202         87 AEVGDYIEEEIESVDF--GRIAAQTAKQVIVQKIREAERERVYEE-YKDRVGEIITGVVKRVERGNIIVDL-GRAEAILP  162 (470)
T ss_pred             ccCCCeEEEEEccccC--ChHHHHHHHHHHHHHHHHHHHHHHHHH-HHhhcCCEEEEEEEEEecCCEEEEE-CCeEEEec
Confidence            7899999999988773  4443 333444333343     22333 32  33     32      899999 6999999 


Q ss_pred             EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc------chhhhc
Q 026737          163 ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL------IRKASK  216 (234)
Q Consensus       163 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~------i~ls~K  216 (234)
                      .|++.                       +.+.+++||+++|+|+++++      |-||++
T Consensus       163 ~sE~i-----------------------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt  199 (470)
T PRK09202        163 RKEQI-----------------------PRENFRPGDRVRAYVYEVRKEARGPQIILSRT  199 (470)
T ss_pred             HHHcC-----------------------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence            45541                       23478999999999999986      556654

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

Probab=96.02  E-value=0.057  Score=44.83  Aligned_cols=84  Identities=12%  Similarity=0.147  Sum_probs=56.8

Q ss_pred             CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccccc
Q 026737          105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSN  183 (234)
Q Consensus       105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~  183 (234)
                      .|+.|.+.|++++.                       +      |+||.+. -++||+ .|++-.+.-.-.+.-..|.-.
T Consensus        81 ~gEVV~GeVv~~~~-----------------------~------G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~  130 (183)
T COG1095          81 RGEVVEGEVVEVVE-----------------------F------GAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGE  130 (183)
T ss_pred             cccEEEEEEEEEee-----------------------c------ceEEEec-cccccccHhhccCcccccCcccceeeec
Confidence            48888888888874                       4      9999996 789999 777755521111222223322


Q ss_pred             CCCCCcceeeeeeCCCEEEEEEeeecc---------chhhhcccc--cchhH
Q 026737          184 APPSGKKFTLLARAGRQVQEIQLSHSL---------IRKASKRHC--NEYWN  224 (234)
Q Consensus       184 ~~~~~~~~~~~~~~G~~v~~~vl~~d~---------i~ls~K~~~--~~p~~  224 (234)
                      .      =...+++||.|+++|+..+.         |-|+|||--  .-+|-
T Consensus       131 ~------tk~~i~~gd~VR~RIv~~s~~~~~~~~~~I~lTmrq~~LGklew~  176 (183)
T COG1095         131 E------TKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMRQPGLGKLEWI  176 (183)
T ss_pred             c------cceEEecCCEEEEEEEEEecccCccccceEEEEeccccCCcchhh
Confidence            1      13389999999999999863         777888863  35663

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

Probab=95.70  E-value=0.0089  Score=57.37  Aligned_cols=68  Identities=29%  Similarity=0.496  Sum_probs=57.8

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      ..+++.|..+.|+     +||+||+++     ..+.|++|-++++..      ..|.+|+++-+++..+-+.++.|.|..
T Consensus       117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln-----~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~  185 (715)
T COG1107         117 MEDVEAGKYYKGIVSRVEKYGVFVELN-----SHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEP  185 (715)
T ss_pred             hhhcccceeeeccccchhhhcceeecC-----hhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceee
Confidence            4578999999999     999999997     479999999998863      227899999999999998889888877


Q ss_pred             eecc
Q 026737          128 KQLE  131 (234)
Q Consensus       128 K~~~  131 (234)
                      ..+.
T Consensus       186 ~~~~  189 (715)
T COG1107         186 VGLD  189 (715)
T ss_pred             cCCc
Confidence            6554

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

Probab=95.39  E-value=0.045  Score=39.70  Aligned_cols=36  Identities=25%  Similarity=0.438  Sum_probs=23.9

Q ss_pred             eeEEEEEceeccccccc--chhhhhCCCCEEEEEEEEE
Q 026737           81 HLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKI  116 (234)
Q Consensus        81 g~~glv~isels~~~~~--~~~~~~~vGd~v~vkVl~i  116 (234)
                      ...|++|.+++-.....  .+.+.|++||.|+|+|++.
T Consensus        45 ~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl   82 (82)
T PF10447_consen   45 PFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL   82 (82)
T ss_dssp             SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred             ccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence            47899999987665443  4678899999999999974

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.

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

Probab=95.29  E-value=0.012  Score=51.33  Aligned_cols=66  Identities=15%  Similarity=0.186  Sum_probs=52.2

Q ss_pred             ceeeeec--CCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccc
Q 026737          149 PYLKSFY--KKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNE  221 (234)
Q Consensus       149 G~fV~l~--~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~  221 (234)
                      |++|.|-  ++++|++ +||++. +|         +       +.++.+.|+|..=-|.||.+|+    |-||.+++.++
T Consensus        31 Gayv~LlEYnniEGmiLlsELSr-RR---------I-------RSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~e   93 (304)
T KOG2916|consen   31 GAYVKLLEYNNIEGMILLSELSR-RR---------I-------RSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSPE   93 (304)
T ss_pred             cceEeeeecCCcccchhhhHHHH-HH---------H-------HHHHHHHhcCCcceEEEEEEcCCCCceechhccCCHH
Confidence            9999985  4999999 899841 11         1       4466689999999999999998    99999999877


Q ss_pred             hhHHHHhhcc
Q 026737          222 YWNVFHETAI  231 (234)
Q Consensus       222 p~~~~~~~~~  231 (234)
                      --..-.++|.
T Consensus        94 d~~kC~Er~~  103 (304)
T KOG2916|consen   94 DKEKCEERFA  103 (304)
T ss_pred             HHHHHHHHHH
Confidence            6666666553

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=94.74  E-value=0.047  Score=39.59  Aligned_cols=44  Identities=5%  Similarity=0.130  Sum_probs=33.7

Q ss_pred             ceeeeecC-CceEEE--EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFYK-KMDDVR--ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~~-gi~Gl~--~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      |++|.|-+ |++|++  .|+++.++.                 ++++..+ +|....|.|+.+|+
T Consensus        30 ~~YV~LleY~iegmIl~~selsr~ri-----------------rsi~kll-VGk~e~v~ViRVDk   76 (86)
T PHA02858         30 IFYVKLIDYGLEALIVNYVNVNADRA-----------------EKLKKKL-VGKTINVQVIRTDK   76 (86)
T ss_pred             EEEEEEecCccceEEecHHHHhHHHH-----------------Hhhhhhh-cCCeeEEEEEEECC
Confidence            88999865 899998  477743221                 3455577 99999999999997

>PRK11712 ribonuclease G; Provisional

Probab=94.74  E-value=0.23  Score=47.43  Aligned_cols=59  Identities=25%  Similarity=0.511  Sum_probs=44.6

Q ss_pred             cCCCCCcEEEEE-------EeeEEEEEecCCCcceeEEEEEceecccc------------cccchhhhhCCCCEEEEEEE
Q 026737           54 SRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI  114 (234)
Q Consensus        54 ~~~~~G~iv~g~-------~~G~fV~l~~~~g~~g~~glv~isels~~------------~~~~~~~~~~vGd~v~vkVl  114 (234)
                      ....+|.+|.|+       =.+|||+|+     .+-.||+|++++...            ......+.+++||.+-|.|.
T Consensus        34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG-----~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~  108 (489)
T PRK11712         34 KRGIVGNIYKGRVSRVLPGMQAAFVDIG-----LDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVV  108 (489)
T ss_pred             cccccccEEEEEEeecCCCCceeEEeeC-----CCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEE
Confidence            445789999999       336999998     478999999987321            11234566999999999998


Q ss_pred             EEe
Q 026737          115 KID  117 (234)
Q Consensus       115 ~id  117 (234)
                      +--
T Consensus       109 Ke~  111 (489)
T PRK11712        109 KDP  111 (489)
T ss_pred             eCC
Confidence            754

>PRK10811 rne ribonuclease E; Reviewed

Probab=94.72  E-value=0.096  Score=53.36  Aligned_cols=61  Identities=26%  Similarity=0.480  Sum_probs=46.1

Q ss_pred             CCCCcEEEEE-------EeeEEEEEecCCCcceeEEEEEceeccccccc---------chhhhhCCCCEEEEEEEEEeCC
Q 026737           56 VNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKIDRE  119 (234)
Q Consensus        56 ~~~G~iv~g~-------~~G~fV~l~~~~g~~g~~glv~isels~~~~~---------~~~~~~~vGd~v~vkVl~id~~  119 (234)
                      ..+|.||.|+       =.++||+|+     .+..||+|+++....++.         .....+++||.|-|.|.+--..
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDIG-----~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~g  110 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERG  110 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEec-----CCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccC
Confidence            3589999999       447999998     368999999998654322         2245688999999999885543


Q ss_pred             CC
Q 026737          120 KS  121 (234)
Q Consensus       120 ~~  121 (234)
                      ++
T Consensus       111 tK  112 (1068)
T PRK10811        111 NK  112 (1068)
T ss_pred             CC
Confidence            33

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

Probab=94.69  E-value=0.077  Score=39.13  Aligned_cols=79  Identities=13%  Similarity=0.058  Sum_probs=48.9

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      .++||.|-++|.++..  .+..+.+-.+..                   ..+.....|++ +|+.+.. .          
T Consensus         4 P~~GDiVig~V~~v~~--~~~~v~I~~v~~-------------------~~l~~~~~g~l~~~dv~~~-~----------   51 (92)
T cd05791           4 PKVGSIVIARVTRINP--RFAKVDILCVGG-------------------RPLKESFRGVIRKEDIRAT-E----------   51 (92)
T ss_pred             CCCCCEEEEEEEEEcC--CEEEEEEEEecC-------------------eecCCCcccEEEHHHcccc-c----------
Confidence            3789999999999863  344443322210                   12234567888 5654311 0          


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKR  217 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~  217 (234)
                          ....++.+.+++||-|+|+|++++.   +.||++.
T Consensus        52 ----~d~~~~~~~f~~GDiV~AkVis~~~~~~~~Lst~~   86 (92)
T cd05791          52 ----KDKVEMYKCFRPGDIVRAKVISLGDASSYYLSTAE   86 (92)
T ss_pred             ----cchHHHHhhcCCCCEEEEEEEEcCCCCCcEEEecC
Confidence                0112356689999999999999963   6666653

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

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=94.09  E-value=0.15  Score=47.89  Aligned_cols=67  Identities=9%  Similarity=0.050  Sum_probs=49.9

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCC---CeEEEEE
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK---SRITLSI  127 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~---~ri~LS~  127 (234)
                      -++|+++.|+     ..+++|+++..-|..+++|++|.++..      |.+.|++||.++|.|.++....   -+|.||+
T Consensus       150 ~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilSR  223 (449)
T PRK12329        150 DLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVSR  223 (449)
T ss_pred             HhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence            4789999999     557999983100101389999988754      5577999999999999998652   4688887


Q ss_pred             e
Q 026737          128 K  128 (234)
Q Consensus       128 K  128 (234)
                      .
T Consensus       224 t  224 (449)
T PRK12329        224 A  224 (449)
T ss_pred             C
Confidence            3

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=93.72  E-value=0.17  Score=46.54  Aligned_cols=57  Identities=18%  Similarity=0.091  Sum_probs=44.6

Q ss_pred             hhh--CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEEE-cccccccccccccc
Q 026737          101 DIL--NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRI-TRQGFEKRVVSQDL  177 (234)
Q Consensus       101 ~~~--~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~~-s~~~~~~~~~~~~~  177 (234)
                      +.|  +.|+.|.++|.+++.                       .      |+||++ +|++|+++ +++.          
T Consensus       128 ~ef~~k~GeiV~G~V~~~~~-----------------------~------~~~Vdl-g~vEa~LP~~E~i----------  167 (362)
T PRK12327        128 NEFSEREGDIVTGVVQRRDN-----------------------R------FVYVNL-GKIEAVLPPAEQI----------  167 (362)
T ss_pred             HHHHHhcCCEEEEEEEEEeC-----------------------C------cEEEEe-CCeEEEecHHHcC----------
Confidence            336  899999999998763                       2      789999 57999995 4431          


Q ss_pred             ccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          178 QLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                                   +.+.+++||++++.|++++.
T Consensus       168 -------------p~e~~~~Gd~Ika~V~~V~~  187 (362)
T PRK12327        168 -------------PGETYKHGDRIKVYVVKVEK  187 (362)
T ss_pred             -------------CCCCCCCCCEEEEEEEEEec
Confidence                         13468999999999999984

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=93.51  E-value=0.22  Score=46.63  Aligned_cols=79  Identities=13%  Similarity=0.096  Sum_probs=50.1

Q ss_pred             chhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccc
Q 026737           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQD  176 (234)
Q Consensus        98 ~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~  176 (234)
                      .+.....+|+.+.++|.++.+                       .+.    ||||++..|-.||+ +++.......    
T Consensus        18 ~~~~~~~vGnIY~GrV~~i~p-----------------------~l~----aAFVdiG~~k~gfL~~~d~~~~~~~----   66 (414)
T TIGR00757        18 RPKSRQLKGNIYKGRVTRILP-----------------------SLQ----AAFVDIGLEKNGFLHASDIGPNYEC----   66 (414)
T ss_pred             cCcCcCCCCCEEEEEEeeecC-----------------------CCc----eEEEEcCCCceEEEEHHHcCchhhc----
Confidence            344445789999999998875                       111    89999999999999 7776321000    


Q ss_pred             cccccccCCCCCcceeeeeeCCCEEEEEEeee
Q 026737          177 LQLWLSNAPPSGKKFTLLARAGRQVQEIQLSH  208 (234)
Q Consensus       177 ~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~  208 (234)
                      ... .........++...+++||.|-|.|.+-
T Consensus        67 ~~~-~~~~~~~~~~i~~~l~~G~~IlVQV~Ke   97 (414)
T TIGR00757        67 LAP-AEAKREAGPSISELLRPGQSVLVQVVKE   97 (414)
T ss_pred             ccc-ccccccccCCHHHhCcCCCEEEEEEeeC
Confidence            000 0000000124566899999999998873

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=93.04  E-value=0.25  Score=45.11  Aligned_cols=64  Identities=16%  Similarity=0.140  Sum_probs=48.0

Q ss_pred             hhh--CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccc-eeeeecCCceEEE-Eccccccccccccc
Q 026737          101 DIL--NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP-YLKSFYKKMDDVR-ITRQGFEKRVVSQD  176 (234)
Q Consensus       101 ~~~--~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G-~fV~l~~gi~Gl~-~s~~~~~~~~~~~~  176 (234)
                      +.|  +.|+.|.++|.+++.                       .      | +||++ +|++|++ .+++.         
T Consensus       125 ~ey~~k~GeiV~G~V~~v~~-----------------------~------g~v~Vdi-G~~ea~LP~~E~i---------  165 (341)
T TIGR01953       125 DEFSSKEGEIISGTVKRVNR-----------------------R------GNLYVEL-GKTEGILPKKEQI---------  165 (341)
T ss_pred             HHHHhhcCCEEEEEEEEEec-----------------------C------CcEEEEE-CCeEEEecHHHcC---------
Confidence            345  499999999999864                       1      4 58999 5999999 45431         


Q ss_pred             cccccccCCCCCcceeeeeeCCCEEEEEEeeecc------chhhhcc
Q 026737          177 LQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL------IRKASKR  217 (234)
Q Consensus       177 ~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~------i~ls~K~  217 (234)
                                    +.+.+++||++++.|++++.      |-||.+.
T Consensus       166 --------------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~  198 (341)
T TIGR01953       166 --------------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH  198 (341)
T ss_pred             --------------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence                          12358999999999999984      6666653

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.

>PRK05054 exoribonuclease II; Provisional

Probab=91.09  E-value=0.87  Score=45.06  Aligned_cols=55  Identities=5%  Similarity=-0.110  Sum_probs=34.1

Q ss_pred             ceeeeecC-CceEEE-Eccccccc--cccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFYK-KMDDVR-ITRQGFEK--RVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~~-gi~Gl~-~s~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      |+||+|++ |++||+ +|.+..+.  ..-.++- ..+...    +  ...++.||+|+|+|.++|.
T Consensus       576 G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~-~~~~~~----~--~~~~~lGd~V~V~v~~vd~  634 (644)
T PRK05054        576 GMRVRLLENGAVAFIPASFLHAVRDELVCNQEN-GTVQIK----G--ETVYKLGDVIDVTLAEVRM  634 (644)
T ss_pred             cEEEEEeCCceEEEEEccccCCCccceEEcccc-ceEEEe----C--CEEEcCCCEEEEEEEEEcc
Confidence            99999976 899999 77663221  1000000 000000    1  1378999999999999985

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

Probab=88.98  E-value=1.9  Score=35.98  Aligned_cols=81  Identities=19%  Similarity=0.250  Sum_probs=48.9

Q ss_pred             hhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec-CCceEEEEccccccccccccccc
Q 026737          100 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY-KKMDDVRITRQGFEKRVVSQDLQ  178 (234)
Q Consensus       100 ~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~-~gi~Gl~~s~~~~~~~~~~~~~~  178 (234)
                      ....+.|+.|-++|+++..  .+..+.+-.++..+                 -++. .+.-++.+|+.+..         
T Consensus        59 ~~~~K~GdiV~grV~~v~~--~~a~V~i~~ve~~~-----------------r~~~~~~~~~ihvs~~~~~---------  110 (188)
T COG1096          59 PPLPKGGDIVYGRVTDVRE--QRALVRIVGVEGKE-----------------RELATSGAADIHVSQVRDG---------  110 (188)
T ss_pred             CCCCCCCCEEEEEEeeccc--eEEEEEEEEEeccc-----------------ccCCCCceeeEEEEecccc---------
Confidence            3457889999999999863  34443332222111                 0111 13333446665321         


Q ss_pred             cccccCCCCCcceeeeeeCCCEEEEEEeee-ccchhhhc
Q 026737          179 LWLSNAPPSGKKFTLLARAGRQVQEIQLSH-SLIRKASK  216 (234)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~-d~i~ls~K  216 (234)
                       +.       .++++.+++||-|+|+|++. +++.||.+
T Consensus       111 -~~-------~~~~d~f~~GDivrA~Vis~~~~~~Lst~  141 (188)
T COG1096         111 -YV-------EKLSDAFRIGDIVRARVISTGDPIQLSTK  141 (188)
T ss_pred             -cc-------cccccccccccEEEEEEEecCCCeEEEec
Confidence             11       34667999999999999998 66666654

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

Probab=87.92  E-value=3.3  Score=35.90  Aligned_cols=73  Identities=12%  Similarity=0.046  Sum_probs=49.0

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      .++||.|-.+|+++-+.                             +-.|++..-..+++ +|++-            |-
T Consensus        62 P~~gD~VIG~I~~v~~~-----------------------------~W~VDI~sp~~A~L~ls~~~------------~r  100 (239)
T COG1097          62 PEVGDVVIGKIIEVGPS-----------------------------GWKVDIGSPYPALLSLSDFL------------RR  100 (239)
T ss_pred             CCCCCEEEEEEEEEccc-----------------------------ceEEEcCCccceEeehhhhh------------cc
Confidence            46799999999988541                             33577766677777 66651            11


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKR  217 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~  217 (234)
                      .. +....++...+++||-|-|+|..+|.   ..|.+|.
T Consensus       101 ~~-~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~  138 (239)
T COG1097         101 KF-ENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD  138 (239)
T ss_pred             cc-cccccccccccccCCEEEEEEEEccCCCceEEEeec
Confidence            10 11124566799999999999999997   5555543

>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=87.07  E-value=1.7  Score=30.73  Aligned_cols=53  Identities=13%  Similarity=0.070  Sum_probs=32.1

Q ss_pred             ceeeeecC-CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEE-EEEEeeecc--chhhhc
Q 026737          149 PYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV-QEIQLSHSL--IRKASK  216 (234)
Q Consensus       149 G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v-~~~vl~~d~--i~ls~K  216 (234)
                      +++|++.+ |+.|++ ...++. ..-.++.  .|            .-+++||++ ++.+|....  |.++.|
T Consensus        15 ~l~v~l~~~~l~a~l~~~HLsD-~~~k~~~--~~------------~klrvG~~L~~~lvL~~~~r~i~lt~K   72 (72)
T cd05699          15 GLEVAILPEEIRAFLPTMHLSD-HVSNCPL--LW------------HCLQEGDTIPNLMCLSNYKGRIILTKK   72 (72)
T ss_pred             cEEEEecCCCcEEEEEccccCC-chhhCHH--HH------------hhhhcCCCccceEEEeccccEEEEecC
Confidence            77899988 999999 444432 1111111  12            146999999 888882221  555543

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.

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=86.03  E-value=2  Score=42.95  Aligned_cols=56  Identities=14%  Similarity=0.074  Sum_probs=36.8

Q ss_pred             ceeeeecC-CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      |+||+|.+ |++|++ +|.+..+-....+.-  ..    ....+....++.||.|++++.+++.
T Consensus       637 g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~--~~----l~~~~~~~~~~lgd~v~v~v~~v~~  694 (706)
T COG0557         637 GFFVELPELGLEGLVHISSLPDDYYHFDERG--QA----LVGEKSGKVYRLGDEVKVKVTSVDL  694 (706)
T ss_pred             cEEEEecccccccceEcccCCCceeeecccc--ce----eeccccccccccCCEEEEEEEEEcc
Confidence            99999977 799999 888743222111000  00    0113445578999999999999985

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

Probab=85.85  E-value=7.6  Score=28.20  Aligned_cols=68  Identities=6%  Similarity=0.066  Sum_probs=41.3

Q ss_pred             CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccc-cccccccc
Q 026737          105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVS-QDLQLWLS  182 (234)
Q Consensus       105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~-~~~~~~~~  182 (234)
                      .|+.+.++|.++++                       .      |+|+.+ +.+++|+ .+.+-.+--... +..-.|. 
T Consensus         1 kgEVi~g~V~~v~~-----------------------~------G~~v~~-Gpl~~f~~~~~ip~~~~~~~~~~~~~~~-   49 (88)
T cd04462           1 KGEVVDAIVTSVNK-----------------------T------GFFAEV-GPLSIFISRHLIPSDMEFDPNASPPCFT-   49 (88)
T ss_pred             CCcEEEEEEEEEec-----------------------c------EEEEEE-cCceEEEEeeecCccceECCcCCCCeEe-
Confidence            47888888888875                       3      889998 4567776 333211100001 1111342 


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeec
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHS  209 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d  209 (234)
                       .+     -...++.|+.|+++|+.+.
T Consensus        50 -~~-----~~~~i~~g~~VR~rV~~v~   70 (88)
T cd04462          50 -SN-----EDIVIKKDTEVRLKIIGTR   70 (88)
T ss_pred             -CC-----CcEEECCCCEEEEEEEEEE
Confidence             11     1458999999999998885

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.

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

Probab=84.40  E-value=3.9  Score=33.36  Aligned_cols=60  Identities=18%  Similarity=0.236  Sum_probs=41.1

Q ss_pred             cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc----cccccc-------hhhhhCCCCEEEEEEEEEe
Q 026737           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS----WDLIQD-------IRDILNEGDEVRVKVIKID  117 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels----~~~~~~-------~~~~~~vGd~v~vkVl~id  117 (234)
                      -++-.|+++.|+     +.|+|++++      .++.++.---..    ...-.+       -.+..++|.+|++||+...
T Consensus        77 FkpfKGEVvdgvV~~Vnk~G~F~~~G------Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr  150 (170)
T KOG3298|consen   77 FKPFKGEVVDGVVTKVNKMGVFARSG------PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR  150 (170)
T ss_pred             EeecCCcEEEEEEEEEeeeeEEEecc------ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence            356789999998     899999997      477776433222    111112       1235789999999999886


Q ss_pred             CC
Q 026737          118 RE  119 (234)
Q Consensus       118 ~~  119 (234)
                      .+
T Consensus       151 ~~  152 (170)
T KOG3298|consen  151 VD  152 (170)
T ss_pred             Ee
Confidence            53

>TIGR02062 RNase_B exoribonuclease II

Probab=82.76  E-value=4.8  Score=39.86  Aligned_cols=55  Identities=4%  Similarity=-0.028  Sum_probs=32.9

Q ss_pred             ceeeeec-CCceEEE-EccccccccccccccccccccCCCCCcce--eeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFY-KKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKF--TLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~-~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~G~~v~~~vl~~d~  210 (234)
                      |+||+|. .|++||+ ++.+....     +  .|.-..+.....+  ...++.||+|+|+|.++|.
T Consensus       572 g~~v~l~~~~~~g~v~~~~l~~~~-----~--~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~  630 (639)
T TIGR02062       572 GMRVRLLENGAIAFIPAAFLHANR-----E--ELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRM  630 (639)
T ss_pred             cEEEEEecCceEEEEEhhhcCCCC-----c--ceEEcccccEEEEeccEEEecCCEEEEEEEEecc
Confidence            9999995 4899999 66653210     0  0100000000001  1269999999999999985

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.

>COG4044 Uncharacterized protein conserved in archaea [Function unknown]

Probab=80.77  E-value=2.5  Score=35.97  Aligned_cols=74  Identities=24%  Similarity=0.367  Sum_probs=52.3

Q ss_pred             hcCCCCCcEEEEE-------EeeEEEEEecCCCcceeEEEEEceecccccccch-hh---hh--CCCCEEEEEEEEEeCC
Q 026737           53 SSRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-RD---IL--NEGDEVRVKVIKIDRE  119 (234)
Q Consensus        53 ~~~~~~G~iv~g~-------~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~-~~---~~--~vGd~v~vkVl~id~~  119 (234)
                      +.++++|+++-|+       -||+||+++ +.|....++++|..+|....-..| ++   .|  -.-..++|-|.++|..
T Consensus        70 l~~~~~Gdv~vGrl~~l~~vgyg~yvdig-V~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~  148 (247)
T COG4044          70 LSKVEEGDVYVGRLIDLGKVGYGAYVDIG-VLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKL  148 (247)
T ss_pred             cccCCCCcEEEEEEeeeccceeEEEcccc-ccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccch
Confidence            3788999999999       889999996 344235689999998876554444 22   22  2346788889888876


Q ss_pred             CCeEEEEE
Q 026737          120 KSRITLSI  127 (234)
Q Consensus       120 ~~ri~LS~  127 (234)
                      .+.|...+
T Consensus       149 ~~EIea~l  156 (247)
T COG4044         149 AQEIEARL  156 (247)
T ss_pred             hhhhhhhh
Confidence            66665443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	234
2k4k_A	130	Solution Structure Of Gsp13 From Bacillus Subtilis		5e-10
2aho_B	266	Structure Of The Archaeal Initiation Factor Eif2 Al		4e-06
3aev_A	275	Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex		7e-06
1yz6_A	274	Crystal Structure Of Intact Alpha Subunit Of Aif2 F		8e-06
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		2e-05
3bzc_A	785	Crystal Structure Of The Tex Protein From Pseudomon		4e-05
2oce_A	780	Crystal Structure Of Tex Family Protein Pa5201 From		5e-05
1sro_A	76	S1 Rna Binding Domain, Nmr, 20 Structures Length =		1e-04

>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis Length = 130

Iteration: 1
 Score = 61.2 bits (147), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 52/87 (59%), Gaps = 10/87 (11%)
Query: 53  SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGD 107
           +++  V  ++ G+      YGAF+ L          GLVH+SEV+   ++DI + L+ GD
Sbjct: 2   AAKFEVGSVYTGKVTGLQAYGAFVALD-----EETQGLVHISEVTHGFVKDINEHLSVGD 56
Query: 108 EVRVKVIKIDREKSRITLSIKQLEEDP 134
           EV+VKV+ +D EK +I+LSI+  +  P
Sbjct: 57  EVQVKVLAVDEEKGKISLSIRATQAAP 83

>pdb|2AHO|B Chain B, Structure Of The Archaeal Initiation Factor Eif2 Alpha- Gamma Heterodimer From Sulfolobus Solfataricus Complexed With Gdpnp Length = 266

Iteration: 1
 Score = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 43/68 (63%), Gaps = 3/68 (4%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYG+++ L   D    L   +  SEVS   +++IRD+L E  +V VKVI++DR K  + +
Sbjct: 24  DYGSYVSL---DEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDV 80
Query: 126 SIKQLEED 133
           S+K++ +D
Sbjct: 81  SLKKVTDD 88

>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From Pyrococcus Horikoshii Ot3 Length = 275

Iteration: 1
 Score = 47.4 bits (111), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 3/65 (4%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           +YGAF+ L   D        +H+SEV+   +++IRD L EG +V  KVI++D  K  I L
Sbjct: 24  NYGAFLEL---DEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDL 80
Query: 126 SIKQL 130
           S++++
Sbjct: 81  SLRRV 85

>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From Pyrococcus Abyssi Length = 274

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 3/65 (4%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           +YGAF+ L   D        +H+SEV+   +++IRD L EG +V  KVI++D  K  I L
Sbjct: 23  NYGAFLEL---DEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDL 79
Query: 126 SIKQL 130
           S++++
Sbjct: 80  SLRRV 84

>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase Length = 723

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 28/85 (32%), Positives = 49/85 (57%), Gaps = 11/85 (12%)
Query: 53  SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGD 107
           ++ + V  ++ G+     D+GAF+ +          GLVH+S+++   ++ + D L  G 
Sbjct: 622 TAEIEVGRVYTGKVTRIVDFGAFVAIGGGK-----EGLVHISQIADKRVEKVTDYLQMGQ 676
Query: 108 EVRVKVIKIDREKSRITLSIKQLEE 132
           EV VKV+++DR+  RI LSIK+  E
Sbjct: 677 EVPVKVLEVDRQ-GRIRLSIKEATE 700

>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas Aeruginosa, Crystal Form I Length = 785

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/63 (33%), Positives = 41/63 (65%), Gaps = 5/63 (7%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           ++GAF+ +       H  GLVH+S +S   ++D  +++  GD V+VKV+++D  ++R+ L
Sbjct: 667 NFGAFVDIGV-----HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGL 721
Query: 126 SIK 128
           S++
Sbjct: 722 SMR 724

>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From Pseudomonas Aeruginosa Length = 780

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 21/63 (33%), Positives = 41/63 (65%), Gaps = 5/63 (7%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           ++GAF+ +       H  GLVH+S +S   ++D  +++  GD V+VKV+++D  ++R+ L
Sbjct: 668 NFGAFVDIGV-----HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGL 722
Query: 126 SIK 128
           S++
Sbjct: 723 SMR 725

>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures Length = 76

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 11/81 (13%)
Query: 54  SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
           + + V  ++ G+     D+GAF+ +          GLVH+S+++   ++ + D L  G E
Sbjct: 1   AEIEVGRVYTGKVTRIVDFGAFVAIGGGK-----EGLVHISQIADKRVEKVTDYLQMGQE 55
Query: 109 VRVKVIKIDREKSRITLSIKQ 129
           V VKV+++DR+  RI LSIK+
Sbjct: 56  VPVKVLEVDRQ-GRIRLSIKE 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	234
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	4e-22
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	9e-22
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	2e-04
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	2e-21
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	7e-21
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	1e-05
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	4e-19
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	2e-18
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	2e-18
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	7e-18
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	8e-17
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	5e-16
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	9e-16
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	3e-15
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	9e-15
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	4e-13
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	8e-12
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	1e-07
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	1e-07
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	3e-07
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	7e-07
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	3e-06
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	2e-05
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	4e-05
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	5e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-04

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130

 Score = 87.1 bits (216), Expect = 4e-22
 Identities = 32/87 (36%), Positives = 52/87 (59%), Gaps = 10/87 (11%)

Query: 53  SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGD 107
           +++  V  ++ G+      YGAF+ L          GLVH+SEV+   ++DI + L+ GD
Sbjct: 2   AAKFEVGSVYTGKVTGLQAYGAFVAL-----DEETQGLVHISEVTHGFVKDINEHLSVGD 56

Query: 108 EVRVKVIKIDREKSRITLSIKQLEEDP 134
           EV+VKV+ +D EK +I+LSI+  +  P
Sbjct: 57  EVQVKVLAVDEEKGKISLSIRATQAAP 83

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 85.3 bits (212), Expect = 9e-22
 Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 10/91 (10%)

Query: 49  WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDIL 103
           +N + +      I  G+       GA + L   DG+    G +  SE S D ++D   +L
Sbjct: 22  FNNWVALNKKGAIVTGKVTAVDAKGATVELA--DGV---EGYLRASEASRDRVEDATLVL 76

Query: 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
           + GDEV  K   +DR+   I+LS++  +E  
Sbjct: 77  SVGDEVEAKFTGVDRKNRAISLSVRAKDEAD 107

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 0/29 (0%), Positives = 4/29 (13%)

Query: 114 IKIDREKSRITLSIKQLEEDPLLETLEKV 142
           +         +  +           +   
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMFNNWVALN 29

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 Length = 182

 Score = 86.8 bits (215), Expect = 2e-21
 Identities = 23/90 (25%), Positives = 47/90 (52%), Gaps = 8/90 (8%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
            VED+ +       + GA++ L   + +    G++ +SE+S   I+ I  ++  G    V
Sbjct: 14  EVEDVVMVNVRSIAEMGAYVSLLEYNNI---EGMILLSELSRRRIRSINKLIRIGRNECV 70

Query: 112 KVIKIDREKSRITLSIKQLEEDPLLETLEK 141
            VI++D+EK  I LS +++  +  ++  +K
Sbjct: 71  VVIRVDKEKGYIDLSKRRVSPEEAIKCEDK 100

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A Length = 175

 Score = 85.2 bits (211), Expect = 7e-21
 Identities = 22/90 (24%), Positives = 48/90 (53%), Gaps = 8/90 (8%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
            ++DI +       + GA++ L   D +    G++ +SE+S   I+ I+ ++  G     
Sbjct: 14  EIDDIVMVNVQQIAEMGAYVKLLEYDNI---EGMILLSELSRRRIRSIQKLIRVGKNDVA 70

Query: 112 KVIKIDREKSRITLSIKQLEEDPLLETLEK 141
            V+++D+EK  I LS +++  + +++  EK
Sbjct: 71  VVLRVDKEKGYIDLSKRRVSSEDIIKCEEK 100

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A Length = 175

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 13/123 (10%), Positives = 30/123 (24%), Gaps = 13/123 (10%)

Query: 12  KSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-DY 67
           +SI ++ +   G      V++ ++E   +  S++        K   +            Y
Sbjct: 56  RSIQKLIR--VGKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRY 113

Query: 68  GAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
            A       + LY                     +              I+     +   
Sbjct: 114 CAEKFQIPLEELYK------TIAWPLSRKFGHAYEAFKLSIIDETVWEGIEPPSKDVLDE 167

Query: 127 IKQ 129
           +K 
Sbjct: 168 LKN 170

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 78.8 bits (195), Expect = 4e-19
 Identities = 32/92 (34%), Positives = 46/92 (50%), Gaps = 11/92 (11%)

Query: 49  WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDI 102
           W   + R        GR     DYG F+ +   +G+    GLVHVSE+ W         +
Sbjct: 21  WVAIAKRYPEGTKLTGRVTNLTDYGCFVEIE--EGV---EGLVHVSEMDWTNKNIHPSKV 75

Query: 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
           +N GD V V V+ ID E+ RI+L +KQ + +P
Sbjct: 76  VNVGDVVEVMVLDIDEERRRISLGLKQCKANP 107

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B* Length = 266

 Score = 80.8 bits (199), Expect = 2e-18
 Identities = 32/140 (22%), Positives = 63/140 (45%), Gaps = 21/140 (15%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
           +  +I +       DYG+++ L    GL      +  SEVS   +++IRD+L E  +V V
Sbjct: 10  SEGEILIATVKQVFDYGSYVSLDEYGGL---QAFLPWSEVSSKWVKNIRDVLKENRKVIV 66

Query: 112 KVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKR 171
           KVI++DR K  + +S+K++ +D   +   +             +KK+  +    +   ++
Sbjct: 67  KVIRVDRRKGTVDVSLKKVTDDERRKKNLQ-------------WKKIQRLDKILELVSQK 113

Query: 172 VVSQDLQLWLSNAPPSGKKF 191
           +   +   W   A     K+
Sbjct: 114 LKLSEKDAWEQVAWKLEAKY 133

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1 Length = 308

 Score = 81.2 bits (200), Expect = 2e-18
 Identities = 25/90 (27%), Positives = 49/90 (54%), Gaps = 8/90 (8%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
            VED+ +       + GA++ L   + +    G++H+SE+S   I+ I  ++  G    V
Sbjct: 12  EVEDVVMVNVRSIQEMGAYVSLLEYNNI---EGMIHLSELSRRRIRSINKLIRIGRNECV 68

Query: 112 KVIKIDREKSRITLSIKQLEEDPLLETLEK 141
           KVI++D+EK  I LS +++  +  ++  +K
Sbjct: 69  KVIRVDKEKGYIDLSKRRVSPEEAIKCEDK 98

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

 Score = 75.5 bits (186), Expect = 7e-18
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 6/71 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID--REKSRI 123
           DYGAFI +          GLVH + +S   +    +I++ GD+V VK+I  +   ++ ++
Sbjct: 35  DYGAFIKI----PGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKV 90

Query: 124 TLSIKQLEEDP 134
           +LS+K + +  
Sbjct: 91  SLSMKVVNQGT 101

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 72.3 bits (178), Expect = 8e-17
 Identities = 20/92 (21%), Positives = 45/92 (48%), Gaps = 10/92 (10%)

Query: 49  WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDI 102
                    + DI+ G+      +G F+  +         GLVH+SE+  +  + ++ D+
Sbjct: 3   SGSSGEEPTIGDIYNGKVTSIMQFGCFV--QLEGLRKRWEGLVHISELRREGRVANVADV 60

Query: 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
           +++G  V+VKV+       + +LS+K ++++ 
Sbjct: 61  VSKGQRVKVKVLSFTGT--KTSLSMKDVDQET 90

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 75.6 bits (187), Expect = 5e-16
 Identities = 27/86 (31%), Positives = 47/86 (54%), Gaps = 15/86 (17%)

Query: 56  VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
             V  I+ G+     D+GAF++  F   DGL      VHVS++S + +    D+L EG  
Sbjct: 635 AEVGKIYDGKVVKVVDFGAFVNF-FGAKDGL------VHVSQISNERVAKPSDVLKEGQM 687

Query: 109 VRVKVIKIDREKSRITLSIKQLEEDP 134
           V+VK++  D  + +  LS+K ++++ 
Sbjct: 688 VKVKLLGFDD-RGKTKLSMKVVDQET 712

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 74.8 bits (185), Expect = 9e-16
 Identities = 28/86 (32%), Positives = 48/86 (55%), Gaps = 15/86 (17%)

Query: 56  VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
           + V  ++ G+     D+GAF+ +     +GL      VH+S+++   ++ + D L  G E
Sbjct: 625 IEVGRVYTGKVTRIVDFGAFVAI-GGGKEGL------VHISQIADKRVEKVTDYLQMGQE 677

Query: 109 VRVKVIKIDREKSRITLSIKQLEEDP 134
           V VKV+++DR + RI LSIK+  E  
Sbjct: 678 VPVKVLEVDR-QGRIRLSIKEATEQS 702

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80

 Score = 67.3 bits (165), Expect = 3e-15
 Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 9/68 (13%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
            YGAFI+L        + GL+   ++    +++    LN GDE+ V+ I +  EK  I  
Sbjct: 18  KYGAFINL-----NEQVRGLLRPRDMISLRLEN----LNVGDEIIVQAIDVRPEKREIDF 68

Query: 126 SIKQLEED 133
               LE  
Sbjct: 69  KYIPLEHH 76

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Length = 275

 Score = 70.4 bits (172), Expect = 9e-15
 Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 8/90 (8%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
              +  V       +YGAF+ L    G       +H+SEV+   +++IRD L EG +V  
Sbjct: 10  EEGEFVVATVKRIHNYGAFLELDEYPGK---EAFMHISEVASTWVRNIRDYLKEGQKVVA 66

Query: 112 KVIKIDREKSRITLSIKQLEEDPLLETLEK 141
           KVI++D  K  I LS++++ +      L++
Sbjct: 67  KVIRVDPRKGHIDLSLRRVTQQQRKAKLQE 96

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Length = 757

 Score = 67.2 bits (165), Expect = 4e-13
 Identities = 21/90 (23%), Positives = 44/90 (48%), Gaps = 19/90 (21%)

Query: 56  VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDL----IQDIRDILN 104
             V +  +G       +GAF+ L  P  DGL      +H+S++        ++++ D+L 
Sbjct: 665 PEVGERILGSVVKTTTFGAFVSL-LPGKDGL------LHISQIRKLAGGKRVENVEDVLG 717

Query: 105 EGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
            G +V+V++ +ID  + +++L      E+ 
Sbjct: 718 VGQKVQVEIAEIDS-RGKLSLIPVIEGEEA 746

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A Length = 785

 Score = 63.4 bits (155), Expect = 8e-12
 Identities = 22/69 (31%), Positives = 44/69 (63%), Gaps = 5/69 (7%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           ++GAF+ +    G+ H  GLVH+S +S   ++D  +++  GD V+VKV+++D  ++R+ L
Sbjct: 667 NFGAFVDI----GV-HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGL 721

Query: 126 SIKQLEEDP 134
           S++  +   
Sbjct: 722 SMRMSDTPG 730

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219

 Score = 51.0 bits (122), Expect = 1e-07
 Identities = 15/102 (14%), Positives = 34/102 (33%), Gaps = 13/102 (12%)

Query: 81   HLTGLVHVSEVSWDLIQD-IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETL 139
             +  +V+    +   ++    +I   G     KVI ID       +S+   +    ++  
Sbjct: 925  EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDHD----VKQQ 980

Query: 140  EKVIPQGLEPYLKSFYKKMDDVRI--------TRQGFEKRVV 173
               I    +P +    ++++D            R     RV+
Sbjct: 981  YVPISYSKDPSIWDLKQELEDAEEERKLMMAEARAKRTHRVI 1022

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030

 Score = 50.7 bits (121), Expect = 1e-07
 Identities = 16/117 (13%), Positives = 35/117 (29%), Gaps = 18/117 (15%)

Query: 66   DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-IRDILNEGDEVRVKVIKIDREKSRIT 124
                            +  +V+    +   ++    +I   G     KVI ID       
Sbjct: 918  HNDIICTTNS-----EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAE 972

Query: 125  LSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRI--------TRQGFEKRVV 173
            +S+   + D  ++     I    +P +    ++++D            R     RV+
Sbjct: 973  VSLL--DHD--VKQQYVPISYSKDPSIWDLKQELEDAEEERKLMMAEARAKRTHRVI 1025

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E Length = 180

 Score = 48.4 bits (115), Expect = 3e-07
 Identities = 26/124 (20%), Positives = 58/124 (46%), Gaps = 14/124 (11%)

Query: 20  GLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           GL  +I++VK  +    +     +  +  ++  +    V+++  G      +YG F++L 
Sbjct: 43  GLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDNYGVFVNLG 102

Query: 75  FPDGLYHLTGL----VHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREK----SRITL 125
             DGL H++ +    +    V   +  +  + ++ +GD+VR +VI +         RI L
Sbjct: 103 PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTGRLPRIAL 162

Query: 126 SIKQ 129
           +++Q
Sbjct: 163 TMRQ 166

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1 Length = 187

 Score = 47.2 bits (112), Expect = 7e-07
 Identities = 30/154 (19%), Positives = 62/154 (40%), Gaps = 26/154 (16%)

Query: 2   SPSHSCKEPQKSIHEIAK-----------GLTGSIISVKVIQANEEMKKLVFSEKDAVWN 50
            P    K+ ++++ +I             G   SI+ VK I   + +     +    V+ 
Sbjct: 14  PPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFE 73

Query: 51  KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL----VHVSEVSWDLI-QDIR 100
                  + ++  G      ++G+F+ L   DGL H++ +    V        +I ++  
Sbjct: 74  TLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETG 133

Query: 101 DILNEGDEVRVKVIKIDREKSR-----ITLSIKQ 129
            +L  GD VR +++ I  +  R     I L+++Q
Sbjct: 134 KVLEIGDYVRARIVAISLKAERKRGSKIALTMRQ 167

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Length = 285

 Score = 46.1 bits (109), Expect = 3e-06
 Identities = 19/124 (15%), Positives = 40/124 (32%), Gaps = 17/124 (13%)

Query: 25  IISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGL 79
            I ++V + +     L + E      + +        +       +  G F++L  P+  
Sbjct: 119 YIRLEVDKKDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYL--PENN 176

Query: 80  YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETL 139
               G +H SE               G  +  +VI        + LS+K    + L    
Sbjct: 177 ML--GFIHPSE--------RYAEPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDA 226

Query: 140 EKVI 143
           + ++
Sbjct: 227 QMIL 230

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5 Length = 119

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 11/79 (13%), Positives = 29/79 (36%), Gaps = 5/79 (6%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           D+G  + +    G+      + + +    +  ++    L  G  +   V K+      ++
Sbjct: 34  DHGYLVDI----GVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVS 89

Query: 125 LSIKQLEEDPLLETLEKVI 143
           LS+   E    + T ++  
Sbjct: 90  LSVGHSEVSTAIATEQQSW 108

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A Length = 179

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 15/91 (16%)

Query: 51  KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGL-----YHLTGLVHVSEVSWDLIQDIR 100
                +   D+ +GR     +  A I +    G          G++HVS V    +++I 
Sbjct: 50  SPIPEIVKGDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEIS 109

Query: 101 DILNEGDEVRVKVIKIDREKSRITLSIKQLE 131
           + +   D ++ +VI        + LS K+ E
Sbjct: 110 EAVGYLDILKARVI-----GDNLRLSTKEEE 135

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 172

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 21/152 (13%), Positives = 43/152 (28%), Gaps = 24/152 (15%)

Query: 2   SPSHSCKEPQKSIHEIAK--------GLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYS 53
            PS+     Q  +             G  G II V      +  K  V   +     +  
Sbjct: 15  HPSYFGPRMQDYLKAKLLADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVK 74

Query: 54  SRVNVEDIFVG----------RDYGAFIHLRFPDGLYHLTGL----VHVSEVSWDLIQDI 99
            R  +   F G             G F ++   +       +          +       
Sbjct: 75  YRAVLWRPFRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGE 134

Query: 100 RDILNEGDEVRVKVI--KIDREKSRITLSIKQ 129
             ++ +G  VR+K++  + D  +     ++K+
Sbjct: 135 DQVIEKGSNVRLKIVGTRTDATEIFAIATMKE 166

>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 = 39.8 bits (92), Expect = 6e-04
 Identities = 41/287 (14%), Positives = 82/287 (28%), Gaps = 88/287 (30%)

Query: 6   SCKEP-------QKSIHEIAKGLT-----GSIISVKVIQANEEMKKLVFSEK-------- 45
           +C  P       QK +++I    T      S I +++     E+++L+ S+         
Sbjct: 191 NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL 250

Query: 46  DAVWNK-------YSSRV-------NVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEV 91
             V N         S ++        V D                  L        + + 
Sbjct: 251 LNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY 310

Query: 92  SWDLIQD-------------------IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 132
                QD                   IRD L   D    K +  D+  + I  S+  LE 
Sbjct: 311 LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD--NWKHVNCDKLTTIIESSLNVLEP 368

Query: 133 DPLLETLEKVIPQGLEPYLKSFYKKM----DDVRITRQGFE---KRVVSQDLQLWLSNAP 185
                              +  + ++        I           V+  D+ + ++   
Sbjct: 369 A----------------EYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKL- 411

Query: 186 PSGKKFTLLARAGRQVQEIQLS-HSLIRKASKRHCNEYWNVFHETAI 231
               K++L+    +Q +E  +S  S+  +  K      + + H + +
Sbjct: 412 ---HKYSLVE---KQPKESTISIPSIYLE-LKVKLENEYAL-HRSIV 450

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	234
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.9
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.81
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.73
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.67
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.66
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.64
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.63
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.62
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.62
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.62
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.56
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.55
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.53
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.52
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.44
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.43
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.4
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.39
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.34
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.31
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.28
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.26
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	99.2
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.2
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.19
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.17
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.17
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.16
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.15
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.15
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.14
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.14
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	99.1
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.09
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	99.06
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.02
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.99
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.97
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	98.96
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	98.93
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.87
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.86
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.84
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.74
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.73
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.69
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.69
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.68
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.64
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.43
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.39
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.39
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	98.32
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.23
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.12
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.11
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.07
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.03
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.02
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.98
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.96
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	97.9
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	97.9
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	97.82
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	97.79
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	97.77
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.74
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	97.74
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.72
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	97.65
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	97.57
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.54
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	97.52
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.34
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	97.22
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	96.7
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	96.5
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	96.46
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	96.41
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	96.12
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	95.7
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	95.47
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	95.28
2r7d_A	469	Ribonuclease II family protein; structural genomic	94.89
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	94.71
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	94.39
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	92.51
1jjg_A	102	M156R; beta barrel, S1 motif, OB fold, MYXV156R, N	92.03
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	88.63

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

Probab=99.90  E-value=1.3e-23  Score=184.58  Aligned_cols=164  Identities=13%  Similarity=0.075  Sum_probs=133.2

Q ss_pred             CCCCEEEEEEEEEeCCCCEEEEEechhhHhhhhcCCCCCcEEEEE------EeeEEEEEecCCCcceeEEEEEceecccc
Q 026737           21 LTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD   94 (234)
Q Consensus        21 ~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~------~~G~fV~l~~~~g~~g~~glv~isels~~   94 (234)
                      .+||+++|.|+ .|. .+++++|.+..       .+++|+++.|+      +|||||+++.    ++.+||||+|+++|.
T Consensus        41 ~vGdevev~v~-~d~-~~r~iat~~~p-------~~~~G~~~~g~V~~v~~~~GaFVdiG~----~~~d~lvp~sel~~~  107 (285)
T 3go5_A           41 TVGDTVKGFAY-TDM-KQKLRLTTLEV-------TATQDQFGWGRVTEVRKDLGVFVDTGL----PDKEIVVSLDILPEL  107 (285)
T ss_dssp             CTTSEEEEEEE-ECT-TSCEEEECSCC-------CSCSSSCEEEEEEEEETTTEEEEECSC----TTCCEEEEGGGSCSS
T ss_pred             ccCCEEEEEEE-ECC-CCCEEEecccc-------cccCCCEEEEEEEEEccCceEEEEECC----CCcEEEEEHHHCCcc
Confidence            59999999997 465 55677787643       37899999998      3899999961    148999999999997


Q ss_pred             cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec-ccCcchhhhhccccccc-----c------ceee-eecCCceEE
Q 026737           95 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL-EEDPLLETLEKVIPQGL-----E------PYLK-SFYKKMDDV  161 (234)
Q Consensus        95 ~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~-~~~p~~~~~~~~~~~G~-----~------G~fV-~l~~gi~Gl  161 (234)
                      +..    .+++||.+.++ +.+|+ ++||.+|+|+. ..+||.....+ ++.|.     +      |+|| .+++|++||
T Consensus       108 ~~~----~~~~Gd~v~v~-l~iD~-~~Ri~ls~k~~~~~~~~~~~~~~-~~~G~~V~g~V~~i~~~G~fV~~i~~g~~Gl  180 (285)
T 3go5_A          108 KEL----WPKKGDQLYIR-LEVDK-KDRIWGLLAYQEDFQRLARPAYN-NMQNQNWPAIVYRLKLSGTFVYLPENNMLGF  180 (285)
T ss_dssp             GGG----SCCTTCEEEEE-EEECT-TSCEEEEECCHHHHHHHCCCCCS-CCTTCEEEEEEEEEETTEEEEEETTTTEEEE
T ss_pred             ccc----ccCCCCEEEEE-EEECC-CCcEEEEehhhhhcchhhhhhhh-CCCCCEEEEEEEEEeCCcEEEEEeCCCeEEE
Confidence            542    36899999766 69998 79999999987 46899765555 56652     1      9999 999999999


Q ss_pred             E-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhh
Q 026737          162 R-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHET  229 (234)
Q Consensus       162 ~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~  229 (234)
                      | +|+++                         ..+++||+|+|+|+++|.    |+||+|++...+|+..++.
T Consensus       181 ih~SEl~-------------------------~~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~~~~~~~a~~  228 (285)
T 3go5_A          181 IHPSERY-------------------------AEPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQM  228 (285)
T ss_dssp             ECGGGCS-------------------------SCCCTTCEEEEEEEEEETTTTEEEEECSCCCCCCCCHHHHH
T ss_pred             EEHHHcc-------------------------ccCCCCCEEEEEEEEEECCCCeEEEEeChhhhhccchHHHH
Confidence            9 78762                         147999999999999975    9999999998888877654

>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=99.81  E-value=2.3e-21  Score=159.84  Aligned_cols=110  Identities=23%  Similarity=0.368  Sum_probs=83.1

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~  130 (234)
                      +++|+++.|+     +||+||+|.+.   ++++||||+|+++|.++.++.+.|++||.|+|+|+++|+++++|+||+|++
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~---~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~   89 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEY---NNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRV   89 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTT---TTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTTC
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccC---CCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence            4899999999     99999999311   269999999999999999999999999999999999999999999999999


Q ss_pred             ccCcchhhhhcccccccc------------ceeeeecCCceEEE-Ecccccccc
Q 026737          131 EEDPLLETLEKVIPQGLE------------PYLKSFYKKMDDVR-ITRQGFEKR  171 (234)
Q Consensus       131 ~~~p~~~~~~~~~~~G~~------------G~fV~l~~gi~Gl~-~s~~~~~~~  171 (234)
                      .++||....++ ++.|..            |  ++|++|++||+ +|+.+|.++
T Consensus        90 ~~~p~~~~~~~-~~~g~~v~g~v~~i~~~~g--v~l~~giegl~h~s~~~~~~~  140 (182)
T 1kl9_A           90 SPEEAIKCEDK-FTKSKTVYSILRHVAEVLE--YTKDEQLESLFQRTAWVFDDK  140 (182)
T ss_dssp             CHHHHHHHHHH-HHHHHHHHHHHHHHHHHTT--CCSHHHHHHHHHHTHHHHHHH
T ss_pred             CcChHHHHHHh-ccCCCEEEEEEEEchhhcC--CcccCChhheEEeeecchhhh
Confidence            99999876665 555521            5  78888999999 887755543

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

Probab=99.73  E-value=2.7e-18  Score=131.48  Aligned_cols=89  Identities=36%  Similarity=0.620  Sum_probs=80.2

Q ss_pred             hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc-cccchhhhhCCCCEEEEEEEEEeCCCC
Q 026737           48 VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKS  121 (234)
Q Consensus        48 ~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~-~~~~~~~~~~vGd~v~vkVl~id~~~~  121 (234)
                      +|+.+...+++|+++.|+     +||+||+|+     ++++||||+|++++. +..++.+.|++||.|+|+|+++|.+++
T Consensus        20 p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~-----~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~   94 (115)
T 2khi_A           20 HWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIE-----EGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERR   94 (115)
T ss_dssp             -CCCSSCSSCSSCEEEEEEEEEETTEEEEECS-----TTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTTT
T ss_pred             CHHHHhhcCCCCCEEEEEEEEEECCEEEEEEC-----CCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCCC
Confidence            577777899999999999     999999997     379999999999985 778899999999999999999999999


Q ss_pred             eEEEEEeecccCcchhhhhc
Q 026737          122 RITLSIKQLEEDPLLETLEK  141 (234)
Q Consensus       122 ri~LS~K~~~~~p~~~~~~~  141 (234)
                      +|.||+|++.+|||+++.++
T Consensus        95 rI~lslk~~~~~p~~~~~~~  114 (115)
T 2khi_A           95 RISLGLKQCKANPWQQFAET  114 (115)
T ss_dssp             EEEECCCCCCSSCCCCCCCC
T ss_pred             EEEEEEEecCcCHHHHHHhh
Confidence            99999999999999865543

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

Probab=99.67  E-value=3.2e-16  Score=137.41  Aligned_cols=104  Identities=13%  Similarity=0.121  Sum_probs=91.5

Q ss_pred             CCCCEEEEEEEEEeCCCCEEEEEechh----hHhhhhcCCCCCcEEEEE-----EeeEEE-EEecCCCcceeEEEEEcee
Q 026737           21 LTGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFI-HLRFPDGLYHLTGLVHVSE   90 (234)
Q Consensus        21 ~vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV-~l~~~~g~~g~~glv~ise   90 (234)
                      .+||++.++ +++|+ ++|+++|+|++    +|......+++|++|+|+     +||+|| .++     ++++||||.||
T Consensus       113 ~~Gd~v~v~-l~iD~-~~Ri~ls~k~~~~~~~~~~~~~~~~~G~~V~g~V~~i~~~G~fV~~i~-----~g~~Glih~SE  185 (285)
T 3go5_A          113 KKGDQLYIR-LEVDK-KDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPE-----NNMLGFIHPSE  185 (285)
T ss_dssp             CTTCEEEEE-EEECT-TSCEEEEECCHHHHHHHCCCCCSCCTTCEEEEEEEEEETTEEEEEETT-----TTEEEEECGGG
T ss_pred             CCCCEEEEE-EEECC-CCcEEEEehhhhhcchhhhhhhhCCCCCEEEEEEEEEeCCcEEEEEeC-----CCeEEEEEHHH
Confidence            599999766 79998 78999999754    477778899999999999     999999 996     37999999999


Q ss_pred             cccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhh
Q 026737           91 VSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETL  139 (234)
Q Consensus        91 ls~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~  139 (234)
                      ++.        .+++||+|+|+|+++|++++||+||+|++...+|.+..
T Consensus       186 l~~--------~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~~~~~~~a  226 (285)
T 3go5_A          186 RYA--------EPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDA  226 (285)
T ss_dssp             CSS--------CCCTTCEEEEEEEEEETTTTEEEEECSCCCCCCCCHHH
T ss_pred             ccc--------cCCCCCEEEEEEEEEECCCCeEEEEeChhhhhccchHH
Confidence            984        38999999999999999899999999999888876543

>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=99.66  E-value=3.5e-17  Score=134.04  Aligned_cols=87  Identities=24%  Similarity=0.447  Sum_probs=70.1

Q ss_pred             CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 026737           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (234)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~  131 (234)
                      ++|+++.|+     +||+||+|.+.   ++++||||+|+++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.
T Consensus        14 ~~G~iv~G~V~~i~~fGaFV~L~e~---~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~   90 (175)
T 2a19_A           14 EIDDIVMVNVQQIAEMGAYVKLLEY---DNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVS   90 (175)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTT---TTCEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTTCC
T ss_pred             CCCCEEEEEEEEEecceEEEEEcCC---CCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEecC
Confidence            499999999     99999999310   2699999999999999999999999999999999999999999999999999


Q ss_pred             cCcchhhhhccccccc
Q 026737          132 EDPLLETLEKVIPQGL  147 (234)
Q Consensus       132 ~~p~~~~~~~~~~~G~  147 (234)
                      ++||....++ ++.|.
T Consensus        91 ~~~~~~~~~~-~~~g~  105 (175)
T 2a19_A           91 SEDIIKCEEK-YQKSK  105 (175)
T ss_dssp             HHHHHHHHHH-HHHHH
T ss_pred             cChHHHHHHh-ccCCC
Confidence            9999877666 56663

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

Probab=99.64  E-value=9.4e-17  Score=123.67  Aligned_cols=88  Identities=27%  Similarity=0.369  Sum_probs=78.4

Q ss_pred             hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCC--
Q 026737           48 VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--  120 (234)
Q Consensus        48 ~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~--  120 (234)
                      .|+.+...+++|++|.|+     +||+||+|++    .+.+||||+++++|.++.++.+.|++||.|+|+|+++|.++  
T Consensus        12 ~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g----~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~~   87 (119)
T 2cqo_A           12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPG----CRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDR   87 (119)
T ss_dssp             CCCCSCCSCCTTCEEEEEEEEEETTEEEEECTT----CSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSSC
T ss_pred             chhhhhcccCCCCEEEEEEEEEeCceEEEEECC----CcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccccC
Confidence            467777889999999999     9999999962    13699999999999999999999999999999999999864  


Q ss_pred             CeEEEEEeecccCcchhhh
Q 026737          121 SRITLSIKQLEEDPLLETL  139 (234)
Q Consensus       121 ~ri~LS~K~~~~~p~~~~~  139 (234)
                      ++|.||+|++.++||+...
T Consensus        88 ~~i~LSlk~~~~~~~~~~~  106 (119)
T 2cqo_A           88 IKVSLSMKVVNQGTGKDLD  106 (119)
T ss_dssp             EEEEEESTTBCSSSCCBSC
T ss_pred             ceEEEEEeecccCCccccC
Confidence            7999999999999997643

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

Probab=99.63  E-value=5.7e-16  Score=121.00  Aligned_cols=78  Identities=41%  Similarity=0.747  Sum_probs=73.6

Q ss_pred             cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      ..+++|++|.|+     +||+||+|+     .+++||||+|++++.++.++.+.|++||.|+|+|+++|.++++|.||+|
T Consensus         3 ~~~~vG~iv~G~V~~i~~~G~FV~l~-----~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk   77 (130)
T 2k4k_A            3 AKFEVGSVYTGKVTGLQAYGAFVALD-----EETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIR   77 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEE-----TTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESH
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEEC-----CCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence            468999999998     999999997     3799999999999999999999999999999999999998999999999


Q ss_pred             ecccCcch
Q 026737          129 QLEEDPLL  136 (234)
Q Consensus       129 ~~~~~p~~  136 (234)
                      ++.++||.
T Consensus        78 ~~~~~p~~   85 (130)
T 2k4k_A           78 ATQAAPEK   85 (130)
T ss_dssp             HHHHSCCC
T ss_pred             ecccCccc
Confidence            99999975

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

Probab=99.62  E-value=2.9e-16  Score=118.98  Aligned_cols=86  Identities=28%  Similarity=0.412  Sum_probs=75.1

Q ss_pred             EEechh---hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEE
Q 026737           42 FSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKV  113 (234)
Q Consensus        42 lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkV  113 (234)
                      -|.|++   +|+.+...+++|+++.|+     +||+||+|+     ++++||||++++++.++.++.+.|++||.|+|+|
T Consensus        12 ~~iKq~~~~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~-----~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V   86 (109)
T 2khj_A           12 SGLVPRGSHMFNNWVALNKKGAIVTGKVTAVDAKGATVELA-----DGVEGYLRASEASRDRVEDATLVLSVGDEVEAKF   86 (109)
T ss_dssp             ---------CHHHHTTTCCSSSEEEEEEEEECSSCEEEECS-----TTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEE
T ss_pred             cchhhcccCHHHHHhhcCCCCCEEEEEEEEEECCeEEEEEC-----CCCEEEEEHHHcCcccccChhhccCCCCEEEEEE
Confidence            355554   599999999999999999     999999997     3699999999999999999999999999999999


Q ss_pred             EEEeCCCCeEEEEEeeccc
Q 026737          114 IKIDREKSRITLSIKQLEE  132 (234)
Q Consensus       114 l~id~~~~ri~LS~K~~~~  132 (234)
                      +++|+++++|.||+|++.+
T Consensus        87 ~~vd~~~~ki~LS~k~~~~  105 (109)
T 2khj_A           87 TGVDRKNRAISLSVRAKDE  105 (109)
T ss_dssp             EEEETTTTEEEEETTSSSS
T ss_pred             EEEECCCCEEEEEEeecCh
Confidence            9999988899999998764

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

Probab=99.62  E-value=8.4e-16  Score=112.25  Aligned_cols=76  Identities=33%  Similarity=0.453  Sum_probs=68.6

Q ss_pred             cCCCCCcEEEEE----EeeEEEEEecCCCcceeEEEEEce-ecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        54 ~~~~~G~iv~g~----~~G~fV~l~~~~g~~g~~glv~is-els~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      ...++|+++.|+    +||+||+|.+.   ++++||||+| +++++++.++++.+ +||.|+|+|+++|++++||.||+|
T Consensus         7 ~~~~vG~~~~G~V~v~~fG~FVel~~~---~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lslk   82 (88)
T 1luz_A            7 SLPNAGDVIKGRVYEKDYALYIYLFDY---PHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYK   82 (88)
T ss_dssp             CCCCTTCEEEEEEEEETTEEEEEETTC---TTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEE
T ss_pred             cCCCCCCEEEEEEEEEccEEEEEECCC---CCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEEe
Confidence            457899999998    99999999621   1699999999 99999999999999 999999999999999999999999


Q ss_pred             ecccC
Q 026737          129 QLEED  133 (234)
Q Consensus       129 ~~~~~  133 (234)
                      ++.++
T Consensus        83 ~~~~~   87 (88)
T 1luz_A           83 RMCRH   87 (88)
T ss_dssp             EECSC
T ss_pred             ecCCC
Confidence            98765

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

Probab=99.62  E-value=1e-15  Score=114.84  Aligned_cols=82  Identities=26%  Similarity=0.541  Sum_probs=71.8

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceec-ccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV-SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isel-s~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      ...+++|+++.|+     +||+||+|++..  ++++||||+|++ ++.++.++.+.|++||.|+|+|+++|.  ++|.||
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~--~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~--~~i~LS   82 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLR--KRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG--TKTSLS   82 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEECSSS--SCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET--TEEEEE
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEEcCCC--CCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC--CeeEEE
Confidence            4568999999998     999999997210  169999999999 667889999999999999999999996  699999


Q ss_pred             EeecccCcchhh
Q 026737          127 IKQLEEDPLLET  138 (234)
Q Consensus       127 ~K~~~~~p~~~~  138 (234)
                      +|++.++||...
T Consensus        83 lk~~~~~~~~~~   94 (103)
T 2eqs_A           83 MKDVDQETGEDL   94 (103)
T ss_dssp             STTBCTTTCCBC
T ss_pred             EeecccCCchhc
Confidence            999999999753

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

Probab=99.56  E-value=1.3e-14  Score=103.85  Aligned_cols=70  Identities=31%  Similarity=0.491  Sum_probs=62.7

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      ++++|+++.|+     +||+||+|+     ++++||+|+|++++.++    +.|++||.|+|+|+++|++++||.||+|+
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~-----~~~~Gllh~sel~~~~~----~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~   72 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLN-----EQVRGLLRPRDMISLRL----ENLNVGDEIIVQAIDVRPEKREIDFKYIP   72 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEE-----TTEEEEECGGGCSSCCG----GGCCTTCEEEEEEEEEETTTTEEEEEECS
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEEC-----CCCEEEEEHHHCCcccc----eeeCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            47899999998     999999998     37999999999998876    67999999999999999988999999998


Q ss_pred             cccC
Q 026737          130 LEED  133 (234)
Q Consensus       130 ~~~~  133 (234)
                      +.+.
T Consensus        73 ~~~~   76 (80)
T 2k52_A           73 LEHH   76 (80)
T ss_dssp             CC--
T ss_pred             cccc
Confidence            8753

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

Probab=99.55  E-value=1.1e-15  Score=116.92  Aligned_cols=89  Identities=13%  Similarity=0.172  Sum_probs=61.3

Q ss_pred             EEEeecccCcchhhhhcccccccc-----------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCccee
Q 026737          125 LSIKQLEEDPLLETLEKVIPQGLE-----------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFT  192 (234)
Q Consensus       125 LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~  192 (234)
                      -|+|++..+||...... +..|.+           |+||+|++|++||+ +|+++++.+.                .++.
T Consensus        11 ~~~k~~~~~p~~~~~~~-~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~----------------~~~~   73 (115)
T 2khi_A           11 SSGLVPRGSHWVAIAKR-YPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKN----------------IHPS   73 (115)
T ss_dssp             ----------CCCSSCS-SCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTT----------------CSST
T ss_pred             cchhhcccCCHHHHhhc-CCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccc----------------cCcc
Confidence            36777777887654333 444421           99999999999999 8888543211                2344


Q ss_pred             eeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhc
Q 026737          193 LLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETA  230 (234)
Q Consensus       193 ~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~  230 (234)
                      ..+++||.|+|+|+++|.    |+||+|++.++||+.+.++|
T Consensus        74 ~~~~vGd~V~vkV~~vd~~~~rI~lslk~~~~~p~~~~~~~~  115 (115)
T 2khi_A           74 KVVNVGDVVEVMVLDIDEERRRISLGLKQCKANPWQQFAETH  115 (115)
T ss_dssp             TTCCTTCEEEEEEEEEETTTTEEEECCCCCCSSCCCCCCCCC
T ss_pred             cEECCCCEEEEEEEEEECCCCEEEEEEEecCcCHHHHHHhhC
Confidence            589999999999999985    99999999999999988775

>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=99.53  E-value=3.5e-15  Score=131.91  Aligned_cols=87  Identities=29%  Similarity=0.497  Sum_probs=77.7

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~  130 (234)
                      +++|+++.|+     +||+||+|++.   ++++||||+|+++|.++.++.+.|++||.|.|+|+++|+++++|.||+|++
T Consensus        11 ~~vG~iv~G~V~~I~~fGaFV~L~ey---~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~   87 (308)
T 1q8k_A           11 PEVEDVVMVNVRSIQEMGAYVSLLEY---NNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRV   87 (308)
T ss_dssp             CSSCCEEEEEEEEEETTEEEEESCTT---TSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSC
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEECCC---CCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEec
Confidence            4699999999     89999999511   169999999999999999999999999999999999999999999999999


Q ss_pred             ccCcchhhhhcccccc
Q 026737          131 EEDPLLETLEKVIPQG  146 (234)
Q Consensus       131 ~~~p~~~~~~~~~~~G  146 (234)
                      .++||.....+ ++.|
T Consensus        88 ~~~p~~~~~~~-~~~G  102 (308)
T 1q8k_A           88 SPEEAIKCEDK-FTKS  102 (308)
T ss_dssp             CHHHHHHHHHH-HHHH
T ss_pred             ccChHHHHHHH-ccCC
Confidence            99999877665 4554

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

Probab=99.52  E-value=9.2e-15  Score=127.52  Aligned_cols=87  Identities=30%  Similarity=0.515  Sum_probs=76.9

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~  130 (234)
                      +++|+++.|+     +||+||+|++.+   +++||||+|+++|.++.++.+.|++||.|.|+|+++|+++++|.||+|++
T Consensus         9 p~~Gdiv~G~V~~I~~fGaFV~L~e~~---gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~   85 (275)
T 3aev_A            9 PEEGEFVVATVKRIHNYGAFLELDEYP---GKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRV   85 (275)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTST---TCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTTC
T ss_pred             CCCCCEEEEEEEEEECcEEEEEECCCC---CeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence            4589999999     999999996211   69999999999999999999999999999999999999999999999999


Q ss_pred             ccCcchhhhhcccccc
Q 026737          131 EEDPLLETLEKVIPQG  146 (234)
Q Consensus       131 ~~~p~~~~~~~~~~~G  146 (234)
                      .++||....++ +..|
T Consensus        86 ~~~~~~~~~~~-~~~g  100 (275)
T 3aev_A           86 TQQQRKAKLQE-FKRA  100 (275)
T ss_dssp             CHHHHHHHHHH-HHHH
T ss_pred             CcchhHHHHHh-ccCC
Confidence            99999866554 4443

>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=99.44  E-value=8.3e-14  Score=114.58  Aligned_cols=85  Identities=16%  Similarity=0.156  Sum_probs=66.8

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeee--cCCceEEE-Ecccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSF--YKKMDDVR-ITRQGFEKRVVSQDLQL  179 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l--~~gi~Gl~-~s~~~~~~~~~~~~~~~  179 (234)
                      .++|+.+.++|.++..                       +      |+||+|  .+|++||+ +|+++++.         
T Consensus        13 p~~G~iv~G~V~~I~~-----------------------f------GaFV~L~e~~g~eGLvhiSels~~~---------   54 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAE-----------------------M------GAYVSLLEYNNIEGMILLSELSRRR---------   54 (182)
T ss_dssp             CCTTCEEEEEEEEECS-----------------------S------EEEEEETTTTTEEEEEEGGGC-------------
T ss_pred             CCCCCEEEEEEEEEec-----------------------c------EEEEEEccCCCcEEEEEHHHCCCcc---------
Confidence            4789999999998863                       5      999999  57999999 89985432         


Q ss_pred             ccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcccC
Q 026737          180 WLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAIVN  233 (234)
Q Consensus       180 ~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~~~  233 (234)
                         .     .++...+++||.|+|+|+++|.    |+||+|++.++||+.+.++|++|
T Consensus        55 ---v-----~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~~~~p~~~~~~~~~~g  104 (182)
T 1kl9_A           55 ---I-----RSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKS  104 (182)
T ss_dssp             ----------------CTTCEEEEEEEEEETTTTEEEEESTTCCHHHHHHHHHHHHHH
T ss_pred             ---c-----CCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeecCcChHHHHHHhccCC
Confidence               1     3456699999999999999985    99999999999999999999865

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*

Probab=99.43  E-value=3.6e-14  Score=123.29  Aligned_cols=84  Identities=31%  Similarity=0.498  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      .+++|+++.|+     +||+||+|++.+   +.+||||+|+++|.++.++.+.|++||.|.|+|+++|+++++|.||+|+
T Consensus         8 ~~~vG~iv~G~V~~I~~~GaFV~l~e~~---~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~   84 (266)
T 3cw2_C            8 LPSEGEILIATVKQVFDYGSYVSLDEYG---GLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (266)
T ss_dssp             SCCTTCEEEEEEEECCSSSBEEEETTTT---SEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEESTT
T ss_pred             cCCCCCEEEEEEEEEeccEEEEEEcCCC---CeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            47899999999     999999995111   6999999999999999999999999999999999999989999999999


Q ss_pred             cccCcchhhhhc
Q 026737          130 LEEDPLLETLEK  141 (234)
Q Consensus       130 ~~~~p~~~~~~~  141 (234)
                      +.++||....++
T Consensus        85 ~~~~~~~~~~~~   96 (266)
T 3cw2_C           85 VTDDERRKKNLQ   96 (266)
T ss_dssp             SCTTHHHHHHHH
T ss_pred             cchhhHHHHHHh
Confidence            999999775554

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

Probab=99.40  E-value=2.2e-14  Score=139.20  Aligned_cols=101  Identities=29%  Similarity=0.481  Sum_probs=2.0

Q ss_pred             EEEeCCCCEEEEEech-h-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc
Q 026737           31 IQANEEMKKLVFSEKD-A-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (234)
Q Consensus        31 i~id~~~~~i~lS~k~-~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~   97 (234)
                      +++++ .+.+.++... .       .++.+...+++|++|.|+     +||+||+|.     ++++||||+|+++|.++.
T Consensus       603 idi~d-dG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~-----~g~eGLvHiSels~~rv~  676 (726)
T 4aid_A          603 VDIND-DGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFF-----GAKDGLVHVSQISNERVA  676 (726)
T ss_dssp             ------------CCSCHHHHHHHHHC------------------------------------------------------
T ss_pred             eeEEC-CceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEeccEEEEEEC-----CCcEEEEEHHHcCccccc
Confidence            56664 4555555432 1       256677889999999999     999999997     479999999999999999


Q ss_pred             chhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhh
Q 026737           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET  138 (234)
Q Consensus        98 ~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~  138 (234)
                      ++.+.|++||.|+|||+++|+ ++||.||+|++.++||.+.
T Consensus       677 ~~~d~~kvGD~V~VkVi~iD~-~grI~LS~K~~~~~~G~~~  716 (726)
T 4aid_A          677 KPSDVLKEGQMVKVKLLGFDD-RGKTKLSMKVVDQETGEDL  716 (726)
T ss_dssp             -----------------------------------------
T ss_pred             CccccCCCCCEEEEEEEEECC-CCcEEEEEeecccCcchhh
Confidence            999999999999999999998 8999999999999999754

>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=99.39  E-value=4.2e-13  Score=109.76  Aligned_cols=84  Identities=15%  Similarity=0.171  Sum_probs=68.2

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec--CCceEEE-Eccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY--KKMDDVR-ITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~--~gi~Gl~-~s~~~~~~~~~~~~~~~~  180 (234)
                      ++|+.+.++|.++..                       +      |+||+|.  +|++||+ +|+++++.          
T Consensus        14 ~~G~iv~G~V~~i~~-----------------------f------GaFV~L~e~~gveGLvhiSels~~~----------   54 (175)
T 2a19_A           14 EIDDIVMVNVQQIAE-----------------------M------GAYVKLLEYDNIEGMILLSELSRRR----------   54 (175)
T ss_dssp             CTTCEEEEEEEEEET-----------------------T------EEEEEETTTTTCEEEEECC----------------
T ss_pred             CCCCEEEEEEEEEec-----------------------c------eEEEEEcCCCCcEEEEEHHHcCCcc----------
Confidence            489999999998864                       5      9999995  7999999 89985432          


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcccC
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAIVN  233 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~~~  233 (234)
                      .       .++...+++||.|+|+|+++|.    |+||+|++.++||+.+.++|++|
T Consensus        55 v-------~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~~~~~~~~~~~~~~g  104 (175)
T 2a19_A           55 I-------RSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKS  104 (175)
T ss_dssp             ---------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTTCCHHHHHHHHHHHHHH
T ss_pred             c-------CCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEecCcChHHHHHHhccCC
Confidence            1       2455689999999999999985    99999999999999999999875

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

Probab=99.34  E-value=9.7e-14  Score=134.98  Aligned_cols=101  Identities=30%  Similarity=0.541  Sum_probs=0.0

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc
Q 026737           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (234)
Q Consensus        31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~   97 (234)
                      ++++. .+.+.++....        .++.+...+++|++|+|+     +||+||+|.     ++.+||||+|+++|.++.
T Consensus       593 IdI~~-dg~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~-----~g~eGLvHiSel~~~~v~  666 (723)
T 3cdi_A          593 IEIED-DGTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIG-----GGKEGLVHISQIADKRVE  666 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEecC-CccEEEecCCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEecceEEEEeC-----CCceEEEEHHHcCCcccc
Confidence            45654 45666654432        255667889999999999     999999997     479999999999999999


Q ss_pred             chhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhh
Q 026737           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET  138 (234)
Q Consensus        98 ~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~  138 (234)
                      ++.+.|++||.|+|||+++|. ++||+||+|++.++||...
T Consensus       667 ~~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~~~~~~g~~~  706 (723)
T 3cdi_A          667 KVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKEATEQSQPAA  706 (723)
T ss_dssp             -----------------------------------------
T ss_pred             CcccccCCCCEEEEEEEEECC-CCcEEEEEEeccCCCCccc
Confidence            999999999999999999998 9999999999999998753

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=99.31  E-value=2.7e-14  Score=139.41  Aligned_cols=103  Identities=21%  Similarity=0.407  Sum_probs=38.2

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhh--cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceec----
Q 026737           31 IQANEEMKKLVFSEKDA--------VWNKYS--SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV----   91 (234)
Q Consensus        31 i~id~~~~~i~lS~k~~--------~~~~~~--~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isel----   91 (234)
                      ++++. .+.+.+|....        .++.+.  ..+++|++|.|+     +||+||+|.     ++++||||+|++    
T Consensus       631 IdI~~-dG~v~Is~~~~~~~~~a~~~i~~i~~p~~~~vG~i~~G~V~~i~~fGaFV~l~-----~g~eGLvHiSel~~~~  704 (757)
T 1e3p_A          631 ITIED-DGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGAFVSLL-----PGKDGLLHISQIRKLA  704 (757)
T ss_dssp             C---------CCCBSSHHHHCC---------------------CBEEECC-CSCEECCC--------CCCCC--------
T ss_pred             EEecC-CceEEEecCCHHHHHHHHHHHHHhcchhhcccccEEEEEEEEccccEEEEEEc-----CCcEEEEEhHHhcccc
Confidence            56664 67788887642        123444  678999999998     999999997     479999999999    


Q ss_pred             ccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhh
Q 026737           92 SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLE  140 (234)
Q Consensus        92 s~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~  140 (234)
                      +|.++.++.+.|++||.|+|+|+++|+ ++||+||+|++.++||.....
T Consensus       705 s~~rv~~~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~~~~~pw~~~~~  752 (757)
T 1e3p_A          705 GGKRVENVEDVLGVGQKVQVEIAEIDS-RGKLSLIPVIEGEEAASDEKK  752 (757)
T ss_dssp             -----------CCSSCBCCCCCCCCCS-SCC------------------
T ss_pred             CCCcccCcccccCCCCEEEEEEEEECC-CCCEEEEEecCCCCchhhhhh
Confidence            999999999999999999999999998 999999999999999976443

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=99.28  E-value=5.1e-14  Score=137.42  Aligned_cols=113  Identities=16%  Similarity=0.111  Sum_probs=43.7

Q ss_pred             EeeEEEEEecCCCcceeEEEEEceecccccccchh---------hhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcch
Q 026737           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR---------DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL  136 (234)
Q Consensus        66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~---------~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~  136 (234)
                      ++|+||+|+       .+|.+|++..++.......         ..+++|+.+.++|.++..                  
T Consensus       626 ~~G~~IdI~-------~dG~v~Is~~~~~~~~~a~~~i~~i~~p~~~~vG~i~~G~V~~i~~------------------  680 (757)
T 1e3p_A          626 DTGAEITIE-------DDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTT------------------  680 (757)
T ss_dssp             CCCSCC---------------CCCBSSHHHHCC---------------------CBEEECC-------------------
T ss_pred             hhCCEEEec-------CCceEEEecCCHHHHHHHHHHHHHhcchhhcccccEEEEEEEEccc------------------
Confidence            899999996       4899999998876543221         223444444444444321                  


Q ss_pred             hhhhccccccccceeeeecCCceEEE-Eccc----cccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc-
Q 026737          137 ETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQ----GFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL-  210 (234)
Q Consensus       137 ~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~-  210 (234)
                           +      |+||+|.+|++||+ +|++    +++. +                .++..++++||+|+|+|+++|. 
T Consensus       681 -----f------GaFV~l~~g~eGLvHiSel~~~~s~~r-v----------------~~~~~~~~vGd~V~VkVi~vd~~  732 (757)
T 1e3p_A          681 -----F------GAFVSLLPGKDGLLHISQIRKLAGGKR-V----------------ENVEDVLGVGQKVQVEIAEIDSR  732 (757)
T ss_dssp             -----C------SCEECCC---CCCCC------------------------------------CCSSCBCCCCCCCCCSS
T ss_pred             -----c------EEEEEEcCCcEEEEEhHHhccccCCCc-c----------------cCcccccCCCCEEEEEEEEECCC
Confidence                 3      99999999999999 8998    5432 1                3456689999999999999984 


Q ss_pred             --chhhhcccccchhHHHHhhcc
Q 026737          211 --IRKASKRHCNEYWNVFHETAI  231 (234)
Q Consensus       211 --i~ls~K~~~~~p~~~~~~~~~  231 (234)
                        |+||+|++.++||+...++|+
T Consensus       733 grI~LS~k~~~~~pw~~~~~~~~  755 (757)
T 1e3p_A          733 GKLSLIPVIEGEEAASDEKKDDA  755 (757)
T ss_dssp             CC---------------------
T ss_pred             CCEEEEEecCCCCchhhhhhccc
Confidence              999999999999999998875

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

Probab=99.26  E-value=5.2e-12  Score=94.53  Aligned_cols=80  Identities=19%  Similarity=0.106  Sum_probs=66.6

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC---CceEEE-Eccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK---KMDDVR-ITRQGFEKRVVSQDLQ  178 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~---gi~Gl~-~s~~~~~~~~~~~~~~  178 (234)
                      +++|+.+.++|.++.+                       +      |+||+|.+   +++||+ +|++.++.++      
T Consensus        10 ~~vG~i~~G~V~~v~~-----------------------f------G~FV~l~~~~~~~~Glvhisel~~~~~~------   54 (103)
T 2eqs_A           10 PTIGDIYNGKVTSIMQ-----------------------F------GCFVQLEGLRKRWEGLVHISELRREGRV------   54 (103)
T ss_dssp             CCTTCEEEEEEEEECS-----------------------S------CEEEEECSSSSCCEEEECGGGTSSSSCC------
T ss_pred             CCCCCEEEEEEEEEec-----------------------c------EEEEEEcCCCCCeEEEEEHHHCCCCccc------
Confidence            6789999999998853                       4      99999986   999999 8988433221      


Q ss_pred             cccccCCCCCcceeeeeeCCCEEEEEEeeecc--chhhhcccccchhHHHH
Q 026737          179 LWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL--IRKASKRHCNEYWNVFH  227 (234)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~--i~ls~K~~~~~p~~~~~  227 (234)
                                .++...+++||.|+|+|+++|.  |+||+|++.++||+.+.
T Consensus        55 ----------~~~~~~~~~Gd~V~VkV~~vd~~~i~LSlk~~~~~~~~~~~   95 (103)
T 2eqs_A           55 ----------ANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETGEDLN   95 (103)
T ss_dssp             ----------CCHHHHCCTTCEEEEEEEEEETTEEEEESTTBCTTTCCBCC
T ss_pred             ----------CCcccEeCCCCEEEEEEEEEECCeeEEEEeecccCCchhcC
Confidence                      2455689999999999999986  99999999999998764

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E

Probab=99.20  E-value=5e-12  Score=103.55  Aligned_cols=82  Identities=27%  Similarity=0.563  Sum_probs=67.3

Q ss_pred             HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc-----------cchhhhhCCCCEEEEE
Q 026737           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVK  112 (234)
Q Consensus        49 ~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~-----------~~~~~~~~vGd~v~vk  112 (234)
                      +.....++.+|+++.|+     +||+||+++      +.+||+|+|+++++++           ++..+.|++||.|++|
T Consensus        72 ~~~iv~~p~~Gev~~G~V~~v~~~G~fv~l~------~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~Vrvk  145 (180)
T 4ayb_E           72 FDMITYVPVVQEVVEGEVLQVDNYGVFVNLG------PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRAR  145 (180)
T ss_dssp             EEEEEECCCTTCEEEEEEEEEETTEEEEECS------SSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEE
T ss_pred             hheeeeeccCCCEEEEEEeeeccceEEEEEC------CccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEE
Confidence            44556789999999999     999999996      5899999999999876           4677789999999999


Q ss_pred             EEEEeCC----CCeEEEEEeecc--cCcch
Q 026737          113 VIKIDRE----KSRITLSIKQLE--EDPLL  136 (234)
Q Consensus       113 Vl~id~~----~~ri~LS~K~~~--~~p~~  136 (234)
                      |+++|.+    ..||.||+|+.-  +.+|-
T Consensus       146 V~~v~~~~~~~~~rI~ls~k~~gLG~~~W~  175 (180)
T 4ayb_E          146 VISVASTVTGRLPRIALTMRQPYLGKLEWI  175 (180)
T ss_dssp             EEEECC-------CEEEECCSTTCEEHHHH
T ss_pred             EEEEeCCCCcccCcEEEEcCCCCCCCChhH
Confidence            9999864    458999999843  44454

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

Probab=99.20  E-value=6.4e-12  Score=94.86  Aligned_cols=79  Identities=8%  Similarity=0.004  Sum_probs=53.5

Q ss_pred             EEEEeecccCcchhhhhcccccccc-----------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcce
Q 026737          124 TLSIKQLEEDPLLETLEKVIPQGLE-----------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKF  191 (234)
Q Consensus       124 ~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~  191 (234)
                      +-|+|++.++||..+... +..|.+           |+||+|.+|++||+ +|+++++..                 .++
T Consensus        11 ~~~iKq~~~~p~~~~~~~-~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~-----------------~~~   72 (109)
T 2khj_A           11 SSGLVPRGSHMFNNWVAL-NKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRV-----------------EDA   72 (109)
T ss_dssp             ----------CHHHHTTT-CCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSS-----------------SSG
T ss_pred             ccchhhcccCHHHHHhhc-CCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccc-----------------cCh
Confidence            457899999999876655 555521           99999999999999 888743211                 234


Q ss_pred             eeeeeCCCEEEEEEeeecc----chhhhccccc
Q 026737          192 TLLARAGRQVQEIQLSHSL----IRKASKRHCN  220 (234)
Q Consensus       192 ~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~  220 (234)
                      ...+++||.|+|+|+++|.    |.||+|++.+
T Consensus        73 ~~~~~vGd~V~v~V~~vd~~~~ki~LS~k~~~~  105 (109)
T 2khj_A           73 TLVLSVGDEVEAKFTGVDRKNRAISLSVRAKDE  105 (109)
T ss_dssp             GGSCCTTCEEEEEEEEEETTTTEEEEETTSSSS
T ss_pred             hhccCCCCEEEEEEEEEECCCCEEEEEEeecCh
Confidence            5589999999999999984    9999999864

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

Probab=99.19  E-value=1.1e-11  Score=95.17  Aligned_cols=87  Identities=7%  Similarity=-0.054  Sum_probs=68.5

Q ss_pred             ccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC-CceEEE-Ecccccccccc
Q 026737           96 IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK-KMDDVR-ITRQGFEKRVV  173 (234)
Q Consensus        96 ~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~-gi~Gl~-~s~~~~~~~~~  173 (234)
                      ...+...+++|+.+.++|.++..                       +      |+||+|.+ +++||+ +|+++++..  
T Consensus        13 ~~~~~~~~~vG~iv~G~V~~I~~-----------------------f------GaFV~l~g~~~~Glvhisel~~~~~--   61 (119)
T 2cqo_A           13 PETMENLPALYTIFQGEVAMVTD-----------------------Y------GAFIKIPGCRKQGLVHRTHMSSCRV--   61 (119)
T ss_dssp             CCCSCCSCCTTCEEEEEEEEEET-----------------------T------EEEEECTTCSSCEEEEHHHHCSSCC--
T ss_pred             hhhhhcccCCCCEEEEEEEEEeC-----------------------c------eEEEEECCCcEEEEEEHHHCCcccc--
Confidence            33444557899999999998863                       4      99999955 479999 888853311  


Q ss_pred             ccccccccccCCCCCcceeeeeeCCCEEEEEEeeec------cchhhhcccccchhHHHHh
Q 026737          174 SQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHS------LIRKASKRHCNEYWNVFHE  228 (234)
Q Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d------~i~ls~K~~~~~p~~~~~~  228 (234)
                                     .++...+++||.|+|+|+++|      +|+||+|++.++||+.+..
T Consensus        62 ---------------~~~~~~~~~Gd~V~VkV~~vd~~~~~~~i~LSlk~~~~~~~~~~~~  107 (119)
T 2cqo_A           62 ---------------DKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVNQGTGKDLDP  107 (119)
T ss_dssp             ---------------SCHHHHCCTTCEEEEEEEEEEECSSCEEEEEESTTBCSSSCCBSCT
T ss_pred             ---------------cChhhcCCCCCEEEEEEEEEeccccCceEEEEEeecccCCccccCc
Confidence                           235568999999999999997      3999999999999987653

>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=99.17  E-value=2.1e-11  Score=107.77  Aligned_cols=85  Identities=15%  Similarity=0.132  Sum_probs=72.5

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec--CCceEEE-Ecccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY--KKMDDVR-ITRQGFEKRVVSQDLQL  179 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~--~gi~Gl~-~s~~~~~~~~~~~~~~~  179 (234)
                      +++|+.+.++|.++.+                       +      |+||+|.  +|++||+ +|+++++.         
T Consensus        11 ~~vG~iv~G~V~~I~~-----------------------f------GaFV~L~ey~gveGLvhiSels~~~---------   52 (308)
T 1q8k_A           11 PEVEDVVMVNVRSIQE-----------------------M------GAYVSLLEYNNIEGMIHLSELSRRR---------   52 (308)
T ss_dssp             CSSCCEEEEEEEEEET-----------------------T------EEEEESCTTTSCCEEECGGGTSCSS---------
T ss_pred             CCCCCEEEEEEEEEeC-----------------------c------EEEEEECCCCCeEEEEEhHHcCccc---------
Confidence            4689999999999864                       4      9999998  7999999 89985421         


Q ss_pred             ccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcccC
Q 026737          180 WLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAIVN  233 (234)
Q Consensus       180 ~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~~~  233 (234)
                       .       .++...+++||.|+|+|+++|.    |+||+|++.++||..+.+.|++|
T Consensus        53 -i-------~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~~~~p~~~~~~~~~~G  102 (308)
T 1q8k_A           53 -I-------RSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKS  102 (308)
T ss_dssp             -C-------SCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSCCHHHHHHHHHHHHHH
T ss_pred             -c-------cCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEecccChHHHHHHHccCC
Confidence             1       2355689999999999999985    99999999999999999998865

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=99.17  E-value=2.8e-11  Score=92.75  Aligned_cols=76  Identities=13%  Similarity=0.174  Sum_probs=62.3

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceec-ccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV-SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isel-s~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      ..++++|+++.|+     +||+||+|+  .  .+..|++|.++. +|.++.++.+.|++||.|+|+|+++|.++++|.||
T Consensus        16 ~~~l~~G~i~~G~V~~v~~fG~fV~l~--~--~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~Ls   91 (119)
T 1wi5_A           16 AEALKPGMLLTGTVSSLEDHGYLVDIG--V--DGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS   91 (119)
T ss_dssp             TTTCCTTCEEEEEEEEECSSEEEEECC--C--SSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEE
T ss_pred             HhcCCCCCEEEEEEEEEeCceEEEEEC--C--CCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEEE
Confidence            4679999999999     999999997  1  146777766654 34455678899999999999999999989999999


Q ss_pred             Eeeccc
Q 026737          127 IKQLEE  132 (234)
Q Consensus       127 ~K~~~~  132 (234)
                      +|+...
T Consensus        92 lk~~~l   97 (119)
T 1wi5_A           92 VGHSEV   97 (119)
T ss_dssp             CCCCCS
T ss_pred             Echhhc
Confidence            997543

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=99.16  E-value=4.6e-11  Score=98.27  Aligned_cols=79  Identities=25%  Similarity=0.494  Sum_probs=67.4

Q ss_pred             hhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc-----------chhhhhCCCCEEEEEE
Q 026737           50 NKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKV  113 (234)
Q Consensus        50 ~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~-----------~~~~~~~vGd~v~vkV  113 (234)
                      ......+.+|+++.|+     +||+||+|+      +.+||+|+|++++.++.           ++.+.|++||.|+|+|
T Consensus        73 ~~i~~~~~~Gev~~G~V~~v~~~G~fV~l~------~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV  146 (187)
T 1go3_E           73 ETLVYIPEMYELIEGEVVDVVEFGSFVRLG------PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARI  146 (187)
T ss_dssp             EEEEECCCTTCEEEEEEEEEETTEEEEECS------SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEE
T ss_pred             EEEEEccCCCCEEEEEEEEEeCcEEEEEEc------CccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEE
Confidence            3445678999999999     999999996      49999999999988775           7888999999999999


Q ss_pred             EEEeCCCC-----eEEEEEeecccCc
Q 026737          114 IKIDREKS-----RITLSIKQLEEDP  134 (234)
Q Consensus       114 l~id~~~~-----ri~LS~K~~~~~p  134 (234)
                      +++|.+++     +|.||+|+..-.|
T Consensus       147 ~~vd~~~~~p~~~~I~lS~k~~~LG~  172 (187)
T 1go3_E          147 VAISLKAERKRGSKIALTMRQPYLGK  172 (187)
T ss_dssp             EEEECCC-----CEEEEECCSTTCEE
T ss_pred             EEEEcccCCCCccEEEEEEcCCCCCc
Confidence            99998654     9999999854433

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

Probab=99.15  E-value=2.8e-11  Score=122.97  Aligned_cols=73  Identities=15%  Similarity=0.094  Sum_probs=68.2

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccc-ccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~-~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      .+.+++|+++.|+     +||+||+|+     +|++||||+|++++.+ +.+|.+.|++||.|+|+|+++|.++++|.||
T Consensus       897 ~~~l~~G~iv~G~V~~V~~fGaFV~L~-----~gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LS  971 (1219)
T 3psi_A          897 EKTFFKGSIIPVRVERFWHNDIICTTN-----SEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVS  971 (1219)
T ss_dssp             TTTSCTTCEEEEEEEEECSSCEEEECT-----TSCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEE
T ss_pred             HhhCCCCCEEEEEEEEEecceEEEEeC-----CCceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence            3789999999999     999999997     4799999999999998 8999999999999999999999999999999


Q ss_pred             Eeec
Q 026737          127 IKQL  130 (234)
Q Consensus       127 ~K~~  130 (234)
                      +|..
T Consensus       972 lk~~  975 (1219)
T 3psi_A          972 LLDH  975 (1219)
T ss_dssp             CCHH
T ss_pred             ecHH
Confidence            9853

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

Probab=99.15  E-value=3.7e-12  Score=123.93  Aligned_cols=116  Identities=16%  Similarity=0.142  Sum_probs=0.0

Q ss_pred             EEEEE--EeeEEEEEecCCCcceeEEEEEceecccccc-------cchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 026737           61 IFVGR--DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (234)
Q Consensus        61 iv~g~--~~G~fV~l~~~~g~~g~~glv~isels~~~~-------~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~  131 (234)
                      +++..  ++|+||+++       .+|.++++..++...       ......+++|+.+.++|.++..             
T Consensus       581 ~I~~I~~~~G~~IdI~-------~dg~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~-------------  640 (723)
T 3cdi_A          581 VIRALTEETGTTIEIE-------DDGTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVD-------------  640 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             eeeeeehhhCceEEec-------CCccEEEecCCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEec-------------
Confidence            34444  899999996       479999987666543       2333446778888888877642             


Q ss_pred             cCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          132 EDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       132 ~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                                +      |+||+|.+|++||+ +|+++++.          +       .++...+++||+|+|+|+++|.
T Consensus       641 ----------f------GaFVel~~g~eGLvHiSel~~~~----------v-------~~~~~~~~vGd~V~VkVi~vd~  687 (723)
T 3cdi_A          641 ----------F------GAFVAIGGGKEGLVHISQIADKR----------V-------EKVTDYLQMGQEVPVKVLEVDR  687 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ----------c------eEEEEeCCCceEEEEHHHcCCcc----------c-------cCcccccCCCCEEEEEEEEECC
Confidence                      4      99999999999999 89985432          1       3456689999999999999984


Q ss_pred             ---chhhhcccccchhHHHHhh
Q 026737          211 ---IRKASKRHCNEYWNVFHET  229 (234)
Q Consensus       211 ---i~ls~K~~~~~p~~~~~~~  229 (234)
                         |+||+|++.++||+.+...
T Consensus       688 ~grI~LS~k~~~~~~g~~~~p~  709 (723)
T 3cdi_A          688 QGRIRLSIKEATEQSQPAAAPE  709 (723)
T ss_dssp             ----------------------
T ss_pred             CCcEEEEEEeccCCCCcccCcc
Confidence               9999999999999887543

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

Probab=99.14  E-value=4.9e-11  Score=92.88  Aligned_cols=77  Identities=13%  Similarity=0.041  Sum_probs=64.7

Q ss_pred             hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccc
Q 026737          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       102 ~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~  180 (234)
                      .+++|+.+.++|.++.+                       +      |+||+|.+|++||| +|+++++.          
T Consensus         4 ~~~vG~iv~G~V~~i~~-----------------------~------G~FV~l~~~~~Glihisel~~~~----------   44 (130)
T 2k4k_A            4 KFEVGSVYTGKVTGLQA-----------------------Y------GAFVALDEETQGLVHISEVTHGF----------   44 (130)
T ss_dssp             CCCTTCEEEEEEEEEET-----------------------T------EEEEEEETTEEEEEEGGGTSSSC----------
T ss_pred             cCCCCCEEEEEEEEEeC-----------------------C------eEEEEECCCcEEEEEHHHCCccc----------
Confidence            37899999999998864                       4      99999999999999 88885321          


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhH
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWN  224 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~  224 (234)
                      .       .++...+++||.|+|+|+++|.    |+||+|++.++||+
T Consensus        45 ~-------~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk~~~~~p~~   85 (130)
T 2k4k_A           45 V-------KDINEHLSVGDEVQVKVLAVDEEKGKISLSIRATQAAPEK   85 (130)
T ss_dssp             C-------SCGGGTCCTTCEEEEEEEEEETTTTEEEEESHHHHHSCCC
T ss_pred             c-------cCccccCCCCCEEEEEEEEEeCCCCEEEEEEeecccCccc
Confidence            1       2345589999999999999985    99999999999985

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

Probab=99.14  E-value=4.8e-11  Score=103.97  Aligned_cols=85  Identities=12%  Similarity=0.057  Sum_probs=71.6

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec--CCceEEE-Ecccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY--KKMDDVR-ITRQGFEKRVVSQDLQL  179 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~--~gi~Gl~-~s~~~~~~~~~~~~~~~  179 (234)
                      .++|+.+.++|.++..                       +      |+||+|.  +|++||+ +|+++++.         
T Consensus         9 p~~Gdiv~G~V~~I~~-----------------------f------GaFV~L~e~~gieGlIhiSels~~~---------   50 (275)
T 3aev_A            9 PEEGEFVVATVKRIHN-----------------------Y------GAFLELDEYPGKEAFMHISEVASTW---------   50 (275)
T ss_dssp             CCTTCEEEEEEEEEET-----------------------T------EEEEEETTSTTCEEEEEGGGSCSSC---------
T ss_pred             CCCCCEEEEEEEEEEC-----------------------c------EEEEEECCCCCeEEEEEHHHcCccc---------
Confidence            4689999999999864                       5      9999998  6999999 89885321         


Q ss_pred             ccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcccC
Q 026737          180 WLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAIVN  233 (234)
Q Consensus       180 ~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~~~  233 (234)
                       .       .++...+++||.|+|+|+++|.    |+||+|++.++||....++|++|
T Consensus        51 -v-------~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~~~~~~~~~~~~~~~g  100 (275)
T 3aev_A           51 -V-------RNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQQQRKAKLQEFKRA  100 (275)
T ss_dssp             -C-------SCGGGTCCTTCEEEEEEEEEETTTTEEEEESTTCCHHHHHHHHHHHHHH
T ss_pred             -c-------cCHHhccCCCCEEEEEEEEEECCCCEEEEEEeecCcchhHHHHHhccCC
Confidence             1       2345689999999999999985    99999999999999998888765

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A

Probab=99.10  E-value=2.3e-11  Score=119.10  Aligned_cols=74  Identities=30%  Similarity=0.585  Sum_probs=68.0

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      ..++++|+++.|+     +||+||+|+     .+++||||+|++++.++.++.+.|++||.|+|+|+++|.++++|.||+
T Consensus       649 ~~~l~vG~iv~G~V~~V~~fGaFV~l~-----~~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSl  723 (785)
T 3bzc_A          649 LKDLKPGMVLEGVVTNVTNFGAFVDIG-----VHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSM  723 (785)
T ss_dssp             STTCCTTCBCCCEEEEEETTEEEEECS-----SSSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECC
T ss_pred             hhhcCCCCEEEEEEEEEecCCeEEEeC-----CCcEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEE
Confidence            3568899999888     999999997     368999999999999999999999999999999999999999999999


Q ss_pred             eecc
Q 026737          128 KQLE  131 (234)
Q Consensus       128 K~~~  131 (234)
                      |...
T Consensus       724 k~~~  727 (785)
T 3bzc_A          724 RMSD  727 (785)
T ss_dssp             SSCC
T ss_pred             ecCC
Confidence            9644

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

Probab=99.09  E-value=6.8e-12  Score=121.78  Aligned_cols=114  Identities=20%  Similarity=0.191  Sum_probs=2.9

Q ss_pred             EeeEEEEEecCCCcceeEEEEEceeccc-------ccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhh
Q 026737           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSW-------DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET  138 (234)
Q Consensus        66 ~~G~fV~l~~~~g~~g~~glv~isels~-------~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~  138 (234)
                      ++|+-+++.       -+|.+.+.--+.       .++......+++|+.+.++|.++..                    
T Consensus       598 ~tg~~idi~-------ddG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~--------------------  650 (726)
T 4aid_A          598 TTGAKVDIN-------DDGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVD--------------------  650 (726)
T ss_dssp             -----------------------CCSCHHHHHHHHHC-------------------------------------------
T ss_pred             HHCCceeEE-------CCceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEec--------------------
Confidence            889999886       467777764432       2345555668899999999988753                    


Q ss_pred             hhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---chhh
Q 026737          139 LEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKA  214 (234)
Q Consensus       139 ~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls  214 (234)
                         +      |+||+|.+|++||+ +|+++++..                 .++...+++||.|+|+|+++|.   |+||
T Consensus       651 ---f------GaFVel~~g~eGLvHiSels~~rv-----------------~~~~d~~kvGD~V~VkVi~iD~~grI~LS  704 (726)
T 4aid_A          651 ---F------GAFVNFFGAKDGLVHVSQISNERV-----------------AKPSDVLKEGQMVKVKLLGFDDRGKTKLS  704 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ---c------EEEEEECCCcEEEEEHHHcCcccc-----------------cCccccCCCCCEEEEEEEEECCCCcEEEE
Confidence               5      99999999999999 899854321                 2456689999999999999985   9999


Q ss_pred             hcccccchhHHHHhhccc
Q 026737          215 SKRHCNEYWNVFHETAIV  232 (234)
Q Consensus       215 ~K~~~~~p~~~~~~~~~~  232 (234)
                      +|++.++||+.+.++.++
T Consensus       705 ~K~~~~~~G~~~~~k~~~  722 (726)
T 4aid_A          705 MKVVDQETGEDLSKKEAA  722 (726)
T ss_dssp             ------------------
T ss_pred             EeecccCcchhhhhhhhh
Confidence            999999999999877654

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

Probab=99.06  E-value=1.6e-11  Score=123.12  Aligned_cols=73  Identities=15%  Similarity=0.105  Sum_probs=0.0

Q ss_pred             cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccc-ccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~-~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      ..+++|+++.|+     +||+||+|+     +|++||||+|++++.+ +.+|.+.|++||.|+|+|+++|.++++|.||+
T Consensus       901 ~~l~~G~iv~G~V~~V~~fGaFV~L~-----~gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSl  975 (1030)
T 3psf_A          901 KTFFKGSIIPVRVERFWHNDIICTTN-----SEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSL  975 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhcCCCEEEEEEEEEccCeEEEEeC-----CCcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEe
Confidence            688999999999     999999997     4799999999999998 89999999999999999999999999999999


Q ss_pred             eecc
Q 026737          128 KQLE  131 (234)
Q Consensus       128 K~~~  131 (234)
                      |+..
T Consensus       976 k~~d  979 (1030)
T 3psf_A          976 LDHD  979 (1030)
T ss_dssp             ----
T ss_pred             chHH
Confidence            9754

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2

Probab=99.02  E-value=4.1e-10  Score=94.41  Aligned_cols=77  Identities=19%  Similarity=0.205  Sum_probs=65.9

Q ss_pred             cCCCCCcEEEEE-----EeeEEEEEecCCC---cceeEEEEEceeccccccc--chhhhhCCCCEEEEEEEEEeCCCCeE
Q 026737           54 SRVNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRI  123 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g---~~g~~glv~isels~~~~~--~~~~~~~vGd~v~vkVl~id~~~~ri  123 (234)
                      ..+++|++|.|+     ++|+||+|.+.++   ..+.+|+||++|+++.+..  ++.+.|++||.|+|+|++++..++++
T Consensus        77 y~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i  156 (209)
T 2nn6_I           77 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNY  156 (209)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEE
T ss_pred             CCCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeE
Confidence            357999999999     9999999953210   0157899999999999888  89999999999999999999877799


Q ss_pred             EEEEeec
Q 026737          124 TLSIKQL  130 (234)
Q Consensus       124 ~LS~K~~  130 (234)
                      .||+|+.
T Consensus       157 ~LS~k~~  163 (209)
T 2nn6_I          157 LLTTAEN  163 (209)
T ss_dssp             EEECCSS
T ss_pred             EEEEecC
Confidence            9999875

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

Probab=98.99  E-value=7.4e-10  Score=90.71  Aligned_cols=70  Identities=27%  Similarity=0.393  Sum_probs=60.2

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCC-----cceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEE
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDG-----LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT  124 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g-----~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~  124 (234)
                      .++ |++|.|+     ++|+||+|...+|     ..+.+|+||+|++++.++.++.+.|++||.|+|+|++     +++.
T Consensus        55 ~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~-----~~i~  128 (179)
T 3m7n_A           55 IVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG-----DNLR  128 (179)
T ss_dssp             CCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE-----TTTE
T ss_pred             cCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC-----CeEE
Confidence            367 9999999     8999999972100     0068999999999999999999999999999999997     8899


Q ss_pred             EEEeec
Q 026737          125 LSIKQL  130 (234)
Q Consensus       125 LS~K~~  130 (234)
                      ||+|+.
T Consensus       129 LS~k~~  134 (179)
T 3m7n_A          129 LSTKEE  134 (179)
T ss_dssp             EECCST
T ss_pred             EEEecC
Confidence            999874

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*

Probab=98.97  E-value=2e-10  Score=99.72  Aligned_cols=86  Identities=9%  Similarity=-0.015  Sum_probs=72.0

Q ss_pred             hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec--CCceEEE-Eccccccccccccccc
Q 026737          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY--KKMDDVR-ITRQGFEKRVVSQDLQ  178 (234)
Q Consensus       102 ~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~--~gi~Gl~-~s~~~~~~~~~~~~~~  178 (234)
                      .+++|+.+.++|.++.+                       +      |+||+|.  +|++||+ +|+++++.        
T Consensus         8 ~~~vG~iv~G~V~~I~~-----------------------~------GaFV~l~e~~~~~GlihiSels~~~--------   50 (266)
T 3cw2_C            8 LPSEGEILIATVKQVFD-----------------------Y------GSYVSLDEYGGLQAFLPWSEVSSKW--------   50 (266)
T ss_dssp             SCCTTCEEEEEEEECCS-----------------------S------SBEEEETTTTSEECBBCGGGSSCSS--------
T ss_pred             cCCCCCEEEEEEEEEec-----------------------c------EEEEEEcCCCCeEEEEEhHHcCccc--------
Confidence            36789999999988753                       4      9999997  7999999 89885321        


Q ss_pred             cccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcccC
Q 026737          179 LWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAIVN  233 (234)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~~~  233 (234)
                        .       .++...+++||.|.|+|+++|.    |+||+|++.++||+.+.+.|+++
T Consensus        51 --v-------~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~~~~~~~~~~~~~~~~~  100 (266)
T 3cw2_C           51 --V-------KNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKKVTDDERRKKNLQWKKI  100 (266)
T ss_dssp             --C-------CCHHHHSCTTCEEEEEECCCCSSSCCCBEESTTSCTTHHHHHHHHHHHH
T ss_pred             --c-------cCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEEecchhhHHHHHHhcccc
Confidence              1       3456689999999999999985    99999999999999998888654

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

Probab=98.96  E-value=4.4e-10  Score=81.70  Aligned_cols=71  Identities=14%  Similarity=0.257  Sum_probs=57.3

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC--CceEEE-Ec-cccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK--KMDDVR-IT-RQGFEKRVVSQDLQ  178 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~--gi~Gl~-~s-~~~~~~~~~~~~~~  178 (234)
                      .++|+.+.++|. +..                       +      |+||+|.+  |++||+ +| +++++..       
T Consensus         9 ~~vG~~~~G~V~-v~~-----------------------f------G~FVel~~~~~~eGLvhis~el~~~~~-------   51 (88)
T 1luz_A            9 PNAGDVIKGRVY-EKD-----------------------Y------ALYIYLFDYPHFEAILAESVKMHMDRY-------   51 (88)
T ss_dssp             CCTTCEEEEEEE-EET-----------------------T------EEEEEETTCTTSEEEEGGGSSCCHHHH-------
T ss_pred             CCCCCEEEEEEE-EEc-----------------------c------EEEEEECCCCCeEEEEEeeHHhCcccc-------
Confidence            468999999998 864                       5      99999974  899999 89 9854321       


Q ss_pred             cccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccc
Q 026737          179 LWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNE  221 (234)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~  221 (234)
                                .+++..+ .||+|+|+|+++|.    |+||+|++.++
T Consensus        52 ----------~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lslk~~~~~   87 (88)
T 1luz_A           52 ----------VEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKRMCRH   87 (88)
T ss_dssp             ----------HHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEEECSC
T ss_pred             ----------cCHhHEe-CCCEEEEEEEEEECCCCEEEEEEeecCCC
Confidence                      1234466 99999999999985    99999998764

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

Probab=98.93  E-value=1.9e-09  Score=76.66  Aligned_cols=69  Identities=7%  Similarity=-0.013  Sum_probs=56.7

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.+.++|.++.+                       +      |+||+|.++++||+ +|+++++.           
T Consensus         3 ~~~G~iv~G~V~~v~~-----------------------~------G~fV~l~~~~~Gllh~sel~~~~-----------   42 (80)
T 2k52_A            3 VEPGKFYKGVVTRIEK-----------------------Y------GAFINLNEQVRGLLRPRDMISLR-----------   42 (80)
T ss_dssp             CCTTCEEEEEEEEEET-----------------------T------EEEEEEETTEEEEECGGGCSSCC-----------
T ss_pred             CCCCCEEEEEEEEEeC-----------------------C------EEEEEECCCCEEEEEHHHCCccc-----------
Confidence            5789999999998864                       4      99999999999999 88874211           


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNE  221 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~  221 (234)
                               + ..+++||+|+|+|+++|.    |+||+|++.+.
T Consensus        43 ---------~-~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~~~~~   76 (80)
T 2k52_A           43 ---------L-ENLNVGDEIIVQAIDVRPEKREIDFKYIPLEHH   76 (80)
T ss_dssp             ---------G-GGCCTTCEEEEEEEEEETTTTEEEEEECSCC--
T ss_pred             ---------c-eeeCCCCEEEEEEEEEECCCCEEEEEEeecccc
Confidence                     1 368999999999999985    99999998753

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...

Probab=98.87  E-value=2.7e-09  Score=86.62  Aligned_cols=65  Identities=15%  Similarity=0.136  Sum_probs=53.5

Q ss_pred             hhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccch----------hhhhCCCCEEEEEEEE
Q 026737           51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----------RDILNEGDEVRVKVIK  115 (234)
Q Consensus        51 ~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~----------~~~~~vGd~v~vkVl~  115 (234)
                      .......+|++++|+     +||+||+++     + .+||||+|++++.+..++          ++.+++||.|+++|++
T Consensus        76 ~~~~~~~~Gev~~G~V~~v~~fG~FV~l~-----~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~  149 (171)
T 1y14_B           76 AVVFKPFKGEVVDGTVVSCSQHGFEVQVG-----P-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEG  149 (171)
T ss_dssp             EEEECCCTTCEEEEEEEEEETTEEEEEET-----T-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEE
T ss_pred             EEEccCCCCCEEEEEEEEEecCEEEEEec-----C-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEE
Confidence            345678999999999     999999997     4 999999999986543222          2669999999999999


Q ss_pred             EeCCCC
Q 026737          116 IDREKS  121 (234)
Q Consensus       116 id~~~~  121 (234)
                      +|.+.+
T Consensus       150 vd~~~~  155 (171)
T 1y14_B          150 CISQVS  155 (171)
T ss_dssp             EEEETT
T ss_pred             EEcCCC
Confidence            998664

>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1

Probab=98.86  E-value=1.8e-09  Score=90.82  Aligned_cols=79  Identities=18%  Similarity=0.127  Sum_probs=63.0

Q ss_pred             hhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchh----------hhhCCCCEEEEEEEE
Q 026737           51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR----------DILNEGDEVRVKVIK  115 (234)
Q Consensus        51 ~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~----------~~~~vGd~v~vkVl~  115 (234)
                      .......+|++++|+     +||+||+|+     + .+||||+|++++.+..++.          +.+++||.|+++|++
T Consensus        76 ~i~~~p~vGev~~G~V~~vt~fG~FVelg-----~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~  149 (215)
T 2b8k_G           76 AVVFKPFKGEVVDGTVVSCSQHGFEVQVG-----P-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEG  149 (215)
T ss_dssp             EEEECCCTTEEEEEEEEEEETTEEEEECT-----T-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEE
T ss_pred             hheeccCCCCEEEEEEEEEecceEEEEec-----C-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEE
Confidence            345568999999999     999999997     4 8999999999865443332          569999999999999


Q ss_pred             EeCCCC---eEEEEEeecccCcch
Q 026737          116 IDREKS---RITLSIKQLEEDPLL  136 (234)
Q Consensus       116 id~~~~---ri~LS~K~~~~~p~~  136 (234)
                      +|.+.+   +|. |+|+...-||.
T Consensus       150 vd~~~~~i~~Ig-Smk~~~LG~~~  172 (215)
T 2b8k_G          150 CISQVSSIHAIG-SIKEDYLGAIS  172 (215)
T ss_dssp             EEEETTEEEEEE-ECCSTTCEEC-
T ss_pred             EEcCCCccEEEE-EcCCCCCCCcc
Confidence            998764   677 88876655654

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1

Probab=98.84  E-value=3.5e-09  Score=85.89  Aligned_cols=71  Identities=15%  Similarity=0.262  Sum_probs=56.3

Q ss_pred             hhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccch------------hhhhCCCCEEEEEEE
Q 026737           52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI------------RDILNEGDEVRVKVI  114 (234)
Q Consensus        52 ~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~------------~~~~~vGd~v~vkVl  114 (234)
                      ......+|++++|+     +||+||+|+      ..+||||+|++++.+..++            ...|++||.|+++|+
T Consensus        75 ~~~~~~~Gev~~G~V~~v~~fG~fV~l~------~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~  148 (172)
T 2c35_B           75 IVFRPFKGEVVDAVVTQVNKVGLFTEIG------PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIV  148 (172)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEEET------TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEE
T ss_pred             EEeeCCCCCEEEEEEEEEeCCEEEEEEC------CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEE
Confidence            34567899999999     999999996      4679999999986533222            457999999999999


Q ss_pred             EEeCCCC---eEEEEEee
Q 026737          115 KIDREKS---RITLSIKQ  129 (234)
Q Consensus       115 ~id~~~~---ri~LS~K~  129 (234)
                      ++|.+.+   ++. |+|+
T Consensus       149 ~vd~~~~~~~~ig-sm~~  165 (172)
T 2c35_B          149 GTRVDKNDIFAIG-SLMD  165 (172)
T ss_dssp             EEEEETTEEEEEE-ECCS
T ss_pred             EEEcCCCCcEEEE-EecC
Confidence            9998765   444 6654

>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=98.74  E-value=7.1e-09  Score=89.15  Aligned_cols=70  Identities=26%  Similarity=0.373  Sum_probs=63.0

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc---cchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI---QDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~---~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      .+++|++|.|+     ++|+||+|+     .+.+|++|++++++.+.   .++.+.|++||.|.|+|++++. .+++.||
T Consensus        71 ~p~~GDiV~G~V~~v~~~ga~VdI~-----~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~-~~~i~LS  144 (251)
T 2je6_I           71 YPKINDIVIGLVEDVEIYGWVVDIK-----APYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLS  144 (251)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS-----SSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEE
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEcC-----CCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECC-CCcEEEE
Confidence            57999999999     899999997     36899999999998877   7888899999999999999996 5799999


Q ss_pred             Eeec
Q 026737          127 IKQL  130 (234)
Q Consensus       127 ~K~~  130 (234)
                      +|+.
T Consensus       145 ~r~~  148 (251)
T 2je6_I          145 VKGK  148 (251)
T ss_dssp             CCST
T ss_pred             Eccc
Confidence            9864

>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=98.73  E-value=6.9e-09  Score=92.76  Aligned_cols=98  Identities=17%  Similarity=0.141  Sum_probs=74.4

Q ss_pred             cccCCCCEEEEEEEEEeCCCCEEEEEechhh--------HhhhhcCCC--CCcEEEEE-----EeeEEEEEecCCCccee
Q 026737           18 AKGLTGSIISVKVIQANEEMKKLVFSEKDAV--------WNKYSSRVN--VEDIFVGR-----DYGAFIHLRFPDGLYHL   82 (234)
Q Consensus        18 ~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~~--------~~~~~~~~~--~G~iv~g~-----~~G~fV~l~~~~g~~g~   82 (234)
                      .+..+|+++++.|...|. +++.+.+.|+..        .+.++..|+  .|++++|+     ++|+||+++      +.
T Consensus        85 ~~~~vGd~ie~~I~~~df-gR~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlG------k~  157 (344)
T 1hh2_P           85 PLAEVGSIVKKELNVKNF-GRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIG------KL  157 (344)
T ss_dssp             TTCCTTCEEEEECCCCCS-SSCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEET------TE
T ss_pred             ccccCCCEEEEEEccccC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeC------Ce
Confidence            345699999999987664 333444445432        223455665  89999999     889999996      69


Q ss_pred             EEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCC--eEEEEEe
Q 026737           83 TGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIK  128 (234)
Q Consensus        83 ~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~--ri~LS~K  128 (234)
                      +|++|.+|++      |.+.|++||.|+|.|++++.+++  +|.||.+
T Consensus       158 EgiLp~sE~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt  199 (344)
T 1hh2_P          158 ETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRR  199 (344)
T ss_dssp             EEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESS
T ss_pred             EEEEeHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEee
Confidence            9999999987      56789999999999999997655  5666665

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=98.69  E-value=4.4e-09  Score=85.48  Aligned_cols=68  Identities=18%  Similarity=0.258  Sum_probs=56.0

Q ss_pred             HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccch----------hhhhCCCCEEEEEE
Q 026737           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----------RDILNEGDEVRVKV  113 (234)
Q Consensus        49 ~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~----------~~~~~vGd~v~vkV  113 (234)
                      +.....+...|++++|+     +||+||+++      ..+||||+|++++.+..++          .+.+++||.|++||
T Consensus        75 f~~ivf~p~~Gev~~G~V~~v~~fG~FV~l~------~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV  148 (172)
T 3h0g_G           75 YRAVLWRPFRGEVVDAIVTTVNKMGFFANIG------PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKI  148 (172)
T ss_dssp             EEEEEECCCTTCEEECCCCEEETTEEECCBT------TBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEE
T ss_pred             EEEeeeccCCCCEEEEEEEEEEcceEEEEeC------CeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEE
Confidence            34456678999999999     999999996      4779999999986544333          56899999999999


Q ss_pred             EEEeCCCCe
Q 026737          114 IKIDREKSR  122 (234)
Q Consensus       114 l~id~~~~r  122 (234)
                      +++|.+.++
T Consensus       149 ~~vd~~~~~  157 (172)
T 3h0g_G          149 VGTRTDATE  157 (172)
T ss_dssp             EEEEESSSC
T ss_pred             EEEECCCCC
Confidence            999987744

>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=98.69  E-value=3.1e-08  Score=84.06  Aligned_cols=70  Identities=26%  Similarity=0.356  Sum_probs=62.6

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc-cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~-~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      .+++|++|.|+     ++|+||+|+     ...+|++|+++++.. +..++++.|++||.|.|+|++++. .+++.||+|
T Consensus        54 ~p~~GDiV~G~V~~v~~~~a~V~I~-----~~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~-~~~i~LS~r  127 (229)
T 2ba0_A           54 TPSVGDVVIGIIREVAANGWAVDIY-----SPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMK  127 (229)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS-----SSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECC
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC-----CCeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECC-CCcEEEEEc
Confidence            47999999999     899999997     358999999999974 678899999999999999999996 589999998


Q ss_pred             ec
Q 026737          129 QL  130 (234)
Q Consensus       129 ~~  130 (234)
                      +.
T Consensus       128 ~~  129 (229)
T 2ba0_A          128 DR  129 (229)
T ss_dssp             SS
T ss_pred             cc
Confidence            64

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

Probab=98.68  E-value=3.5e-08  Score=73.38  Aligned_cols=78  Identities=22%  Similarity=0.276  Sum_probs=57.6

Q ss_pred             CCCCcEEEEE--------EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           56 VNVEDIFVGR--------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        56 ~~~G~iv~g~--------~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      ...++.++|+        .|| |+.-.  +|  +.++|+|+|++.+..+  ....+++||.|+..|..+.+         
T Consensus        11 ~~~~~~~~G~Vk~fn~~kGfG-FI~~~--~g--g~dvfvH~s~l~~~~~--~~~~l~~Ge~V~g~V~~i~~---------   74 (101)
T 2bh8_A           11 RLQSGKMTGIVKWFNADKGFG-FITPD--DG--SKDVFVHFSAGSSGAA--VRGNPQQGDRVEGKIKSITD---------   74 (101)
T ss_dssp             -----CEEEEEEEEEGGGTEE-EEEES--SS--SCEEEEECCCSCSSSC--CCCCCCTTCEEEEEEEECCS---------
T ss_pred             ccccccceeEEEEEECCCCCE-EEEeC--CC--CcEEEEEEEEEecCCc--cccCCCCCCEEEEEEEEeCC---------
Confidence            3456677787        578 88865  22  5899999999998753  11336799999999987653         


Q ss_pred             eecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccc
Q 026737          128 KQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFE  169 (234)
Q Consensus       128 K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~  169 (234)
                                    +      |+||+|.++++||+ +|+++|.
T Consensus        75 --------------f------G~fv~l~~~~eGlvhis~i~~~   97 (101)
T 2bh8_A           75 --------------F------GIFIGLDGGIDGLVHLSDISWA   97 (101)
T ss_dssp             --------------E------EEEECTTSCEEEEEEEEEEEEC
T ss_pred             --------------c------EEEEEcCCCceEEEEHHHCccC
Confidence                          5      99999999999999 9998543

>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=98.64  E-value=2.1e-08  Score=85.41  Aligned_cols=70  Identities=17%  Similarity=0.339  Sum_probs=61.3

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc----cccchhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~----~~~~~~~~~~vGd~v~vkVl~id~~~~ri~L  125 (234)
                      .+++|++|.|+     ++|+||+|+     .+.+|++|+++++.+    +..++.+.|++||.|.|+|++++. .+++.|
T Consensus        63 ~p~~GDiV~G~V~~v~~~~~~V~I~-----~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~-~~~i~L  136 (235)
T 2z0s_A           63 VPQAGDVVIGLIQSVGIMNWFVDIN-----SPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPLL  136 (235)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECS-----SSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEEE
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeC-----CCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECC-CCcEEE
Confidence            57999999999     899999997     368999999999873    456788899999999999999996 569999


Q ss_pred             EEeec
Q 026737          126 SIKQL  130 (234)
Q Consensus       126 S~K~~  130 (234)
                      |+|+.
T Consensus       137 S~k~~  141 (235)
T 2z0s_A          137 TVQGE  141 (235)
T ss_dssp             ECCSS
T ss_pred             EEecc
Confidence            99853

>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=98.43  E-value=2.9e-07  Score=70.16  Aligned_cols=74  Identities=9%  Similarity=-0.004  Sum_probs=57.1

Q ss_pred             hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec-CCceEEEEccccccccccccccccc
Q 026737          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY-KKMDDVRITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       102 ~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~-~gi~Gl~~s~~~~~~~~~~~~~~~~  180 (234)
                      .+++|+.+.++|.++..                       +      |+||+|. +++.||+++++..          .|
T Consensus        18 ~l~~G~i~~G~V~~v~~-----------------------f------G~fV~l~~~~~~~l~~~~~~~----------~~   58 (119)
T 1wi5_A           18 ALKPGMLLTGTVSSLED-----------------------H------GYLVDIGVDGTRAFLPLLKAQ----------EY   58 (119)
T ss_dssp             TCCTTCEEEEEEEEECS-----------------------S------EEEEECCCSSCEEEEEHHHHH----------HH
T ss_pred             cCCCCCEEEEEEEEEeC-----------------------c------eEEEEECCCCeEEEEEEeccc----------cc
Confidence            47899999999998853                       5      9999998 5888888776521          24


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccc
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHC  219 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~  219 (234)
                      ....     ++...+++||.|+|+|+++|.    |.||+|+..
T Consensus        59 ~~~~-----~~~~~~~~Gd~V~vkV~~vd~~~~~i~Lslk~~~   96 (119)
T 1wi5_A           59 IRQK-----NKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSE   96 (119)
T ss_dssp             HHHH-----SSSCCCCTTCEEEEEEEECCTTSCEEEEECCCCC
T ss_pred             cccc-----CccCEeCCCCEEEEEEEEEeCCCCEEEEEEchhh
Confidence            3211     234589999999999999984    999999763

>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=98.39  E-value=8.1e-07  Score=72.72  Aligned_cols=87  Identities=9%  Similarity=0.031  Sum_probs=61.3

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      ..+|+.+.++|.++.+                       +      |+||+|.+ ++||+ +|++..+...-.++-..|.
T Consensus        79 ~~~Gev~~G~V~~v~~-----------------------~------G~fV~l~~-~eglvhis~l~~~~~~~d~~~~~~~  128 (187)
T 1go3_E           79 PEMYELIEGEVVDVVE-----------------------F------GSFVRLGP-LDGLIHVSQIMDDYVSYDPKREAII  128 (187)
T ss_dssp             CCTTCEEEEEEEEEET-----------------------T------EEEEECSS-SEEEEEGGGSCSSCEEECCC--CEE
T ss_pred             cCCCCEEEEEEEEEeC-----------------------c------EEEEEEcC-ccEEEEhHHhCCCcceECCccceEE
Confidence            5679999999988864                       4      99999965 99999 7888544321111111333


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeec---------cchhhhccc--ccchhHH
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHS---------LIRKASKRH--CNEYWNV  225 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d---------~i~ls~K~~--~~~p~~~  225 (234)
                      .      .+....+++||.|+|+|+++|         +|+||+|+.  .+.+|-.
T Consensus       129 ~------~~~~~~~~~Gd~V~vkV~~vd~~~~~p~~~~I~lS~k~~~LG~~~w~~  177 (187)
T 1go3_E          129 G------KETGKVLEIGDYVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIE  177 (187)
T ss_dssp             E------TTTCCEECTTCEEEEEEEEEECCC-----CEEEEECCSTTCEEHHHHH
T ss_pred             e------cCCCeEEcCCCEEEEEEEEEEcccCCCCccEEEEEEcCCCCCcHHHHh
Confidence            2      134568999999999999997         388999994  4566643

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E

Probab=98.39  E-value=6.3e-07  Score=72.96  Aligned_cols=86  Identities=14%  Similarity=0.120  Sum_probs=62.3

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      ..+|+.+.++|.++..                       +      |+||++. +++||+ +|++..+.....+.-..|.
T Consensus        79 p~~Gev~~G~V~~v~~-----------------------~------G~fv~l~-~~~glvh~s~l~~d~~~~d~~~~~~~  128 (180)
T 4ayb_E           79 PVVQEVVEGEVLQVDN-----------------------Y------GVFVNLG-PMDGLVHISQITDDTLKYDNVRGIIF  128 (180)
T ss_dssp             CCTTCEEEEEEEEEET-----------------------T------EEEEECS-SSEEEEEGGGSCSSCEEECSSSCCEE
T ss_pred             ccCCCEEEEEEeeecc-----------------------c------eEEEEEC-CccceEEeeecCCCccccchhcceEE
Confidence            4579999999988874                       4      9999995 599999 8988665442222211222


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc--------chhhhcc--cccchhH
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL--------IRKASKR--HCNEYWN  224 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~--------i~ls~K~--~~~~p~~  224 (234)
                      -      .+....++.||+|+++|+++|.        |+||||+  |-+-+|=
T Consensus       129 g------~~~~~~~~~Gd~VrvkV~~v~~~~~~~~~rI~ls~k~~gLG~~~W~  175 (180)
T 4ayb_E          129 G------EKSKKVIQKGDKVRARVISVASTVTGRLPRIALTMRQPYLGKLEWI  175 (180)
T ss_dssp             E------TTTCCCCCTTCEEEEEEEEECC-------CEEEECCSTTCEEHHHH
T ss_pred             E------eccCeEECCCCEEEEEEEEEeCCCCcccCcEEEEcCCCCCCCChhH
Confidence            2      1234589999999999999972        9999999  5666773

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

Probab=98.32  E-value=5.3e-07  Score=91.91  Aligned_cols=73  Identities=10%  Similarity=0.049  Sum_probs=59.3

Q ss_pred             hhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccc
Q 026737          101 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQL  179 (234)
Q Consensus       101 ~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~  179 (234)
                      +.+++|+.+.++|.++..                       +      |+||+|+.|++||| +|+++++..+       
T Consensus       898 ~~l~~G~iv~G~V~~V~~-----------------------f------GaFV~L~~gveGLVHiSelsd~~~v-------  941 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWH-----------------------N------DIICTTNSEVECVVNAQRHAGAQLR-------  941 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECS-----------------------S------CEEEECTTSCEEEECTTSSSSTTSC-------
T ss_pred             hhCCCCCEEEEEEEEEec-----------------------c------eEEEEeCCCceEEEEHHHcCCCccc-------
Confidence            347899999999998853                       4      99999999999999 8998543211       


Q ss_pred             ccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccc
Q 026737          180 WLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRH  218 (234)
Q Consensus       180 ~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~  218 (234)
                               .++..++++||.|+|+|+++|.    |+||+|..
T Consensus       942 ---------~~p~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~  975 (1219)
T 3psi_A          942 ---------RPANEIYEIGKTYPAKVIYIDYANITAEVSLLDH  975 (1219)
T ss_dssp             ---------SCSTTTSCTTCEEEEEEEEEEGGGTEEEEECCHH
T ss_pred             ---------CCHHHcCCCCCEEEEEEEEEECCCCEEEEEecHH
Confidence                     2234589999999999999985    99999865

>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A

Probab=98.23  E-value=1.5e-06  Score=83.80  Aligned_cols=69  Identities=12%  Similarity=0.082  Sum_probs=56.9

Q ss_pred             CCCCCc--EEEEE-----EeeEEEEEecCCCcceeEEEEEceeccc--cccc----------chhhhhCCCCEEEEEEEE
Q 026737           55 RVNVED--IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLIQ----------DIRDILNEGDEVRVKVIK  115 (234)
Q Consensus        55 ~~~~G~--iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~--~~~~----------~~~~~~~vGd~v~vkVl~  115 (234)
                      +-++|+  +++|+     +||+||+|..    +|++||||+|++++  +++.          +....|++||.|+|+|++
T Consensus       555 ~~~vGe~~~f~g~V~~V~~~G~fV~L~~----~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~  630 (644)
T 2id0_A          555 KDKAGTDTRFAAEIVDISRGGMRVRLVD----NGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAE  630 (644)
T ss_dssp             GGGTTSCCCEEEEEEEEETTEEEEEETT----TCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEE
T ss_pred             hhccCCCceEEEEEEEEeCCceEEEEcC----CcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEE
Confidence            457888  88887     9999999952    47999999999973  3311          345679999999999999


Q ss_pred             EeCCCCeEEEEE
Q 026737          116 IDREKSRITLSI  127 (234)
Q Consensus       116 id~~~~ri~LS~  127 (234)
                      +|.++++|.|++
T Consensus       631 vd~~~~~I~~~l  642 (644)
T 2id0_A          631 VRMETRSIIARP  642 (644)
T ss_dssp             EETTTTEEEEEE
T ss_pred             EeCCCCEEEEEE
Confidence            999999999987

>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=98.12  E-value=3.5e-06  Score=70.41  Aligned_cols=73  Identities=12%  Similarity=0.001  Sum_probs=56.3

Q ss_pred             hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec--------CCceEEE-Eccccccccc
Q 026737          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY--------KKMDDVR-ITRQGFEKRV  172 (234)
Q Consensus       102 ~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~--------~gi~Gl~-~s~~~~~~~~  172 (234)
                      .+++||.|.++|+++..                       +      |+||+|.        .+++|++ +|++++... 
T Consensus        78 ~p~vGDvV~G~V~~v~~-----------------------~------~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~-  127 (209)
T 2nn6_I           78 LPDVGAIVTCKVSSINS-----------------------R------FAKVHILYVGSMPLKNSFRGTIRKEDVRATEK-  127 (209)
T ss_dssp             CCCTTCEEEEEEEEECS-----------------------S------EEEEEEEESSSSCCCCSSCSCEEEEGGGTCSS-
T ss_pred             CCCCCCEEEEEEEEEEC-----------------------c------eEEEEECccccccccCCceeEEEHHHcccccc-
Confidence            47899999999999864                       3      6677753        5889999 888753221 


Q ss_pred             cccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccc
Q 026737          173 VSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRH  218 (234)
Q Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~  218 (234)
                                  +  .-++.+.+++||.|+|+|++++.    ++||+|+.
T Consensus       128 ------------~--~~~~~~~l~~GD~V~akVisi~~~~~~i~LS~k~~  163 (209)
T 2nn6_I          128 ------------D--KVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAEN  163 (209)
T ss_dssp             ------------C--CCCGGGTCCSSSEEEEEEEEEETTTTEEEEECCSS
T ss_pred             ------------c--ccchhhhcCCCCEEEEEEEEEeCCCCeEEEEEecC
Confidence                        0  02466789999999999999974    89999985

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

Probab=98.11  E-value=3.7e-07  Score=91.77  Aligned_cols=72  Identities=10%  Similarity=0.047  Sum_probs=0.0

Q ss_pred             hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccc
Q 026737          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       102 ~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~  180 (234)
                      .+++|+.+.++|.++..                       +      |+||+|+.|++||| +|+++++..+        
T Consensus       902 ~l~~G~iv~G~V~~V~~-----------------------f------GaFV~L~~gveGLVHiSelsd~~~v--------  944 (1030)
T 3psf_A          902 TFFKGSIIPVRVERFWH-----------------------N------DIICTTNSEVECVVNAQRHAGAQLR--------  944 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HhcCCCEEEEEEEEEcc-----------------------C------eEEEEeCCCcEEEEEHHHcCCCccc--------
Confidence            36889999999887642                       4      99999999999999 8998543211        


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccc
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRH  218 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~  218 (234)
                              .++..++++||.|+|+|+++|.    |+||+|+.
T Consensus       945 --------~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~  978 (1030)
T 3psf_A          945 --------RPANEIYEIGKTYPAKVIYIDYANITAEVSLLDH  978 (1030)
T ss_dssp             ------------------------------------------
T ss_pred             --------CCHHHcCCCCCEEEEEEEEEECCCCEEEEEechH
Confidence                    2345689999999999999984    99999976

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

Probab=98.07  E-value=5.8e-06  Score=67.39  Aligned_cols=68  Identities=12%  Similarity=0.067  Sum_probs=53.9

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC----------CceEEE-Ecccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK----------KMDDVR-ITRQGFEKR  171 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~----------gi~Gl~-~s~~~~~~~  171 (234)
                      .+ ||.|.++|.++..                       +      |+||+|..          +++||+ +|++++.. 
T Consensus        56 p~-GdiV~G~V~~V~~-----------------------~------ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~-  104 (179)
T 3m7n_A           56 VK-GDVVLGRVVDLRN-----------------------S------IALIEVSSKKGENRGPSNRGIGILHVSNVDEGY-  104 (179)
T ss_dssp             CT-TCEEEEEEEEECS-----------------------S------EEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSC-
T ss_pred             CC-CCEEEEEEEEEeC-----------------------C------cEEEEEccccCcccccccCeeEEEEHHHcCcch-
Confidence            46 9999999999864                       3      77777766          899999 78874321 


Q ss_pred             ccccccccccccCCCCCcceeeeeeCCCEEEEEEeeeccchhhhccc
Q 026737          172 VVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRH  218 (234)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~i~ls~K~~  218 (234)
                                 .     .++.+.+++||.|+|+|++ ..++||+|+.
T Consensus       105 -----------~-----~~~~~~~~~GD~V~akVi~-~~i~LS~k~~  134 (179)
T 3m7n_A          105 -----------V-----KEISEAVGYLDILKARVIG-DNLRLSTKEE  134 (179)
T ss_dssp             -----------C-----SSGGGTCCTTCEEEEEEEE-TTTEEECCST
T ss_pred             -----------h-----hCHhhcCCCCCEEEEEEEC-CeEEEEEecC
Confidence                       1     2456689999999999999 6699999975

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A

Probab=98.03  E-value=6.3e-06  Score=77.28  Aligned_cols=74  Identities=23%  Similarity=0.387  Sum_probs=60.1

Q ss_pred             hhcCCCCCcEEEEE-----Ee--eEEEEEecCCCcceeEEEEEceecccccc---------cchhhhhCCCCEEEEEEEE
Q 026737           52 YSSRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWDLI---------QDIRDILNEGDEVRVKVIK  115 (234)
Q Consensus        52 ~~~~~~~G~iv~g~-----~~--G~fV~l~~~~g~~g~~glv~isels~~~~---------~~~~~~~~vGd~v~vkVl~  115 (234)
                      ......+|.+|.|+     ++  ||||+++     ++.+||+|++++++.++         .++.+.+++||.|.|+|++
T Consensus        39 ~~~~~~vGnIY~GkV~rv~p~~~aAFVdiG-----~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~K  113 (517)
T 2bx2_L           39 PGHEQKKANIYKGKITRIEPSLEAAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDK  113 (517)
T ss_dssp             SSSCCCTTCEEEEEEEEEETTTTEEEEESS-----SSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEE
T ss_pred             CCCcCCCCCEEEEEEEEeccCCceEEEEeC-----CCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEe
Confidence            34457899999999     77  9999998     47899999999998874         3466789999999999999


Q ss_pred             EeCCCCeEEEEEeec
Q 026737          116 IDREKSRITLSIKQL  130 (234)
Q Consensus       116 id~~~~ri~LS~K~~  130 (234)
                      ....++...||..-.
T Consensus       114 e~~g~KGa~lTt~is  128 (517)
T 2bx2_L          114 EERGNKGAALTTFIS  128 (517)
T ss_dssp             CCCTTCCCEEESSCC
T ss_pred             eccccCCceEEeeEE
Confidence            887666666666543

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=98.02  E-value=5.6e-06  Score=68.81  Aligned_cols=61  Identities=11%  Similarity=0.213  Sum_probs=51.6

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc-------------------cchhhhhCCCCE
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDE  108 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~-------------------~~~~~~~~vGd~  108 (234)
                      .-+..+|+++.|+     ++|+||+|+      .++|++|++++.+++.                   ++....|++||.
T Consensus        76 ~f~p~~GEv~~G~Vs~vt~~GifV~lg------~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~  149 (203)
T 3ayh_B           76 IFRPFRGEVMLGKIKSCSEEGIRVTIS------FFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEE  149 (203)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS------SCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCE
T ss_pred             EEccCCCCEEEEEEEEEeccEEEEEEe------CceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCE
Confidence            4467999999999     999999996      5899999999977654                   344567999999


Q ss_pred             EEEEEEEEeCC
Q 026737          109 VRVKVIKIDRE  119 (234)
Q Consensus       109 v~vkVl~id~~  119 (234)
                      |++||++++..
T Consensus       150 VrvrV~~v~~~  160 (203)
T 3ayh_B          150 IRFQIESEDFV  160 (203)
T ss_dssp             EEEEEEEEEEC
T ss_pred             EEEEEEEEEcc
Confidence            99999999873

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

Probab=97.98  E-value=7.6e-06  Score=60.61  Aligned_cols=70  Identities=23%  Similarity=0.283  Sum_probs=47.8

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEE-----------echhhHhhh-hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEE
Q 026737           22 TGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKY-SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTG   84 (234)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS-----------~k~~~~~~~-~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~g   84 (234)
                      .++.+..+|...|.+++-=-+.           .....+..+ ...+++|++|++.     +||+||+|.     ++++|
T Consensus        13 ~~~~~~G~Vk~fn~~kGfGFI~~~~gg~dvfvH~s~l~~~~~~~~~l~~Ge~V~g~V~~i~~fG~fv~l~-----~~~eG   87 (101)
T 2bh8_A           13 QSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFGIFIGLD-----GGIDG   87 (101)
T ss_dssp             ---CEEEEEEEEEGGGTEEEEEESSSSCEEEEECCCSCSSSCCCCCCCTTCEEEEEEEECCSEEEEECTT-----SCEEE
T ss_pred             ccccceeEEEEEECCCCCEEEEeCCCCcEEEEEEEEEecCCccccCCCCCCEEEEEEEEeCCcEEEEEcC-----CCceE
Confidence            5666777777776555432222           222222222 2679999999998     799999996     37999


Q ss_pred             EEEceecccccc
Q 026737           85 LVHVSEVSWDLI   96 (234)
Q Consensus        85 lv~isels~~~~   96 (234)
                      |||+|+++|.++
T Consensus        88 lvhis~i~~~~~   99 (101)
T 2bh8_A           88 LVHLSDISWAQA   99 (101)
T ss_dssp             EEEEEEEEECCC
T ss_pred             EEEHHHCccCcC
Confidence            999999999875

>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=97.96  E-value=2.5e-05  Score=70.07  Aligned_cols=83  Identities=10%  Similarity=0.163  Sum_probs=56.9

Q ss_pred             hhhhcCCC--CCcEEEEE--E-------eeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeC
Q 026737           50 NKYSSRVN--VEDIFVGR--D-------YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDR  118 (234)
Q Consensus        50 ~~~~~~~~--~G~iv~g~--~-------~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~  118 (234)
                      +..+..|+  +|++++|+  .       +++||+|++  +..+.+|++|.+|+.      |.+.|++||.|+|.|++++.
T Consensus       120 ~~i~~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~--~~~k~EgiLP~~Eqi------P~E~~~~GDrVkvyV~~V~~  191 (366)
T 1k0r_A          120 ERTYGEFSTREGEIVAGVIQRDSRANARGLVVVRIGT--ETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTR  191 (366)
T ss_dssp             -------CCCTTCEEEEEEECCHHHHHTTCEEEEECC--SSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEEC
T ss_pred             HHHHHHHHhcCCCEEEEEEEEccccccCCeEEEEeCC--CccceEEEEcHHHcC------CCccCCCCCEEEEEEEEEec
Confidence            34555665  99999999  3       589999971  001399999999986      45789999999999999998


Q ss_pred             CCCeEEEEEeecccCcchhhhh
Q 026737          119 EKSRITLSIKQLEEDPLLETLE  140 (234)
Q Consensus       119 ~~~ri~LS~K~~~~~p~~~~~~  140 (234)
                      +++...+.+....++.....++
T Consensus       192 ~~kgpqI~LSRT~p~lv~~Lfe  213 (366)
T 1k0r_A          192 GAREPLITLSRTHPNLVRKLFS  213 (366)
T ss_dssp             CSSSCEEEEESSCHHHHHHHHH
T ss_pred             CCCccEEEEEeCChHHHHHHHH
Confidence            7655555555555555444343

>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=97.90  E-value=2.4e-06  Score=83.81  Aligned_cols=71  Identities=15%  Similarity=0.085  Sum_probs=55.5

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.+.++|.++..                       +      |+||+|..+++||| +|++++ .++         
T Consensus       652 l~vG~iv~G~V~~V~~-----------------------f------GaFV~l~~~~eGLVhiS~Lsd-~~v---------  692 (785)
T 3bzc_A          652 LKPGMVLEGVVTNVTN-----------------------F------GAFVDIGVHQDGLVHISALSE-KFV---------  692 (785)
T ss_dssp             CCTTCBCCCEEEEEET-----------------------T------EEEEECSSSSEEEEETTTSCS-SCC---------
T ss_pred             cCCCCEEEEEEEEEec-----------------------C------CeEEEeCCCcEEEEEHHHcCc-ccc---------
Confidence            5677777777776642                       4      99999988999999 898853 121         


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHC  219 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~  219 (234)
                             .++...+++||.|+|+|+++|.    |+||+|...
T Consensus       693 -------~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSlk~~~  727 (785)
T 3bzc_A          693 -------KDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMSD  727 (785)
T ss_dssp             -------SCHHHHCCTTCCCCCBEEEEETTTTEEEECCSSCC
T ss_pred             -------CChhheeCCCCEEEEEEEEEECCCCEEEEEEecCC
Confidence                   2345689999999999999985    999999643

>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=97.90  E-value=2.7e-05  Score=65.24  Aligned_cols=91  Identities=7%  Similarity=-0.132  Sum_probs=57.6

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      ..+|+.+.++|.++..                       +      |+||+|.+ ++||+ +|++. +.....+.-..|.
T Consensus        81 p~vGev~~G~V~~vt~-----------------------f------G~FVelg~-~dGlVhiS~l~-d~~~~d~~~~~w~  129 (215)
T 2b8k_G           81 PFKGEVVDGTVVSCSQ-----------------------H------GFEVQVGP-MKVFVTKHLMP-QDLTFNAGSNPPS  129 (215)
T ss_dssp             CCTTEEEEEEEEEEET-----------------------T------EEEEECTT-SEEEEEGGGSC-SSCCCBSSCSSCE
T ss_pred             cCCCCEEEEEEEEEec-----------------------c------eEEEEecC-cEEEEEHHHCC-ccceeccccccce
Confidence            3689999999988864                       4      99999988 99999 88884 2211100101111


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc-------chhhhcccccchhHHHHhhcc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL-------IRKASKRHCNEYWNVFHETAI  231 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~-------i~ls~K~~~~~p~~~~~~~~~  231 (234)
                      -...    +  .+++.||.|+++|+++|.       |. |||+-.--||+....+.+
T Consensus       130 ~~~~----~--~~~~~Gd~VrVkV~~vd~~~~~i~~Ig-Smk~~~LG~~~~~~~~~~  179 (215)
T 2b8k_G          130 YQSS----E--DVITIKSRIRVKIEGCISQVSSIHAIG-SIKEDYLGAISHEKRRWK  179 (215)
T ss_dssp             EECS----S--CEEETTCEEEEEEEEEEEETTEEEEEE-ECCSTTCEEC--------
T ss_pred             eecc----c--cEECCCCEEEEEEEEEEcCCCccEEEE-EcCCCCCCCcchhhHHHH
Confidence            1110    1  479999999999999984       66 888876677765544443

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=97.82  E-value=1.2e-05  Score=78.85  Aligned_cols=65  Identities=17%  Similarity=0.199  Sum_probs=46.4

Q ss_pred             cEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc--cccc-----------cc----hhhhhCCCCEEEEEEEEEe
Q 026737           60 DIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS--WDLI-----------QD----IRDILNEGDEVRVKVIKID  117 (234)
Q Consensus        60 ~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels--~~~~-----------~~----~~~~~~vGd~v~vkVl~id  117 (234)
                      +++.|+     ++|+||.|..    .|++|+||+++++  .+++           .+    ....|++||.|+|+|+.+|
T Consensus       671 ~~~~g~V~~V~~~G~fV~l~~----~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd  746 (760)
T 2vnu_D          671 STETGYVIKVFNNGIVVLVPK----FGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVM  746 (760)
T ss_dssp             SEEEEEEEEEETTEEEEEETT----TTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC---
T ss_pred             eEEEEEEEEEECCeEEEEEeC----CCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCCEEEEEEEEEE
Confidence            688887     9999999972    3799999999996  4331           12    2477999999999999999


Q ss_pred             CC---CCeEEEEEe
Q 026737          118 RE---KSRITLSIK  128 (234)
Q Consensus       118 ~~---~~ri~LS~K  128 (234)
                      .+   ++||.||+|
T Consensus       747 ~~~~~~~kI~lslk  760 (760)
T 2vnu_D          747 DPITSKRKAELLLK  760 (760)
T ss_dssp             -----CCEEEC---
T ss_pred             CccccCCcEEEEeC
Confidence            87   699999986

>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=97.79  E-value=3.8e-05  Score=65.81  Aligned_cols=74  Identities=8%  Similarity=-0.106  Sum_probs=57.9

Q ss_pred             hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccc
Q 026737          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       102 ~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~  180 (234)
                      ..++||.|.++|.++..                       +      |+||++..+.+|++ +|+++..          +
T Consensus        71 ~p~~GDiV~G~V~~v~~-----------------------~------ga~VdI~~~~~GlL~isei~~~----------~  111 (251)
T 2je6_I           71 YPKINDIVIGLVEDVEI-----------------------Y------GWVVDIKAPYKAYLPASNLLGR----------S  111 (251)
T ss_dssp             CCCTTCEEEEEEEEECS-----------------------S------EEEEECSSSSCEEEEHHHHHTS----------C
T ss_pred             CCCCCCEEEEEEEEEeC-----------------------c------eEEEEcCCCeEEEEEHHHhcCC----------c
Confidence            35899999999999864                       3      89999988999999 7887421          1


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhccc
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRH  218 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~  218 (234)
                      .   +.. .++...+++||.|+|+|++++.   +.||+|+.
T Consensus       112 ~---~~~-~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~~  148 (251)
T 2je6_I          112 I---NVG-EDLRRYLDVGDYVIARIENFDRSIDPVLSVKGK  148 (251)
T ss_dssp             C---CTT-CCCSSSCCTTCEEEEEEEEEETTEEEEEECCST
T ss_pred             c---ccc-cchhhcCCCCCEEEEEEEEECCCCcEEEEEccc
Confidence            1   111 3466689999999999999985   88888764

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=97.77  E-value=1.4e-05  Score=80.34  Aligned_cols=66  Identities=18%  Similarity=0.214  Sum_probs=54.0

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc--cccc-----------cc----hhhhhCCCCEEEEEEEEE
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS--WDLI-----------QD----IRDILNEGDEVRVKVIKI  116 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels--~~~~-----------~~----~~~~~~vGd~v~vkVl~i  116 (234)
                      |+++.|+     +||+||.|..    .|++|+||+++++  .+++           .+    ....|++||.|+|+|..+
T Consensus       887 ge~~~g~V~~V~~~G~fV~L~~----~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~v  962 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLVPK----FGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSV  962 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEECTT----TCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCC
T ss_pred             ceEEEEEEEEEcCCeEEEEEcC----CCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEE
Confidence            8899998     9999999972    3799999999997  4431           12    346799999999999999


Q ss_pred             eCC---CCeEEEEEe
Q 026737          117 DRE---KSRITLSIK  128 (234)
Q Consensus       117 d~~---~~ri~LS~K  128 (234)
                      |.+   ++||.||+|
T Consensus       963 d~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          963 MDPITSKRKAELLLK  977 (977)
T ss_dssp             CCSSSCCCCCCEEEC
T ss_pred             cCcccCCCceEEEeC
Confidence            864   389999987

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=97.74  E-value=2e-05  Score=66.22  Aligned_cols=64  Identities=8%  Similarity=0.090  Sum_probs=51.3

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc--------------cchhhhhCCCCEEEEEE
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI--------------QDIRDILNEGDEVRVKV  113 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~--------------~~~~~~~~vGd~v~vkV  113 (234)
                      .-+..+|+++.|+     +||+||+|.+     .++|++|++++..++.              ++....|++||.|+++|
T Consensus        76 ~f~p~vGEv~~G~Is~Vt~fGifVeL~g-----~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV  150 (218)
T 2ckz_B           76 VFKPFLGEIVTGWISKCTAEGIKVSLLG-----IFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRI  150 (218)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECTT-----SCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEE
T ss_pred             EecCCCCCEEEEEEEEEccCcEEEEccC-----ccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEE
Confidence            4568899999999     9999999951     4899999999976553              22345699999999999


Q ss_pred             EEEeCCCC
Q 026737          114 IKIDREKS  121 (234)
Q Consensus       114 l~id~~~~  121 (234)
                      .+++...+
T Consensus       151 ~~v~~~~~  158 (218)
T 2ckz_B          151 EREVFVDV  158 (218)
T ss_dssp             EEEEECCC
T ss_pred             EEEEcccC
Confidence            99997543

>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=97.74  E-value=9.3e-05  Score=59.60  Aligned_cols=70  Identities=6%  Similarity=-0.111  Sum_probs=47.3

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~  182 (234)
                      .+|+.+.++|.++..                       +      |+||++.+ ++||+ +|++. +.....+.-..|.-
T Consensus        82 ~~Gev~~G~V~~v~~-----------------------f------G~FV~l~~-~dglvhis~l~-~~~~~d~~~~~~~~  130 (171)
T 1y14_B           82 FKGEVVDGTVVSCSQ-----------------------H------GFEVQVGP-MKVFVTKHLMP-QDLTFNAGSNPPSY  130 (171)
T ss_dssp             CTTCEEEEEEEEEET-----------------------T------EEEEEETT-EEEEEEGGGSC-TTCEECC-----CE
T ss_pred             CCCCEEEEEEEEEec-----------------------C------EEEEEecC-eEEEEEHHHCC-CCceECcccCceEE
Confidence            579999999988864                       4      99999988 99999 78874 22110000011111


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      ...      ..+++.||.|+++|+++|.
T Consensus       131 ~~~------~~~~~~Gd~V~vkV~~vd~  152 (171)
T 1y14_B          131 QSS------EDVITIKSRIRVKIEGCIS  152 (171)
T ss_dssp             ECS------SCEECTTCEEEEEEEEEEE
T ss_pred             ecc------ceEECCCCEEEEEEEEEEc
Confidence            110      1479999999999999985

>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=97.72  E-value=1.9e-05  Score=69.62  Aligned_cols=69  Identities=22%  Similarity=0.282  Sum_probs=56.4

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc----cc------cchhhhhCCCCEEEEEEEEEeCC
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LI------QDIRDILNEGDEVRVKVIKIDRE  119 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~----~~------~~~~~~~~vGd~v~vkVl~id~~  119 (234)
                      .+++|++|.|+     .+|+||+|.     ...+|++|+|+++..    +.      .+..+.|++||.|.|+|++++. 
T Consensus        92 ~P~vGDvViG~Vt~V~~~~a~VdI~-----s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~-  165 (308)
T 2nn6_H           92 IGEVGDIVVGRITEVQQKRWKVETN-----SRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-  165 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECS-----SSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEEC-----CCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCC-
Confidence            57999999998     899999997     247899999998753    22      2456889999999999999995 


Q ss_pred             CCeEEEEEee
Q 026737          120 KSRITLSIKQ  129 (234)
Q Consensus       120 ~~ri~LS~K~  129 (234)
                      .+++.||+|+
T Consensus       166 ~~~i~LStr~  175 (308)
T 2nn6_H          166 DGAVSLHTRS  175 (308)
T ss_dssp             TTEEEEECCS
T ss_pred             CCCEEEEecC
Confidence            7899999985

>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=97.65  E-value=8.3e-05  Score=62.83  Aligned_cols=71  Identities=14%  Similarity=0.057  Sum_probs=56.2

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      .++||.|.++|.++..                       +      |+||++....+|++ +|+++...         +.
T Consensus        55 p~~GDiV~G~V~~v~~-----------------------~------~a~V~I~~~~~g~l~isev~~~~---------~~   96 (229)
T 2ba0_A           55 PSVGDVVIGIIREVAA-----------------------N------GWAVDIYSPYQAFLPVSENPEMK---------PN   96 (229)
T ss_dssp             CCTTCEEEEEEEEECS-----------------------S------EEEEECSSSSCEEEEGGGCTTCC---------TT
T ss_pred             CCCCCEEEEEEEEEeC-----------------------C------eEEEEeCCCeEEEEEHHHccccc---------cc
Confidence            5889999999999864                       3      88999988899999 78774111         11


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhccc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRH  218 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~  218 (234)
                             .++...+++||.|.|+|++++.   +.||+|+.
T Consensus        97 -------~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~~  129 (229)
T 2ba0_A           97 -------KKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDR  129 (229)
T ss_dssp             -------SCGGGTCCTTCEEEEEEEEECTTCCEEEECCSS
T ss_pred             -------cchhcccCCCCEEEEEEEEECCCCcEEEEEccc
Confidence                   3455689999999999999975   88888764

>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=97.57  E-value=8.9e-05  Score=62.83  Aligned_cols=74  Identities=9%  Similarity=0.054  Sum_probs=56.5

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      .++||.|.++|.++..                       +      |+||++..+.+|++ +|+++. ++.         
T Consensus        64 p~~GDiV~G~V~~v~~-----------------------~------~~~V~I~~~~~g~l~isei~~-~~~---------  104 (235)
T 2z0s_A           64 PQAGDVVIGLIQSVGI-----------------------M------NWFVDINSPYVAVLSVQDFLG-RPF---------  104 (235)
T ss_dssp             CCTTCCEEEEEEEECS-----------------------S------EEEEECSSSSCEEEEHHHHHT-SCC---------
T ss_pred             CCCCCEEEEEEEEEeC-----------------------C------eEEEEeCCCeEEEEEHHHhCC-Ccc---------
Confidence            5789999999988864                       3      89999988999999 788742 111         


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhccc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRH  218 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~  218 (234)
                         +....++...+++||.|.|+|++++.   +.||+|+.
T Consensus       105 ---~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k~~  141 (235)
T 2z0s_A          105 ---NPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGE  141 (235)
T ss_dssp             ---CTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSS
T ss_pred             ---ccchhhHhhcCCCCCEEEEEEEEECCCCcEEEEEecc
Confidence               01113456689999999999999975   88888764

>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=97.54  E-value=8.5e-05  Score=60.30  Aligned_cols=65  Identities=15%  Similarity=0.174  Sum_probs=55.3

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcc-eeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLY-HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~-g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      .+++|++|.|.     .++++|+|+     + ..+|++|++++. ...++.+..|++||.|.|+|.+++. ...+.||
T Consensus         4 ~P~~gDvViG~V~~v~~~~~~VdI~-----~~~~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV~~~~~-~~~~~Lt   74 (175)
T 2ja9_A            4 IPSVNDFVIGVIIGTFSDSYKVSLQ-----NFSSSVSLSYMAFP-NASKKNRPTLQVGDLVYARVCTAEK-ELEAEIE   74 (175)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESS-----TTSCCEEEETTSST-TCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEE
T ss_pred             cCCCcCEEEEEEEEEECcEEEEEEC-----CCCccEEEEHHHCC-chhhhhhccCCCCCEEEEEEEEecC-CCceEEE
Confidence            46899999999     789999997     4 589999999876 3346677889999999999999986 5688888

>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=97.52  E-value=0.00027  Score=56.78  Aligned_cols=70  Identities=7%  Similarity=0.075  Sum_probs=46.4

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccc--cccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVS--QDLQLW  180 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~--~~~~~~  180 (234)
                      .+|+.+.++|.++..                       +      |+||+|. .++||+ +|++. +.....  +....|
T Consensus        80 ~~Gev~~G~V~~v~~-----------------------f------G~fV~l~-~~~glvhis~l~-~~~~~d~~~~~~~~  128 (172)
T 2c35_B           80 FKGEVVDAVVTQVNK-----------------------V------GLFTEIG-PMSCFISRHSIP-SEMEFDPNSNPPCY  128 (172)
T ss_dssp             CTTCEEEEEEEEEET-----------------------T------EEEEEET-TEEEEEEGGGSC-TTEEEESSSSSCEE
T ss_pred             CCCCEEEEEEEEEeC-----------------------C------EEEEEEC-CEEEEEEHHHCC-CCcEECCCCCccEE
Confidence            478888888877764                       4      9999995 677999 78874 221100  000133


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      ...      +-...++.||.|+++|+++|.
T Consensus       129 ~~~------~~~~~~~~Gd~V~vkV~~vd~  152 (172)
T 2c35_B          129 KTM------DEDIVIQQDDEIRLKIVGTRV  152 (172)
T ss_dssp             EET------TSCSEEETTCEEEEEEEEEEE
T ss_pred             EeC------CCCEEECCCCEEEEEEEEEEc
Confidence            321      113489999999999999985

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=97.34  E-value=0.00059  Score=58.20  Aligned_cols=67  Identities=18%  Similarity=0.206  Sum_probs=53.4

Q ss_pred             CCCCcEEEEE--E-------eeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCC--CeEE
Q 026737           56 VNVEDIFVGR--D-------YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRIT  124 (234)
Q Consensus        56 ~~~G~iv~g~--~-------~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~--~ri~  124 (234)
                      -++|++++|+  .       ..+||+|+.  +..+.+|++|.+|+.      |.+.|++||.|+|.|++++...  .+|.
T Consensus         5 ~r~GeIVtG~V~r~~~~v~~~~ViVdlG~--~~~k~EgiLP~~Eqi------p~E~~~~GDrIkayV~~V~~~~~gpqIi   76 (251)
T 2asb_A            5 TREGEIVAGVIQRDSRANARGLVVVRIGT--ETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLIT   76 (251)
T ss_dssp             CCTTCEEEEEEECCHHHHHTTCEEEEECS--SSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEE
T ss_pred             hcCCCEEEEEEEEccccccCCeEEEEeCC--CCcceEEEEcHHHcC------CCccCCCCCEEEEEEEEEEcCCCCCEEE
Confidence            4689999998  2       269999971  001489999999876      5678999999999999999754  7899


Q ss_pred             EEEeec
Q 026737          125 LSIKQL  130 (234)
Q Consensus       125 LS~K~~  130 (234)
                      ||....
T Consensus        77 LSRt~p   82 (251)
T 2asb_A           77 LSRTHP   82 (251)
T ss_dssp             EESSCH
T ss_pred             EEeccH
Confidence            998643

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=97.22  E-value=0.00023  Score=57.38  Aligned_cols=52  Identities=6%  Similarity=-0.028  Sum_probs=35.1

Q ss_pred             ceeeeecCCceEEE-Ecccccccccccc--ccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQ--DLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      |+||+|. .++||+ +|++. +...-.+  ....| .       +....++.||+|+++|+++|.
T Consensus        99 G~FV~l~-~~~glVh~s~l~-~~~~~d~~~~~~~~-~-------~~~~~~~~Gd~VrvkV~~vd~  153 (172)
T 3h0g_G           99 GFFANIG-PLNVFVSSHLVP-PDMKFDPTANPPNY-S-------GEDQVIEKGSNVRLKIVGTRT  153 (172)
T ss_dssp             EEECCBT-TBCCEEEGGGSC-TTCCCBSSSSSCBE-E-------SSSCEECSSCCEEEEEEEEEE
T ss_pred             eEEEEeC-CeEEEEEHHHCC-CccccCcccccceE-e-------cCCcEECCCCEEEEEEEEEEC
Confidence            9999996 588999 78873 3221111  01123 1       123489999999999999985

>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=96.70  E-value=0.00017  Score=64.31  Aligned_cols=91  Identities=14%  Similarity=-0.024  Sum_probs=58.0

Q ss_pred             hhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchh-----hhhccc-ccc-----cc------ceeeeecCCceEEE-
Q 026737          101 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE-----TLEKVI-PQG-----LE------PYLKSFYKKMDDVR-  162 (234)
Q Consensus       101 ~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~-----~~~~~~-~~G-----~~------G~fV~l~~gi~Gl~-  162 (234)
                      ..+.+||.+++.|...|. .+....+.|+....-+.+     .++.+. ..|     ++      |+||++. +++|++ 
T Consensus        85 ~~~~vGd~ie~~I~~~df-gR~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlG-k~EgiLp  162 (344)
T 1hh2_P           85 PLAEVGSIVKKELNVKNF-GRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIG-KLETRLP  162 (344)
T ss_dssp             TTCCTTCEEEEECCCCCS-SSCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEET-TEEEEEE
T ss_pred             ccccCCCEEEEEEccccC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeC-CeEEEEe
Confidence            347899999999988775 333333435433222111     122211 123     22      7999996 999999 


Q ss_pred             EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc------chhhhc
Q 026737          163 ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL------IRKASK  216 (234)
Q Consensus       163 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~------i~ls~K  216 (234)
                      .+++.                       +.+.+++||+|+|.|+++++      |.||.+
T Consensus       163 ~sE~i-----------------------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt  199 (344)
T 1hh2_P          163 KKEWI-----------------------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRR  199 (344)
T ss_dssp             GGGSC-----------------------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESS
T ss_pred             HHHcC-----------------------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEee
Confidence            56651                       12378999999999999984      666655

>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=96.50  E-value=0.0053  Score=59.10  Aligned_cols=74  Identities=8%  Similarity=-0.042  Sum_probs=50.3

Q ss_pred             CCCC--EEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec-CCceEEE-Ecccccccccccccccc
Q 026737          104 NEGD--EVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY-KKMDDVR-ITRQGFEKRVVSQDLQL  179 (234)
Q Consensus       104 ~vGd--~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~-~gi~Gl~-~s~~~~~~~~~~~~~~~  179 (234)
                      ++|+  .+.++|.++..                       +      |+||+|. .|++||+ +|++...+        .
T Consensus       557 ~vGe~~~f~g~V~~V~~-----------------------~------G~fV~L~~~gieGlVhis~l~~~~--------d  599 (644)
T 2id0_A          557 KAGTDTRFAAEIVDISR-----------------------G------GMRVRLVDNGAIAFIPAPFLHAVR--------D  599 (644)
T ss_dssp             GTTSCCCEEEEEEEEET-----------------------T------EEEEEETTTCCEEEEEGGGTCSCG--------G
T ss_pred             ccCCCceEEEEEEEEeC-----------------------C------ceEEEEcCCcEEEEEEchhccCcC--------c
Confidence            5788  88888888753                       4      9999994 6999999 88874200        1


Q ss_pred             ccccCCCCCc----ceeeeeeCCCEEEEEEeeecc----chhhh
Q 026737          180 WLSNAPPSGK----KFTLLARAGRQVQEIQLSHSL----IRKAS  215 (234)
Q Consensus       180 ~~~~~~~~~~----~~~~~~~~G~~v~~~vl~~d~----i~ls~  215 (234)
                      |.... ....    +....++.||+|+|+|+++|.    |.|++
T Consensus       600 ~~~~d-~~~~~l~~~~~~~~~lGD~V~VkV~~vd~~~~~I~~~l  642 (644)
T 2id0_A          600 ELVCS-QENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARP  642 (644)
T ss_dssp             GEEEE-TTTTEEEETTEEEEETTCEEEEEEEEEETTTTEEEEEE
T ss_pred             eeEEc-ccccEEEecCCCEeCCCCEEEEEEEEEeCCCCEEEEEE
Confidence            21100 0001    124579999999999999985    55543

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=96.46  E-value=0.013  Score=48.38  Aligned_cols=77  Identities=13%  Similarity=0.108  Sum_probs=48.7

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~  182 (234)
                      .+|+.+.++|.++..                       +      |+||+| +.++||+ +|++..+...-.++-..|+-
T Consensus        80 ~~GEv~~G~Vs~vt~-----------------------~------GifV~l-g~~eglv~~~~l~~d~~~fd~~~~~~v~  129 (203)
T 3ayh_B           80 FRGEVMLGKIKSCSE-----------------------E------GIRVTI-SFFDDIFIPKDMLFDPCVFRPDERAWVW  129 (203)
T ss_dssp             CTTCEEEEEEEEEET-----------------------T------EEEEEC-SSCCCEEEEGGGBCTTEEEEGGGTEEEE
T ss_pred             CCCCEEEEEEEEEec-----------------------c------EEEEEE-eCceEEEEcHHhCCCCceECccCceEEe
Confidence            467888888877764                       3      999999 5799999 77775443211111112322


Q ss_pred             c--CCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          183 N--APPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       183 ~--~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      .  .+.-+.+-...++.||.|+++|+.++.
T Consensus       130 ~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~  159 (203)
T 3ayh_B          130 KIEGEDGSEGTELYFDIDEEIRFQIESEDF  159 (203)
T ss_dssp             EECCCTTSCCEEEECCTTCEEEEEEEEEEE
T ss_pred             ecccccccccCCcEEcCCCEEEEEEEEEEc
Confidence            1  000002235689999999999999984

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=96.41  E-value=0.012  Score=49.13  Aligned_cols=75  Identities=13%  Similarity=0.054  Sum_probs=48.8

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~  182 (234)
                      .+|+.+.++|.++..                       +      |+||+|++.++||+ +|++..+...-.++-..|.-
T Consensus        80 ~vGEv~~G~Is~Vt~-----------------------f------GifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg  130 (218)
T 2ckz_B           80 FLGEIVTGWISKCTA-----------------------E------GIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIW  130 (218)
T ss_dssp             CTTCEEEEEEEEEET-----------------------T------EEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEE
T ss_pred             CCCCEEEEEEEEEcc-----------------------C------cEEEEccCccceEEEcHHHCCCCcEEcCcCceEEe
Confidence            468888888887764                       4      99999976789999 77764333211111112322


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      .-+   .+-...++.||.|+++|..++.
T Consensus       131 ~~~---e~t~~~~~~Gd~VrvrV~~v~~  155 (218)
T 2ckz_B          131 PMD---EETKLYFDVNEKIRFRIEREVF  155 (218)
T ss_dssp             ECC-----CEEEECTTCEEEEEEEEEEE
T ss_pred             ecc---ccCCcEEcCCCEEEEEEEEEEc
Confidence            110   1124579999999999999985

>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=96.12  E-value=0.013  Score=54.89  Aligned_cols=76  Identities=8%  Similarity=0.015  Sum_probs=52.3

Q ss_pred             hhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccc
Q 026737           99 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDL  177 (234)
Q Consensus        99 ~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~  177 (234)
                      ......+|+.++++|.++.+                       .+.    ||||++.+|.+||+ +|++++.......+.
T Consensus        39 ~~~~~~vGnIY~GkV~rv~p-----------------------~~~----aAFVdiG~gk~gfLhisei~~~~~~~~~~~   91 (517)
T 2bx2_L           39 PGHEQKKANIYKGKITRIEP-----------------------SLE----AAFVDYGAERHGFLPLKEIAREYFPANYSA   91 (517)
T ss_dssp             SSSCCCTTCEEEEEEEEEET-----------------------TTT----EEEEESSSSSCEEEEGGGSCGGGCC-----
T ss_pred             CCCcCCCCCEEEEEEEEecc-----------------------CCc----eEEEEeCCCcEEEEEHHHcChhhhcccccc
Confidence            33445789999999998875                       112    99999999999999 788743321000000


Q ss_pred             ccccccCCCCCcceeeeeeCCCEEEEEEeeec
Q 026737          178 QLWLSNAPPSGKKFTLLARAGRQVQEIQLSHS  209 (234)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d  209 (234)
                              ....++++++++||.|.|.|++..
T Consensus        92 --------~~~~~i~d~lk~Gq~VlVQV~Ke~  115 (517)
T 2bx2_L           92 --------HGRPNIKDVLREGQEVIVQIDKEE  115 (517)
T ss_dssp             ----------CCCGGGTCCTTCEEEEEEEECC
T ss_pred             --------ccccchhhhccCCCEEEEEEEeec
Confidence                    001346678999999999999975

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=95.70  E-value=0.018  Score=57.88  Aligned_cols=80  Identities=11%  Similarity=-0.085  Sum_probs=50.4

Q ss_pred             CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC-CceEEE-Ecccc--cccccccccccccc
Q 026737          106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK-KMDDVR-ITRQG--FEKRVVSQDLQLWL  181 (234)
Q Consensus       106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~-gi~Gl~-~s~~~--~~~~~~~~~~~~~~  181 (234)
                      |+...+.|+++..                       +      |+||.|.+ |++||+ +|++.  .+...-.++ +-.+
T Consensus       887 ge~~~g~V~~V~~-----------------------~------G~fV~L~~~giEGlVhis~L~~~~d~y~fde~-~~~L  936 (977)
T 2wp8_J          887 ESTETGYVIKVFN-----------------------N------GIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEV-EYKL  936 (977)
T ss_dssp             TCEEEEEEEEECS-----------------------S------EEEEECTTTCCEEEEEGGGTCSCGGGCEEETT-TTEE
T ss_pred             ceEEEEEEEEEcC-----------------------C------eEEEEEcCCCeEEEEEeccccCCCceeEEccc-ccEE
Confidence            8888888887742                       3      99999987 999999 88874  221100000 0001


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc-------chhhhc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL-------IRKASK  216 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~-------i~ls~K  216 (234)
                      . .....+.....++.||+|+|+|+.+|.       |+|+||
T Consensus       937 ~-g~~~~g~~~~~~~lGD~V~VkV~~vd~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          937 T-FVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK  977 (977)
T ss_dssp             E-ECCTTCCSCEEEETTCEEEEEECCCCCSSSCCCCCCEEEC
T ss_pred             E-eecCCCccCcEEccCCEEEEEEEEEcCcccCCCceEEEeC
Confidence            0 000000023589999999999998852       777776

>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=95.47  E-value=0.025  Score=55.47  Aligned_cols=66  Identities=9%  Similarity=-0.102  Sum_probs=35.1

Q ss_pred             ceeeeecC-CceEEE-Ecccc--ccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc-------chhhhc
Q 026737          149 PYLKSFYK-KMDDVR-ITRQG--FEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL-------IRKASK  216 (234)
Q Consensus       149 G~fV~l~~-gi~Gl~-~s~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~-------i~ls~K  216 (234)
                      |+||.|.+ |++||+ +|++.  .+...-.++ +-.+..... .......++.||+|+|+|+.+|.       |+|++|
T Consensus       684 G~fV~l~~~giEGlVhis~L~~~~d~~~fd~~-~~~l~g~~~-~~~~~~~~~lGD~V~VkV~~vd~~~~~~~kI~lslk  760 (760)
T 2vnu_D          684 GIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEV-EYKLTFVPT-NSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK  760 (760)
T ss_dssp             EEEEEETTTTEEEEEEHHHHCSCGGGCEEETT-TTEEEECCT-TCSSCEEEETTCEEEEEEC--------CCEEEC---
T ss_pred             eEEEEEeCCCcEEEEEeccccCCCceeEEccc-ccEEEEecC-CCccCcEEecCCEEEEEEEEEECccccCCcEEEEeC
Confidence            99999987 999999 78874  221110000 000000000 00024589999999999999862       777775

>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=95.28  E-value=0.011  Score=51.34  Aligned_cols=66  Identities=8%  Similarity=-0.033  Sum_probs=54.1

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      .+++|++|.|+     ...+.|+|.     ....|++|.+++. ...+..+..|++||.|.|+|++++. .+...||.
T Consensus       124 iP~vGDiVIG~Vt~v~~~~~~VdI~-----s~~~a~L~~~~f~-Gatk~~r~~f~~GDlV~ArV~s~~~-~~~~eLsc  194 (289)
T 2nn6_G          124 VPVKGDHVIGIVTAKSGDIFKVDVG-----GSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVC  194 (289)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECS-----SSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEEC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEEC-----CCceeEEehhhcC-cchhhhhhhcCCCCEEEEEEEEcCC-CCceEEEe
Confidence            47999999999     456899997     3578999999866 2345677889999999999999985 56788887

>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A

Probab=94.89  E-value=0.038  Score=51.19  Aligned_cols=60  Identities=13%  Similarity=0.298  Sum_probs=48.0

Q ss_pred             CCCCcEEEEEEeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           56 VNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        56 ~~~G~iv~g~~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      -..|+++.    |++|++.      +.+|+||++++..+.  .....|++||.|+|+|.++|..+++|.+..
T Consensus       401 ~~~g~~f~----g~vv~l~------~~~glV~v~~l~~d~--~~~~~~~lGd~V~V~v~~vd~~~~~i~f~~  460 (469)
T 2r7d_A          401 AQPERVWD----AVVVDRR------GAQATLLIPDLAFDV--QVNTPAAPGTALQVQFADIDLPQMRVRARS  460 (469)
T ss_dssp             TCTTCCEE----EEEEEEE------TTEEEEEEGGGTEEE--EEECCCCTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             hCCCCEEE----EEEEEEe------CcEEEEEECCCCeEE--ecCCcCCCCCEEEEEEEEEccCCCEEEEEE
Confidence            36788887    4678875      368999999998652  223468999999999999999999998865

>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=94.71  E-value=0.012  Score=51.57  Aligned_cols=79  Identities=9%  Similarity=0.078  Sum_probs=50.5

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      .++||.|.++|.++..                       +      ++||+|....+|++ +|+++.+....      +.
T Consensus        93 P~vGDvViG~Vt~V~~-----------------------~------~a~VdI~s~~~~~l~iS~v~f~gg~i------R~  137 (308)
T 2nn6_H           93 GEVGDIVVGRITEVQQ-----------------------K------RWKVETNSRLDSVLLLSSMNLPGGEL------RR  137 (308)
T ss_dssp             CCSSBCCCEEEEEEET-----------------------T------EEEEECSSSSCEEEESSCCC--------------
T ss_pred             CCCCCEEEEEEEEEeC-----------------------c------eEEEEECCCcCCceechhhcccccee------ec
Confidence            4667777777777653                       2      88999977788888 78775432110      00


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKR  217 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~  217 (234)
                      ... ....++...+++||.|.|+|++++.   +.|++|+
T Consensus       138 ~~~-~D~~~m~~~l~vGDlV~ArVisv~~~~~i~LStr~  175 (308)
T 2nn6_H          138 RSA-EDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRS  175 (308)
T ss_dssp             ------CHHHHHHSCSSCEECCEEEEEETTTEEEEECCS
T ss_pred             ccc-hhhhhhhccCCCCCEEEEEEEEcCCCCCEEEEecC
Confidence            000 0013455689999999999999974   8888774

>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=94.39  E-value=0.054  Score=48.54  Aligned_cols=72  Identities=11%  Similarity=-0.036  Sum_probs=49.3

Q ss_pred             CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC---CceEEE-Eccccccccccccccccc
Q 026737          105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK---KMDDVR-ITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~---gi~Gl~-~s~~~~~~~~~~~~~~~~  180 (234)
                      .|+.|.+.|...+.                   ..++.      ++||+|..   +++|++ .+++.             
T Consensus       130 ~GeIVtG~V~r~~~-------------------~v~~~------~v~VdLG~~~~k~EgiLP~~Eqi-------------  171 (366)
T 1k0r_A          130 EGEIVAGVIQRDSR-------------------ANARG------LVVVRIGTETKASEGVIPAAEQV-------------  171 (366)
T ss_dssp             TTCEEEEEEECCHH-------------------HHHTT------CEEEEECCSSSCEEEEECGGGSC-------------
T ss_pred             CCCEEEEEEEEccc-------------------cccCC------eEEEEeCCCccceEEEEcHHHcC-------------
Confidence            89999999977211                   01112      68999975   599999 56541             


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhH
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWN  224 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~  224 (234)
                                +.+.++.||+|+|.|+++++    ..+.+.+..|+...
T Consensus       172 ----------P~E~~~~GDrVkvyV~~V~~~~kgpqI~LSRT~p~lv~  209 (366)
T 1k0r_A          172 ----------PGESYEHGNRLRCYVVGVTRGAREPLITLSRTHPNLVR  209 (366)
T ss_dssp             ----------TTCCCCTTCEEEEEEEEEECCSSSCEEEEESSCHHHHH
T ss_pred             ----------CCccCCCCCEEEEEEEEEecCCCccEEEEEeCChHHHH
Confidence                      13478999999999999986    44555555554443

>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=92.51  E-value=0.16  Score=43.18  Aligned_cols=46  Identities=9%  Similarity=-0.055  Sum_probs=34.4

Q ss_pred             ceeeeecC---CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc------chhhhcc
Q 026737          149 PYLKSFYK---KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL------IRKASKR  217 (234)
Q Consensus       149 G~fV~l~~---gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~------i~ls~K~  217 (234)
                      .+||+|..   +.+|++ .+|+.                       +.+.++.||+|+|.|++++.      |-||...
T Consensus        26 ~ViVdlG~~~~k~EgiLP~~Eqi-----------------------p~E~~~~GDrIkayV~~V~~~~~gpqIiLSRt~   81 (251)
T 2asb_A           26 LVVVRIGTETKASEGVIPAAEQV-----------------------PGESYEHGNRLRCYVVGVTRGAREPLITLSRTH   81 (251)
T ss_dssp             CEEEEECSSSSCEEEEECGGGSC-----------------------TTCCCCTTCEEEEEEEEEECCSSSCEEEEESSC
T ss_pred             eEEEEeCCCCcceEEEEcHHHcC-----------------------CCccCCCCCEEEEEEEEEEcCCCCCEEEEEecc
Confidence            56899965   599999 45431                       23478999999999999975      6666553

>1jjg_A M156R; beta barrel, S1 motif, OB fold, MYXV156R, NESG project, structural genomics, EIF-2A homolog, PSI, protein structure initiative; NMR {Myxoma virus} SCOP: b.40.4.5

Probab=92.03  E-value=0.44  Score=34.14  Aligned_cols=62  Identities=13%  Similarity=0.107  Sum_probs=46.6

Q ss_pred             hcCCCCCcEEEEE----EeeEEEEEecCCCcceeEEEEEce-ecccccccchhhhhCCCCEEEEEEEEEeC
Q 026737           53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDR  118 (234)
Q Consensus        53 ~~~~~~G~iv~g~----~~G~fV~l~~~~g~~g~~glv~is-els~~~~~~~~~~~~vGd~v~vkVl~id~  118 (234)
                      .-++.+|++.+|.    ++-.+|.|.+.   +|.+|++--+ ++-.++..+.++.+ +|..|+++|+.+|.
T Consensus        27 ~~~~~~g~VtkGiVy~kd~~fyV~L~dY---~glEaii~dYvnv~~dr~~klkkkL-VGKtIkVqVIRvD~   93 (102)
T 1jjg_A           27 AMDLSPGSVHEGIVYFKDGIFKVRLLGY---EGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG   93 (102)
T ss_dssp             CCCCCSSCEEEEEEEEETTEEEEECTTT---SSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS
T ss_pred             ccccCCCceEeeEEEEeCCEEEEEecCC---CCceeeeehhhhhhHHHHHHHHHHh-cCceEEEEEEEecc
Confidence            3468999999999    44568888743   2688887533 44455667777777 79999999999986

>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=88.63  E-value=1.2  Score=35.69  Aligned_cols=65  Identities=14%  Similarity=-0.091  Sum_probs=47.7

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC-CceEEE-Eccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~  180 (234)
                      .++||.|.++|.++..                       .      +++|++.+ -.+|++ +|.+.  ..         
T Consensus         5 P~~gDvViG~V~~v~~-----------------------~------~~~VdI~~~~~~a~L~~s~~~--g~---------   44 (175)
T 2ja9_A            5 PSVNDFVIGVIIGTFS-----------------------D------SYKVSLQNFSSSVSLSYMAFP--NA---------   44 (175)
T ss_dssp             CCTTCEEEEEEEEECS-----------------------S------EEEEESSTTSCCEEEETTSST--TC---------
T ss_pred             CCCcCEEEEEEEEEEC-----------------------c------EEEEEECCCCccEEEEHHHCC--ch---------
Confidence            4679999999988753                       2      67899987 799998 56541  10         


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc---chhh
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKA  214 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls  214 (234)
                      .       .+....+++||-|.|+|..++.   +.|+
T Consensus        45 ~-------k~~r~~l~~GDlV~ArV~~~~~~~~~~Lt   74 (175)
T 2ja9_A           45 S-------KKNRPTLQVGDLVYARVCTAEKELEAEIE   74 (175)
T ss_dssp             C-------SSSCCCCCTTCEEEEEEEECCTTSCCEEE
T ss_pred             h-------hhhhccCCCCCEEEEEEEEecCCCceEEE
Confidence            0       2234478999999999999975   6676

---

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	234
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	6e-13
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	4e-11
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	5e-11
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	5e-11
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	3e-10
d1wi5a_	119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	3e-09
d1y14b1	91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	1e-08
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	8e-08
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	1e-07
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	2e-07
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	2e-07
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	3e-07
d2c35b1	94	b.40.4.5 (B:78-171) C-terminal domain of RNA polym	9e-06
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	8e-04
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	0.001
d2ix0a3	87	b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Esche	0.002
d2nn6i1	125	b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H	0.002

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Escherichia coli [TaxId: 562]

 Score = 60.2 bits (146), Expect = 6e-13
 Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 11/81 (13%)

Query: 54  SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
           + + V  ++ G+     D+GAF+ +          GLVH+S+++   ++ + D L  G E
Sbjct: 1   AEIEVGRVYTGKVTRIVDFGAFVAIG-----GGKEGLVHISQIADKRVEKVTDYLQMGQE 55

Query: 109 VRVKVIKIDREKSRITLSIKQ 129
           V VKV+++DR+  RI LSIK+
Sbjct: 56  VPVKVLEVDRQG-RIRLSIKE 75

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} Length = 62

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 54.7 bits (132), Expect = 4e-11
 Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 9/59 (15%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL----IQDIRDILNEGDEVRVKVIKIDREK 120
            +GAF+ L     L    GL+H+S++        ++++ D+L  G +V+V++ +ID   
Sbjct: 8   TFGAFVSL-----LPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRG 61

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 55.7 bits (134), Expect = 5e-11
 Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 10/84 (11%)

Query: 54  SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
             +    +  G      ++GAF+ +       H  GLVH+S +S   ++D  +++  GD 
Sbjct: 14  KDLKPGMVLEGVVTNVTNFGAFVDI-----GVHQDGLVHISALSEKFVKDPYEVVKAGDI 68

Query: 109 VRVKVIKIDREKSRITLSIKQLEE 132
           V+VKV+++D  ++R+ LS++  + 
Sbjct: 69  VKVKVMEVDIPRNRVGLSMRMSDT 92

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 5e-11
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 8/78 (10%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
            VED+ +       + GA++ L   + +    G++ +SE+S   I+ I  ++  G    V
Sbjct: 12  EVEDVVMVNVRSIAEMGAYVSLLEYNNI---EGMILLSELSRRRIRSINKLIRIGRNECV 68

Query: 112 KVIKIDREKSRITLSIKQ 129
            VI++D+EK  I LS ++
Sbjct: 69  VVIRVDKEKGYIDLSKRR 86

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Length = 84

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 53.1 bits (127), Expect = 3e-10
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 8/78 (10%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
           +  +I +       DYG+++ L    GL      +  SEVS   +++IRD+L E  +V V
Sbjct: 10  SEGEILIATVKQVFDYGSYVSLDEYGGL---QAFLPWSEVSSKWVKNIRDVLKENRKVIV 66

Query: 112 KVIKIDREKSRITLSIKQ 129
           KVI++DR K  + +S+K+
Sbjct: 67  KVIRVDRRKGTVDVSLKK 84

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Length = 119

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 3e-09
 Identities = 11/77 (14%), Positives = 29/77 (37%), Gaps = 5/77 (6%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           D+G  + +    G+      + + +    +  ++    L  G  +   V K+      ++
Sbjct: 34  DHGYLVDI----GVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVS 89

Query: 125 LSIKQLEEDPLLETLEK 141
           LS+   E    + T ++
Sbjct: 90  LSVGHSEVSTAIATEQQ 106

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 91

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.1 bits (117), Expect = 1e-08
 Identities = 14/80 (17%), Positives = 25/80 (31%), Gaps = 17/80 (21%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----------DIRDILNEGDEVRVKVIK 115
            +G  + +            V    +  DL               D++     +RVK+  
Sbjct: 16  QHGFEVQVGPMKVF------VTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEG 69

Query: 116 IDREKSRITLSIKQLEEDPL 135
              + S I   I  ++ED L
Sbjct: 70  CISQVSSIHA-IGSIKEDYL 88

>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 = 46.4 bits (110), Expect = 8e-08
 Identities = 12/82 (14%), Positives = 30/82 (36%), Gaps = 15/82 (18%)

Query: 58  VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDE 108
             D+ +G          F+ +           ++ V +           D++ +L  GD 
Sbjct: 7   AGDVVIGLIQSVGIMNWFVDIN-----SPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDY 61

Query: 109 VRVKVIKIDREKSRITLSIKQL 130
           ++ KV+  D+ +    L+++  
Sbjct: 62  IKAKVVAFDKTR-SPLLTVQGE 82

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 83

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 45.8 bits (108), Expect = 1e-07
 Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 12/85 (14%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVR 110
           +V D+ +G        G  +     D        + VSE       +   ++L+ GD + 
Sbjct: 4   SVGDVVIGIIREVAANGWAV-----DIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAII 58

Query: 111 VKVIKIDREKSRITLSIKQLEEDPL 135
            KV+ ID +  ++TL++K     P+
Sbjct: 59  AKVLNIDPKM-KVTLTMKDRICRPI 82

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 106

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 20/99 (20%), Positives = 45/99 (45%), Gaps = 15/99 (15%)

Query: 58  VEDIFVGR-----DYGAFIHLRFPDGLYHLTGL-----VHVSEVSWDLIQDIRDILNEGD 107
           + ++  G      ++G+F+ L   DGL H++ +      +  +    + ++   +L  GD
Sbjct: 3   MYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGD 62

Query: 108 EVRVKVIKIDREK-----SRITLSIKQLEEDPLLETLEK 141
            VR +++ I  +      S+I L+++Q     L    E+
Sbjct: 63  YVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIEEE 101

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 87

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 45.4 bits (107), Expect = 2e-07
 Identities = 17/82 (20%), Positives = 28/82 (34%), Gaps = 14/82 (17%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDE 108
            + DI +G       YG  + ++           +  S +    I      R  L+ GD 
Sbjct: 6   KINDIVIGLVEDVEIYGWVVDIK-----APYKAYLPASNLLGRSINVGEDLRRYLDVGDY 60

Query: 109 VRVKVIKIDREKSRITLSIKQL 130
           V  ++   DR      LS+K  
Sbjct: 61  VIARIENFDRSI-DPVLSVKGK 81

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.9 bits (106), Expect = 3e-07
 Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 21/89 (23%)

Query: 58  VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----------LIQDIRDI 102
           V DI VGR          +          L  ++ +S ++                +R  
Sbjct: 8   VGDIVVGRITEVQQKRWKVET-----NSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGF 62

Query: 103 LNEGDEVRVKVIKIDREKSRITLSIKQLE 131
           L EGD +  +V  +  +   ++L  + L+
Sbjct: 63  LQEGDLISAEVQAVFSDG-AVSLHTRSLK 90

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (96), Expect = 9e-06
 Identities = 13/89 (14%), Positives = 28/89 (31%), Gaps = 12/89 (13%)

Query: 58  VEDIFVGR-----DYGAFIHLRFPDGLYHLTGL-----VHVSEVSWDLI-QDIRDILNEG 106
             ++           G F  +           +        +         D   ++ + 
Sbjct: 4   KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQD 63

Query: 107 DEVRVKVIKIDREKSRITLSIKQLEEDPL 135
           DE+R+K++    +K+ I   I  L +D L
Sbjct: 64  DEIRLKIVGTRVDKNDIFA-IGSLMDDYL 91

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]} Length = 90

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

 Score = 35.2 bits (81), Expect = 8e-04
 Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 11/77 (14%)

Query: 57  NVEDIFVGRDYGAFIHLRFPDGLY-----HLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
           +V D  +G      I   F D          + +        +  +  R  L  GD V  
Sbjct: 6   SVNDFVIGV-----IIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60

Query: 112 KVIKIDREKSRITLSIK 128
           +V   ++E     +   
Sbjct: 61  RVCTAEKE-LEAEIECF 76

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (81), Expect = 0.001
 Identities = 6/77 (7%), Positives = 19/77 (24%), Gaps = 12/77 (15%)

Query: 57  NVEDIFVGRDYGAFIHLRFPDGLY-----HLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
              D  +G      +  +  D             +          +  R  +  GD +  
Sbjct: 5   VKGDHVIGI-----VTAKSGDIFKVDVGGSEPASLSYLSFEGA-TKRNRPNVQVGDLIYG 58

Query: 112 KVIKIDREKSRITLSIK 128
           + +  +++     +   
Sbjct: 59  QFVVANKDM-EPEMVCI 74

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Length = 87

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

 Score = 34.4 bits (79), Expect = 0.002
 Identities = 6/67 (8%), Positives = 16/67 (23%), Gaps = 14/67 (20%)

Query: 71  IHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVIKIDR 118
           + +R  D        +    +               +      +    D + V + ++  
Sbjct: 19  MRVRLVDN--GAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRM 76

Query: 119 EKSRITL 125
           E   I  
Sbjct: 77  ETRSIIA 83

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 125

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 2/51 (3%)

Query: 81  HLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129
              G +   +V        +I      GD V  KVI +   +S   L+  +
Sbjct: 38  SFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAE 88

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	234
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.7
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.67
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.67
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.64
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.56
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.53
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.41
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.41
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.39
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.25
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.2
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.17
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.16
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.16
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.15
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.07
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.04
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.99
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.84
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	98.77
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	98.74
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.69
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	98.68
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	98.51
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.49
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	98.36
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.23
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	97.96
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.86
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	97.84
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	97.64
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	97.4
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.2
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	96.53
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	96.45
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	96.24
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	95.83
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	95.73
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	94.23
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	94.18
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	90.24
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	87.98
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	83.66

>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=99.70  E-value=3.5e-18  Score=119.91  Aligned_cols=71  Identities=38%  Similarity=0.710  Sum_probs=66.1

Q ss_pred             cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K  128 (234)
                      +++++|+++.|+     +||+||+|+     ++++||||+++++|.++.+|++.|++||+++|+|+++|+ ++||.||+|
T Consensus         1 ad~kvG~iv~G~V~~v~~~G~fV~l~-----~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~-~~ri~LS~k   74 (76)
T d1sroa_           1 AEIEVGRVYTGKVTRIVDFGAFVAIG-----GGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIK   74 (76)
T ss_dssp             CCCCTTSEEEEEEEEEETTEEEEECS-----SSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCT-TCCCEEEEC
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEeC-----CCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECC-CCCEEEEEE
Confidence            368999999999     999999997     379999999999999999999999999999999999996 689999999


Q ss_pred             ec
Q 026737          129 QL  130 (234)
Q Consensus       129 ~~  130 (234)
                      ++
T Consensus        75 ~a   76 (76)
T d1sroa_          75 EA   76 (76)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=99.67  E-value=5.7e-17  Score=118.06  Aligned_cols=76  Identities=30%  Similarity=0.603  Sum_probs=71.5

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~  127 (234)
                      ++++++|+++.|+     ++|+||+|+     .+++||||.++++|.++.++.+.|++||.|+|+|+++|+++++|.||+
T Consensus        13 ~~~~k~G~iv~g~V~~v~~~G~~V~l~-----~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~LS~   87 (94)
T d3bzka4          13 LKDLKPGMVLEGVVTNVTNFGAFVDIG-----VHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSM   87 (94)
T ss_dssp             GGGCCTTCEEEEEEEEEETTEEEEECS-----SSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEES
T ss_pred             HhcCCCCCEEEEEEEEEECcEEEEEeC-----CCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEE
Confidence            5789999999999     999999997     379999999999999999999999999999999999999999999999


Q ss_pred             eecccCc
Q 026737          128 KQLEEDP  134 (234)
Q Consensus       128 K~~~~~p  134 (234)
                      |+. ++|
T Consensus        88 K~~-e~P   93 (94)
T d3bzka4          88 RMS-DTP   93 (94)
T ss_dssp             CTT-CCC
T ss_pred             ecc-CCC
Confidence            986 666

>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=99.67  E-value=8.9e-17  Score=115.11  Aligned_cols=70  Identities=31%  Similarity=0.507  Sum_probs=53.4

Q ss_pred             CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      ++|+++.|+     ++|+||+|...   ++++||||+++++|.++.++.+.|++||.|+|+|+++|++++||.||+|+
T Consensus        12 ~~G~iv~G~V~~i~~~G~fV~l~~~---~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~ki~LS~Kq   86 (86)
T d1kl9a2          12 EVEDVVMVNVRSIAEMGAYVSLLEY---NNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTT---TTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCEEEEEEEEEeCCeEEEEEecC---CCEEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEEEEEeeC
Confidence            689999999     99999999621   26999999999999999999999999999999999999999999999985

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.64  E-value=1.3e-16  Score=113.58  Aligned_cols=71  Identities=35%  Similarity=0.574  Sum_probs=60.7

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      +++|++++|+     +||+||+|...   ++++||||.++++|.++.++.+.|++||+++|+|+++|+++++|.||+|+
T Consensus         9 p~~G~iv~G~V~~v~~~G~fV~l~~~---~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2           9 PSEGEILIATVKQVFDYGSYVSLDEY---GGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             CCTTCCCEEEEEEEETTEEEEEETTT---TTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCc---CCEEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence            5689999999     99999999621   26999999999999999999999999999999999999999999999985

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.56  E-value=2.2e-15  Score=111.90  Aligned_cols=79  Identities=29%  Similarity=0.514  Sum_probs=68.4

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc-----------cchhhhhCCCCEEEEEEEEEeCC
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDRE  119 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~-----------~~~~~~~~vGd~v~vkVl~id~~  119 (234)
                      +++|+++.|+     +||+||+|+      +++||||+++|+++++           .++.+.|++||.|+|+|+++|.+
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~------~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~   74 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLG------PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLK   74 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS------SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECC
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEee------CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchh
Confidence            4789999999     999999996      5999999999999886           36778999999999999999988


Q ss_pred             CCe-----EEEEEeecccCcchhhhh
Q 026737          120 KSR-----ITLSIKQLEEDPLLETLE  140 (234)
Q Consensus       120 ~~r-----i~LS~K~~~~~p~~~~~~  140 (234)
                      +++     +.||+|+...+||+...+
T Consensus        75 ~~~~~~~~i~ls~K~~~~~~~e~~~~  100 (106)
T d1go3e1          75 AERKRGSKIALTMRQPYLGKLEWIEE  100 (106)
T ss_dssp             C-----CEEEEECCSTTCEEHHHHHH
T ss_pred             hccccCceeecccccCCCCcchhhhh
Confidence            766     889999999999975433

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.53  E-value=6.3e-15  Score=104.50  Aligned_cols=74  Identities=26%  Similarity=0.359  Sum_probs=66.2

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccc-ccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~-~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      +++|++|.|+     ++|+||+|+     ++++||+|+++++|.. ..++++.|++||.|.|+|+++|+ +++|.||+|+
T Consensus         3 Pk~Gd~V~G~V~~v~~~g~~V~i~-----~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~LS~k~   76 (83)
T d2ba0a1           3 PSVGDVVIGIIREVAANGWAVDIY-----SPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMKD   76 (83)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECS-----SSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECCS
T ss_pred             CCCCCEEEEEEEEEECCEEEEecC-----CCeeEEEecccccccccccChhhhcccccEEEEEEEEECC-CCCEEEEecC
Confidence            6889999999     999999997     3799999999999875 78999999999999999999996 6899999998


Q ss_pred             cccCcc
Q 026737          130 LEEDPL  135 (234)
Q Consensus       130 ~~~~p~  135 (234)
                      ....|+
T Consensus        77 ~~~~k~   82 (83)
T d2ba0a1          77 RICRPI   82 (83)
T ss_dssp             SSCEEE
T ss_pred             CCCCCC
Confidence            765543

>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=99.41  E-value=7.2e-14  Score=99.83  Aligned_cols=70  Identities=26%  Similarity=0.368  Sum_probs=62.5

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc---chhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---DIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~---~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      .+++|+++.|+     ++|+||+|+     .+++||+|+++++|+++.   ++++.|++||.|.|+|+++|+ .+++.||
T Consensus         4 ~Pk~Gdiv~G~V~~i~~~g~fV~i~-----~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~-~~~i~LS   77 (87)
T d2je6i1           4 YPKINDIVIGLVEDVEIYGWVVDIK-----APYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLS   77 (87)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS-----SSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEE
T ss_pred             cCCCCCEEEEEEEEEECCEEEEEeC-----CCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECC-CCCEEEE
Confidence            46889999999     999999997     369999999999998764   677889999999999999996 6899999


Q ss_pred             Eeec
Q 026737          127 IKQL  130 (234)
Q Consensus       127 ~K~~  130 (234)
                      +|+.
T Consensus        78 ~k~~   81 (87)
T d2je6i1          78 VKGK   81 (87)
T ss_dssp             CCST
T ss_pred             EecC
Confidence            9864

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=9.1e-14  Score=105.03  Aligned_cols=78  Identities=13%  Similarity=0.175  Sum_probs=69.3

Q ss_pred             hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccc-ccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (234)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~-~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS  126 (234)
                      ...+++|+++.|+     ++|+||+|+.    .+++||||++++++.+ ..+|.+.|++||.|+|+|+++|++++++.||
T Consensus        16 ~~~l~~G~iv~G~V~~i~~~G~~V~lg~----~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS   91 (119)
T d1wi5a_          16 AEALKPGMLLTGTVSSLEDHGYLVDIGV----DGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS   91 (119)
T ss_dssp             TTTCCTTCEEEEEEEEECSSEEEEECCC----SSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEE
T ss_pred             HhhcCCCCEEEEEEEEEeccEEEEEEec----cccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEE
Confidence            4579999999999     9999999941    2699999999999875 7789899999999999999999999999999


Q ss_pred             EeecccCc
Q 026737          127 IKQLEEDP  134 (234)
Q Consensus       127 ~K~~~~~p  134 (234)
                      +|+.....
T Consensus        92 ~k~~~~~~   99 (119)
T d1wi5a_          92 VGHSEVST   99 (119)
T ss_dssp             CCCCCSCC
T ss_pred             ecHHHhhh
Confidence            99876543

>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=99.39  E-value=1.1e-13  Score=99.09  Aligned_cols=70  Identities=17%  Similarity=0.323  Sum_probs=62.5

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc----chhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----DIRDILNEGDEVRVKVIKIDREKSRITL  125 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~----~~~~~~~vGd~v~vkVl~id~~~~ri~L  125 (234)
                      .+++|++|.|+     ++|+||+|+     ++.+||+|.+++++.++.    ++++.|++||.|.|+|+++|+ .+++.|
T Consensus         4 ~Pk~GdvV~G~V~~v~~~g~fV~i~-----~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~L   77 (88)
T d2z0sa1           4 VPQAGDVVIGLIQSVGIMNWFVDIN-----SPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPLL   77 (88)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECS-----SSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEEE
T ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC-----CCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECC-CCCEEE
Confidence            46899999999     999999997     378999999999998764    677889999999999999996 579999


Q ss_pred             EEeec
Q 026737          126 SIKQL  130 (234)
Q Consensus       126 S~K~~  130 (234)
                      |+|+.
T Consensus        78 s~k~~   82 (88)
T d2z0sa1          78 TVQGE   82 (88)
T ss_dssp             ECCSS
T ss_pred             EEecC
Confidence            99874

>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=99.25  E-value=1.8e-12  Score=90.23  Aligned_cols=70  Identities=19%  Similarity=0.130  Sum_probs=59.7

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      +++|+.+.++|.++.+                       +      |+||+|.+|++||+ +|+++++.           
T Consensus         3 ~kvG~iv~G~V~~v~~-----------------------~------G~fV~l~~~~~Glv~~sels~~~-----------   42 (76)
T d1sroa_           3 IEVGRVYTGKVTRIVD-----------------------F------GAFVAIGGGKEGLVHISQIADKR-----------   42 (76)
T ss_dssp             CCTTSEEEEEEEEEET-----------------------T------EEEEECSSSCCCBCCTTSSCSSC-----------
T ss_pred             CCCCCEEEEEEEEEeC-----------------------c------EEEEEeCCCCEEEEEhHHhCccc-----------
Confidence            6899999999999864                       4      99999999999999 88885432           


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhccc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRH  218 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~  218 (234)
                       .     .+++..+++||+|+|+|+++|+   |+||+||+
T Consensus        43 -~-----~~~~~~~~~G~~v~v~Vi~id~~~ri~LS~k~a   76 (76)
T d1sroa_          43 -V-----EKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEA   76 (76)
T ss_dssp             -C-----SCHHHHCCTTCEEEEEEEECCTTCCCEEEECCC
T ss_pred             -c-----CCHHHccCCCCEEEEEEEEECCCCCEEEEEEcC
Confidence             1     3466789999999999999986   99999985

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.20  E-value=2e-11  Score=90.02  Aligned_cols=92  Identities=10%  Similarity=0.031  Sum_probs=69.0

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~  182 (234)
                      ++||.+.++|.++..                       +      |+||+|. +++||| +|+++++.......-.++..
T Consensus         2 ~~gei~~g~V~~v~~-----------------------~------G~FVel~-~ieGlv~~s~l~~~~~~~~~~~~~~~~   51 (106)
T d1go3e1           2 EMYELIEGEVVDVVE-----------------------F------GSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIG   51 (106)
T ss_dssp             CTTCEEEEEEEEEET-----------------------T------EEEEECS-SSEEEEEGGGSCSSCEEECCC--CEEE
T ss_pred             CCCCEEEEEEEEEee-----------------------e------EEEEEee-CeEEEEEeecccCceeeeccceeEEee
Confidence            579999999998874                       5      9999994 799999 88886543210000000110


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc---------chhhhcccccchhHHHHhhcc
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL---------IRKASKRHCNEYWNVFHETAI  231 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~---------i~ls~K~~~~~p~~~~~~~~~  231 (234)
                            .+....+++||.|+|+|+++|.         |.||+|+...+||+.+++++.
T Consensus        52 ------~~~~~~~~~Gd~v~vkV~~vd~~~~~~~~~~i~ls~K~~~~~~~e~~~~~~~  103 (106)
T d1go3e1          52 ------KETGKVLEIGDYVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIEEEKA  103 (106)
T ss_dssp             ------TTTCCEECTTCEEEEEEEEEECCC-----CEEEEECCSTTCEEHHHHHHHHH
T ss_pred             ------cccccceeecceEEEEEEEEchhhccccCceeecccccCCCCcchhhhhHhh
Confidence                  2345689999999999999973         789999999999999988764

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Streptomyces antibioticus [TaxId: 1890]

Probab=99.17  E-value=2.5e-13  Score=91.07  Aligned_cols=50  Identities=30%  Similarity=0.588  Sum_probs=29.1

Q ss_pred             EeeEEEEEecCCCcceeEEEEEceecccc----cccchhhhhCCCCEEEEEEEEEeCCC
Q 026737           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQDIRDILNEGDEVRVKVIKIDREK  120 (234)
Q Consensus        66 ~~G~fV~l~~~~g~~g~~glv~isels~~----~~~~~~~~~~vGd~v~vkVl~id~~~  120 (234)
                      +|||||+|.     ++++||||+|++||.    ++.+|++.|++||+|+|+|+++|+++
T Consensus         8 ~fG~FV~l~-----~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           8 TFGAFVSLL-----PGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             -CSCEECCC--------CCCCC-------------------CCSSCBCCCCCCCCCSSC
T ss_pred             eceEEEEec-----CCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCCC
Confidence            999999997     479999999999864    67899999999999999999999743

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=7.4e-12  Score=90.66  Aligned_cols=69  Identities=23%  Similarity=0.303  Sum_probs=58.9

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc----------cccchhhhhCCCCEEEEEEEEEeCCC
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----------LIQDIRDILNEGDEVRVKVIKIDREK  120 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~----------~~~~~~~~~~vGd~v~vkVl~id~~~  120 (234)
                      +++|++|.|+     ++|+||+|+     ++.+|++|+|+++|.          .+.++++.|++||.|.|+|+++|. .
T Consensus         6 P~vGdiV~G~V~~v~~~g~~V~I~-----~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~-d   79 (95)
T d2nn6h1           6 GEVGDIVVGRITEVQQKRWKVETN-----SRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-D   79 (95)
T ss_dssp             CCSSBCCCEEEEEEETTEEEEECS-----SSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-T
T ss_pred             CCCCCEEEEEEEEEecCcEEEEeC-----CCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECC-C
Confidence            6789999998     999999997     368999999999763          344678899999999999999997 6


Q ss_pred             CeEEEEEeec
Q 026737          121 SRITLSIKQL  130 (234)
Q Consensus       121 ~ri~LS~K~~  130 (234)
                      +++.||+|..
T Consensus        80 g~i~Ls~r~~   89 (95)
T d2nn6h1          80 GAVSLHTRSL   89 (95)
T ss_dssp             TEEEEECCSS
T ss_pred             CCEEEEeccc
Confidence            9999999864

>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=99.16  E-value=2.5e-11  Score=86.14  Aligned_cols=69  Identities=17%  Similarity=0.208  Sum_probs=51.1

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec--CCceEEE-Ecccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY--KKMDDVR-ITRQGFEKRVVSQDLQL  179 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~--~gi~Gl~-~s~~~~~~~~~~~~~~~  179 (234)
                      .++|+.+.++|.++..                       +      |+||+|.  +|++||| +|+++++.         
T Consensus        11 p~~G~iv~G~V~~i~~-----------------------~------G~fV~l~~~~~i~G~i~~sels~~~---------   52 (86)
T d1kl9a2          11 PEVEDVVMVNVRSIAE-----------------------M------GAYVSLLEYNNIEGMILLSELSRRR---------   52 (86)
T ss_dssp             CCTTCEEEEEEEEECS-----------------------S------EEEEEETTTTTEEEEEEGGGC-------------
T ss_pred             CCCCCEEEEEEEEEeC-----------------------C------eEEEEEecCCCEEEEEEeeeccccc---------
Confidence            3689999999999864                       4      9999997  5899999 78885332         


Q ss_pred             ccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcc
Q 026737          180 WLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKR  217 (234)
Q Consensus       180 ~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~  217 (234)
                         .     .++...+++||+|+|+|+++|+    |.||+||
T Consensus        53 ---~-----~~~~~~~~~Gd~v~~kV~~vd~~~~ki~LS~Kq   86 (86)
T d1kl9a2          53 ---I-----RSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             ----------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             ---c-----ccceEEeecccEEEEEEEEEECCCCEEEEEeeC
Confidence               1     3455689999999999999986    9999997

>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=99.15  E-value=2.5e-11  Score=87.55  Aligned_cols=74  Identities=12%  Similarity=0.040  Sum_probs=61.8

Q ss_pred             hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccc
Q 026737          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       102 ~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~  180 (234)
                      .+++|+.+.++|.++..                       +      |+||+|.+|++|+| .++++++.          
T Consensus        15 ~~k~G~iv~g~V~~v~~-----------------------~------G~~V~l~~~i~G~i~~~~ls~~~----------   55 (94)
T d3bzka4          15 DLKPGMVLEGVVTNVTN-----------------------F------GAFVDIGVHQDGLVHISALSEKF----------   55 (94)
T ss_dssp             GCCTTCEEEEEEEEEET-----------------------T------EEEEECSSSSCEEEEGGGGCSSC----------
T ss_pred             cCCCCCEEEEEEEEEEC-----------------------c------EEEEEeCCCceEEeehhhhhccc----------
Confidence            37899999999999874                       4      99999999999999 67774321          


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccch
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEY  222 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p  222 (234)
                        .     .++...+++||.|+|+|+++|.    |.||+|+. ++|
T Consensus        56 --~-----~~~~~~~~vGq~v~~~V~~id~~~~~i~LS~K~~-e~P   93 (94)
T d3bzka4          56 --V-----KDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMS-DTP   93 (94)
T ss_dssp             --C-----SCHHHHCCTTCEEEEEEEEEETTTTEEEEESCTT-CCC
T ss_pred             --c-----cChhhhhccCcEEEEEEEEEECCCCEEEEEEecc-CCC
Confidence              1     3456789999999999999986    99999986 777

>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=99.07  E-value=1.1e-10  Score=82.10  Aligned_cols=76  Identities=13%  Similarity=0.051  Sum_probs=62.2

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      .++||.|.++|.++.+                       +      |+||++.++++||+ +|+++++..          
T Consensus         3 Pk~Gd~V~G~V~~v~~-----------------------~------g~~V~i~~~~~g~l~~se~s~~~~----------   43 (83)
T d2ba0a1           3 PSVGDVVIGIIREVAA-----------------------N------GWAVDIYSPYQAFLPVSENPEMKP----------   43 (83)
T ss_dssp             CCTTCEEEEEEEEECS-----------------------S------EEEEECSSSSCEEEEGGGCTTCCT----------
T ss_pred             CCCCCEEEEEEEEEEC-----------------------C------EEEEecCCCeeEEEeccccccccc----------
Confidence            3689999999999864                       4      99999999999999 688843321          


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcccccchh
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRHCNEYW  223 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~~~~p~  223 (234)
                        .    .++...+++||.|.|+|+++|+   |.||+|+....|+
T Consensus        44 --~----~~~~~~~~vGd~V~~kV~~vd~~~~i~LS~k~~~~~k~   82 (83)
T d2ba0a1          44 --N----KKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRICRPI   82 (83)
T ss_dssp             --T----SCGGGTCCTTCEEEEEEEEECTTCCEEEECCSSSCEEE
T ss_pred             --c----cChhhhcccccEEEEEEEEECCCCCEEEEecCCCCCCC
Confidence              1    3455689999999999999985   9999999877664

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.04  E-value=6.7e-11  Score=83.37  Aligned_cols=69  Identities=12%  Similarity=0.036  Sum_probs=55.3

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec--CCceEEE-Ecccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY--KKMDDVR-ITRQGFEKRVVSQDLQL  179 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~--~gi~Gl~-~s~~~~~~~~~~~~~~~  179 (234)
                      .++||.+.++|.++..                       +      |+||+|.  +|++||| +|+++++.         
T Consensus         9 p~~G~iv~G~V~~v~~-----------------------~------G~fV~l~~~~gi~Gli~~sels~~~---------   50 (84)
T d2ahob2           9 PSEGEILIATVKQVFD-----------------------Y------GSYVSLDEYGGLQAFLPWSEVSSKW---------   50 (84)
T ss_dssp             CCTTCCCEEEEEEEET-----------------------T------EEEEEETTTTTEEEEECGGGCC------------
T ss_pred             CCCCCEEEEEEEEEEC-----------------------C------EEEEEECCcCCEEEEEEcccccccc---------
Confidence            3589999999998864                       4      9999997  4899999 78885431         


Q ss_pred             ccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcc
Q 026737          180 WLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKR  217 (234)
Q Consensus       180 ~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~  217 (234)
                         .     .++...+++||+|+|+|+++|.    |.||+||
T Consensus        51 ---~-----~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2          51 ---V-----KNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             ----------CHHHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             ---c-----cccceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence               1     2456689999999999999986    9999996

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=98.99  E-value=3.9e-10  Score=80.11  Aligned_cols=63  Identities=11%  Similarity=0.064  Sum_probs=51.9

Q ss_pred             CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc------------chhhhhCCCCEEEEEEEEEeCCCC
Q 026737           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ------------DIRDILNEGDEVRVKVIKIDREKS  121 (234)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~------------~~~~~~~vGd~v~vkVl~id~~~~  121 (234)
                      |+.++|.     +||+||+|..    .+.+||||+|+|++++..            +....|++||.|+|+|+++|++++
T Consensus         4 ~~~F~g~Is~v~~~GifV~L~e----~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r   79 (87)
T d2ix0a3           4 DTRFAAEIVDISRGGMRVRLVD----NGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETR   79 (87)
T ss_dssp             CCCEEEEEEEEETTEEEEEETT----TCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTT
T ss_pred             CCEEEEEEEEEEcCeEEEEEec----CCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccC
Confidence            4556666     9999999962    379999999999987542            234569999999999999999999


Q ss_pred             eEEE
Q 026737          122 RITL  125 (234)
Q Consensus       122 ri~L  125 (234)
                      +|.+
T Consensus        80 ~I~~   83 (87)
T d2ix0a3          80 SIIA   83 (87)
T ss_dssp             EEEE
T ss_pred             eEEE
Confidence            9975

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.84  E-value=3.4e-09  Score=75.48  Aligned_cols=62  Identities=19%  Similarity=0.220  Sum_probs=53.5

Q ss_pred             CCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc----------cchhhhhCCCCEEEEEEEEEeCCCCe
Q 026737           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----------QDIRDILNEGDEVRVKVIKIDREKSR  122 (234)
Q Consensus        58 ~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~----------~~~~~~~~vGd~v~vkVl~id~~~~r  122 (234)
                      .|+++.|+     ++|+||+++      .++||||.+++.+++.          .+..+.|+.||.|++||++++.++++
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg------~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~   76 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVG------PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSS   76 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET------TEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEc------CeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccCc
Confidence            68999998     999999996      4899999999988765          23455699999999999999999999


Q ss_pred             EEE
Q 026737          123 ITL  125 (234)
Q Consensus       123 i~L  125 (234)
                      |..
T Consensus        77 i~~   79 (91)
T d1y14b1          77 IHA   79 (91)
T ss_dssp             EEE
T ss_pred             cEE
Confidence            865

>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=98.77  E-value=5.5e-09  Score=73.78  Aligned_cols=73  Identities=10%  Similarity=-0.081  Sum_probs=57.9

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      .++||.|.++|.++..                       +      |+||++.++++||+ +|+++++..          
T Consensus         5 Pk~Gdiv~G~V~~i~~-----------------------~------g~fV~i~~~~~gll~~s~~~~~~~----------   45 (87)
T d2je6i1           5 PKINDIVIGLVEDVEI-----------------------Y------GWVVDIKAPYKAYLPASNLLGRSI----------   45 (87)
T ss_dssp             CCTTCEEEEEEEEECS-----------------------S------EEEEECSSSSCEEEEHHHHHTSCC----------
T ss_pred             CCCCCEEEEEEEEEEC-----------------------C------EEEEEeCCCEEEEEehHHhCCcee----------
Confidence            3579999999998864                       4      99999999999999 788854321          


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhccc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRH  218 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~  218 (234)
                        ..  ..++...+++||.|.|+|+++|+   +.||+|+.
T Consensus        46 --~~--~~~~~~~~~~Gd~v~~kV~~vd~~~~i~LS~k~~   81 (87)
T d2je6i1          46 --NV--GEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGK   81 (87)
T ss_dssp             --CT--TCCCSSSCCTTCEEEEEEEEEETTEEEEEECCST
T ss_pred             --cc--ccccchhhcccceEEEEEEEECCCCCEEEEEecC
Confidence              11  12345589999999999999986   99999875

>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=98.74  E-value=3.8e-09  Score=79.05  Aligned_cols=76  Identities=12%  Similarity=-0.014  Sum_probs=60.1

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec-CCceEEE-Eccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY-KKMDDVR-ITRQGFEKRVVSQDLQLW  180 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~-~gi~Gl~-~s~~~~~~~~~~~~~~~~  180 (234)
                      +++|+.+.++|.++..                       +      |+||+|. ++++||| +++++++.+.        
T Consensus        19 l~~G~iv~G~V~~i~~-----------------------~------G~~V~lg~~~~~G~l~~~els~~~~~--------   61 (119)
T d1wi5a_          19 LKPGMLLTGTVSSLED-----------------------H------GYLVDIGVDGTRAFLPLLKAQEYIRQ--------   61 (119)
T ss_dssp             CCTTCEEEEEEEEECS-----------------------S------EEEEECCCSSCEEEEEHHHHHHHHHH--------
T ss_pred             cCCCCEEEEEEEEEec-----------------------c------EEEEEEeccccceEEeHHHhcccccc--------
Confidence            7899999999999864                       4      9999994 8999999 7877533211        


Q ss_pred             cccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccccc-chh
Q 026737          181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCN-EYW  223 (234)
Q Consensus       181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~-~p~  223 (234)
                              .++...+++||.|+|+|+++|+    |.||+|+..- .+|
T Consensus        62 --------~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~k~~~~~~~~  101 (119)
T d1wi5a_          62 --------KNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEVSTAI  101 (119)
T ss_dssp             --------HSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCCCSCCCC
T ss_pred             --------CCHHHhcccceEEEEEEEEEeCCCCEEEEEecHHHhhhhh
Confidence                    2234478999999999999986    9999998754 344

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.69  E-value=1.5e-08  Score=72.56  Aligned_cols=63  Identities=14%  Similarity=0.277  Sum_probs=53.5

Q ss_pred             CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc------------cchhhhhCCCCEEEEEEEEEeCC
Q 026737           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVKVIKIDRE  119 (234)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~------------~~~~~~~~vGd~v~vkVl~id~~  119 (234)
                      =.|+++.|+     ++|+||+++      ..+||||.+++.+++.            .+....|+.||.|++||++++.+
T Consensus         3 f~Gev~~g~V~~v~~~G~fv~lg------~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~   76 (94)
T d2c35b1           3 FKGEVVDAVVTQVNKVGLFTEIG------PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVD   76 (94)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEET------TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEE
T ss_pred             CCCCEEEEEEEEEEeeEEEEEec------CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecC
Confidence            468999998     999999996      4899999999998852            23345689999999999999999


Q ss_pred             CCeEEE
Q 026737          120 KSRITL  125 (234)
Q Consensus       120 ~~ri~L  125 (234)
                      .++|..
T Consensus        77 ~~~I~~   82 (94)
T d2c35b1          77 KNDIFA   82 (94)
T ss_dssp             TTEEEE
T ss_pred             cCcceE
Confidence            999864

>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=98.68  E-value=1.3e-08  Score=71.96  Aligned_cols=74  Identities=8%  Similarity=0.000  Sum_probs=58.2

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      .++||.|.++|.++..                       +      |+||+|.++++||+ +|+++++..          
T Consensus         5 Pk~GdvV~G~V~~v~~-----------------------~------g~fV~i~~~~~g~l~~se~~~~~~----------   45 (88)
T d2z0sa1           5 PQAGDVVIGLIQSVGI-----------------------M------NWFVDINSPYVAVLSVQDFLGRPF----------   45 (88)
T ss_dssp             CCTTCCEEEEEEEECS-----------------------S------EEEEECSSSSCEEEEHHHHHTSCC----------
T ss_pred             CCCCCEEEEEEEEEEC-----------------------C------eEEEEeCCCeEEEEehHHhCcccc----------
Confidence            3689999999999864                       4      99999999999999 788753321          


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhccc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRH  218 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~  218 (234)
                      ..   ...++...+++||.|.|+|+++|+   |.||+|+.
T Consensus        46 ~~---~~~~~~~~~~vGd~V~~kV~~vd~~~~i~Ls~k~~   82 (88)
T d2z0sa1          46 NP---AVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGE   82 (88)
T ss_dssp             CT---TTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSS
T ss_pred             cc---cccchhhhcccCcEEEEEEEEECCCCCEEEEEecC
Confidence            10   112455689999999999999986   99999874

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.51  E-value=2.8e-09  Score=70.82  Aligned_cols=49  Identities=12%  Similarity=-0.016  Sum_probs=26.0

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      ||||+|.+|++||| +|++++...        | ..+    .++++.+++||+|+|+|+++|+
T Consensus        10 G~FV~l~~g~~Glihiseis~~~~--------~-~~v----~~~~~~~~~G~~V~vkV~~iD~   59 (62)
T d1e3pa2          10 GAFVSLLPGKDGLLHISQIRKLAG--------G-KRV----ENVEDVLGVGQKVQVEIAEIDS   59 (62)
T ss_dssp             SCEECCC---CCCCC--------------------------------CCSSCBCCCCCCCCCS
T ss_pred             eEEEEecCCceEEEEHHHcccccc--------c-ccc----cCHHHhcCCCCEEEEEEEEEcC
Confidence            99999999999999 899964321        1 111    3567799999999999999984

>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=98.49  E-value=3.4e-08  Score=69.94  Aligned_cols=69  Identities=7%  Similarity=-0.067  Sum_probs=60.3

Q ss_pred             CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      .+++|++|.|+     .+|+||+|+     ++..|++|++++.+ ..++.+..+++||.|.|+|.+++. .+++.||..+
T Consensus         3 ~P~~GD~ViG~V~~~~~~~~~VdI~-----s~~~a~L~~~~f~g-~~k~~r~~l~~GD~V~arV~~v~~-~~~~~Lscvd   75 (88)
T d2nn6g1           3 VPVKGDHVIGIVTAKSGDIFKVDVG-----GSEPASLSYLSFEG-ATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCID   75 (88)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECS-----SSSCCCEESCSSSC-CSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECSB
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEcC-----CCeeEEEeHHHcCc-cccccCcccCCCCEEEEEEEEeCC-CCCEEEEEEc
Confidence            36899999999     889999997     46899999999964 577888899999999999999996 7899998765


Q ss_pred             c
Q 026737          130 L  130 (234)
Q Consensus       130 ~  130 (234)
                      .
T Consensus        76 ~   76 (88)
T d2nn6g1          76 S   76 (88)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=98.36  E-value=6.4e-08  Score=69.37  Aligned_cols=79  Identities=8%  Similarity=0.089  Sum_probs=56.3

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~  182 (234)
                      ++||.|.++|.++..                       +      |+||+|..+.+|++ +|+++++....       .+
T Consensus         7 ~vGdiV~G~V~~v~~-----------------------~------g~~V~I~~~~~g~l~is~i~~~~~~~-------rr   50 (95)
T d2nn6h1           7 EVGDIVVGRITEVQQ-----------------------K------RWKVETNSRLDSVLLLSSMNLPGGEL-------RR   50 (95)
T ss_dssp             CSSBCCCEEEEEEET-----------------------T------EEEEECSSSSCEEEESSCCC---------------
T ss_pred             CCCCEEEEEEEEEec-----------------------C------cEEEEeCCCceEEEEHHHcccccccc-------cc
Confidence            579999999988864                       3      89999999999999 89886532210       00


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhccc
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRH  218 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~  218 (234)
                      ..+....++...+++||.|.|+|++++.   |.||+|..
T Consensus        51 ~~~~~~~~~~~~~~~Gd~V~~kV~~v~~dg~i~Ls~r~~   89 (95)
T d2nn6h1          51 RSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSL   89 (95)
T ss_dssp             -----CHHHHHHSCSSCEECCEEEEEETTTEEEEECCSS
T ss_pred             ccchhhhhhhhhcccccEEEEEEEEECCCCCEEEEeccc
Confidence            0001113466789999999999999986   99998864

>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=4.2e-07  Score=64.41  Aligned_cols=68  Identities=15%  Similarity=0.125  Sum_probs=59.8

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      +++|++|.|+     ..+.||+|+     +...|++|.++......++.+..|++||.|.|+|.++++ .+.+.||.+.
T Consensus         5 P~~gD~ViG~V~~~~~~~~~vdI~-----~~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~-~~~~~Lsc~~   77 (90)
T d2ja9a1           5 PSVNDFVIGVIIGTFSDSYKVSLQ-----NFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEK-ELEAEIECFD   77 (90)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEESS-----TTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEESSC
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEcC-----CcchhhhhhhhccCccccccCCccCCCCEEEEEEEEECC-CCCEEEEEec
Confidence            6899999999     779999997     358899998887777888889999999999999999996 7889998754

>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=97.96  E-value=1.5e-05  Score=55.78  Aligned_cols=57  Identities=2%  Similarity=-0.232  Sum_probs=38.6

Q ss_pred             ceeeeecC-CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          149 PYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       149 G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      |+||+|.+ +++||+ +|.+.++...-...-+. +..    ..+....++.||+|+|+|+++|.
T Consensus        18 GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~-l~~----~~~~~~~~~~Gd~V~V~v~~vd~   76 (87)
T d2ix0a3          18 GMRVRLVDNGAIAFIPAPFLHAVRDELVCSQEN-GTV----QIKGETVYKVTDVIDVTIAEVRM   76 (87)
T ss_dssp             EEEEEETTTCCEEEEEGGGTCSCGGGEEEETTT-TEE----EETTEEEEETTCEEEEEEEEEET
T ss_pred             eEEEEEecCCcEEEEEehhCCCceEEEeccceE-EEE----EEcccEEEECCCEEEEEEEEEec
Confidence            99999965 899999 89997665421100000 000    02234579999999999999996

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.86  E-value=1.9e-05  Score=58.85  Aligned_cols=74  Identities=20%  Similarity=0.232  Sum_probs=57.3

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCC---cceeEEEEEceeccc--ccccchhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSW--DLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g---~~g~~glv~isels~--~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~L  125 (234)
                      +++|++|.|+     ...++|+|...+|   ...+.|++|.+++..  ....++.+.|++||.|+|+|+++...+..+.|
T Consensus         5 P~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~~~L   84 (125)
T d2nn6i1           5 PDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLL   84 (125)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCccEEE
Confidence            5789999998     7778999853222   114679999998843  34457889999999999999999875567888


Q ss_pred             EEee
Q 026737          126 SIKQ  129 (234)
Q Consensus       126 S~K~  129 (234)
                      |.++
T Consensus        85 st~~   88 (125)
T d2nn6i1          85 TTAE   88 (125)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            8865

>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=97.84  E-value=3.1e-05  Score=52.18  Aligned_cols=59  Identities=19%  Similarity=0.157  Sum_probs=48.1

Q ss_pred             CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCC--eEEEE
Q 026737           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLS  126 (234)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~--ri~LS  126 (234)
                      -++|+++.|+     +..++|+|+      +.+|++|.+|..      |.+.|++||.|+|-|.+++...+  +|.||
T Consensus         6 ~~~geiv~G~V~r~~~~~~~Vdlg------~~eaiLp~~eqi------p~E~~~~Gdrik~~i~~V~~~~kgpqI~lS   71 (72)
T d1hh2p1           6 ELKGTVTTAEVIRVMGEWADIRIG------KLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVS   71 (72)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEET------TEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             hccCcEEEEEEEEEcCCCEEEEEC------CcEEECCHHHcC------CCCCCCCCCEEEEEEEEEEEcCCCCeEEEe
Confidence            4789999999     667899997      699999998865      66889999999999999986443  45554

>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=97.64  E-value=9.6e-05  Score=51.56  Aligned_cols=69  Identities=6%  Similarity=-0.128  Sum_probs=47.4

Q ss_pred             CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccccc
Q 026737          105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSN  183 (234)
Q Consensus       105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~  183 (234)
                      +|+.+.++|.++.+                       +      |+||++. .++||+ ++++..+ ..-.++-..|.-.
T Consensus         3 ~Gev~~g~I~~v~~-----------------------~------G~fv~lg-~~eg~i~~~~l~~~-~~~d~~~~~~~~~   51 (91)
T d1y14b1           3 KGEVVDGTVVSCSQ-----------------------H------GFEVQVG-PMKVFVTKHLMPQD-LTFNAGSNPPSYQ   51 (91)
T ss_dssp             TTCEEEEEEEEEET-----------------------T------EEEEEET-TEEEEEEGGGSCTT-CEECC-----CEE
T ss_pred             CCCEEEEEEEEEEe-----------------------e------EEEEEEc-CeEEEEEhhhcCcc-eEEccccceeEec
Confidence            58999999998875                       4      9999995 689999 7777544 3211111122221


Q ss_pred             CCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          184 APPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       184 ~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                            +-...++.||.|+++|++++.
T Consensus        52 ------~~~~~~~~Gd~VrvkV~~v~~   72 (91)
T d1y14b1          52 ------SSEDVITIKSRIRVKIEGCIS   72 (91)
T ss_dssp             ------CSSCEECTTCEEEEEEEEEEE
T ss_pred             ------ccCeEEeCCCEEEEEEEEEec
Confidence                  123479999999999999985

>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=97.40  E-value=0.00033  Score=49.05  Aligned_cols=70  Identities=9%  Similarity=0.078  Sum_probs=50.1

Q ss_pred             CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccc-ccccccccccc
Q 026737          105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKR-VVSQDLQLWLS  182 (234)
Q Consensus       105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~-~~~~~~~~~~~  182 (234)
                      +|+.+.++|.++++                       +      |+||++. .++||+ ++.+..+-. ...+....|..
T Consensus         4 ~Gev~~g~V~~v~~-----------------------~------G~fv~lg-~~~~~v~~~~l~~d~~y~~~~~~~~~~~   53 (94)
T d2c35b1           4 KGEVVDAVVTQVNK-----------------------V------GLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKT   53 (94)
T ss_dssp             TTCEEEEEEEEEET-----------------------T------EEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEE
T ss_pred             CCCEEEEEEEEEEe-----------------------e------EEEEEec-CceEEEEhhhcCcceeecccccceEEEc
Confidence            58999999999875                       4      9999995 689999 777765532 22222223432


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      .      +-...++.||.|+++|+.++.
T Consensus        54 ~------~~~~~~~~Gd~VrvkV~~v~~   75 (94)
T d2c35b1          54 M------DEDIVIQQDDEIRLKIVGTRV   75 (94)
T ss_dssp             T------TSCSEEETTCEEEEEEEEEEE
T ss_pred             c------cceEEEeCCCEEEEEEEEEec
Confidence            2      223478999999999999875

>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=97.20  E-value=0.00058  Score=46.15  Aligned_cols=62  Identities=19%  Similarity=0.266  Sum_probs=46.4

Q ss_pred             CCCcEEEEE----Ee-----eEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCC--CeEEE
Q 026737           57 NVEDIFVGR----DY-----GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITL  125 (234)
Q Consensus        57 ~~G~iv~g~----~~-----G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~--~ri~L  125 (234)
                      ++|+++.|+    +.     -++|+|+...  .+.+|++|.+|.-      |.+.|++||.|+|.|.+++...  -+|.|
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~--~~~EaiLp~~eqi------p~E~y~~Gdrik~~i~~V~~~~kGp~Iil   74 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTET--KASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITL   74 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSS--SCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEE
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCC--CCEEEECCHHHcC------CCcccCCCCEEEEEEEEEEecCCCCEEEE
Confidence            679999999    22     2799996211  2599999988754      6678999999999999998643  34444


Q ss_pred             E
Q 026737          126 S  126 (234)
Q Consensus       126 S  126 (234)
                      |
T Consensus        75 S   75 (76)
T d2asba1          75 S   75 (76)
T ss_dssp             E
T ss_pred             e
Confidence            4

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.53  E-value=0.0017  Score=44.90  Aligned_cols=68  Identities=9%  Similarity=-0.128  Sum_probs=51.0

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      .++||.|-++|.++..                       .      ++||++.....|++ +|++.  .+         .
T Consensus         4 P~~GD~ViG~V~~~~~-----------------------~------~~~VdI~s~~~a~L~~~~f~--g~---------~   43 (88)
T d2nn6g1           4 PVKGDHVIGIVTAKSG-----------------------D------IFKVDVGGSEPASLSYLSFE--GA---------T   43 (88)
T ss_dssp             CCSSEEEEEEEEEEET-----------------------T------EEEEECSSSSCCCEESCSSS--CC---------S
T ss_pred             CCCCCEEEEEEEEEeC-----------------------C------eEEEEcCCCeeEEEeHHHcC--cc---------c
Confidence            4679999999988753                       2      78999999999998 67651  11         1


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKR  217 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~  217 (234)
                             .+....+++||.|-|+|.++++   +.|+...
T Consensus        44 -------k~~r~~l~~GD~V~arV~~v~~~~~~~Lscvd   75 (88)
T d2nn6g1          44 -------KRNRPNVQVGDLIYGQFVVANKDMEPEMVCID   75 (88)
T ss_dssp             -------SCSSSSSCTTCEEEEEEEECCTTSCCEEECSB
T ss_pred             -------cccCcccCCCCEEEEEEEEeCCCCCEEEEEEc
Confidence                   1223468999999999999987   7776654

>d1luza_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Vaccinia virus [TaxId: 10245]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Vaccinia virus [TaxId: 10245]

Probab=96.45  E-value=0.0083  Score=40.35  Aligned_cols=73  Identities=33%  Similarity=0.458  Sum_probs=56.8

Q ss_pred             CCCCCcEEEEE----EeeEEEEEecCCCcceeEEEEEce-ecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737           55 RVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (234)
Q Consensus        55 ~~~~G~iv~g~----~~G~fV~l~~~~g~~g~~glv~is-els~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~  129 (234)
                      -+.+|++.+|.    ++-.+|.|.+.   +|.+|++--+ ++..++..+.++.+ +|.+|+++|+.+|.-+|.|.++.|.
T Consensus         5 lPnigdVtkGiVy~kd~~fyV~L~dY---~g~ea~l~dy~~~~~d~~~klk~kL-VGKtIkvqVIR~d~lKGYIDVr~~~   80 (85)
T d1luza_           5 LPNAGDVIKGRVYEKDYALYIYLFDY---PHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKR   80 (85)
T ss_dssp             CCCTTCEEEEEEEEETTEEEEEETTC---TTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEE
T ss_pred             cCCCCceeeeEEEEeCCEEEEEecCC---CCceEEeeehhhhhhHHHHHHHHHh-cCceEEEEEEEEcceeeEEEehhhh
Confidence            46899999999    55568899743   2688887533 44445666777776 7999999999999999999999987


Q ss_pred             cc
Q 026737          130 LE  131 (234)
Q Consensus       130 ~~  131 (234)
                      ..
T Consensus        81 ~~   82 (85)
T d1luza_          81 MC   82 (85)
T ss_dssp             EC
T ss_pred             hh
Confidence            54

>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=96.24  E-value=0.0065  Score=42.01  Aligned_cols=69  Identities=16%  Similarity=0.005  Sum_probs=49.4

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEEEccccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~~s~~~~~~~~~~~~~~~~~~  182 (234)
                      .++||.|-++|.++..                       .      +.||+|.....|++++.+..+...          
T Consensus         5 P~~gD~ViG~V~~~~~-----------------------~------~~~vdI~~~~~~~L~~~~~f~g~~----------   45 (90)
T d2ja9a1           5 PSVNDFVIGVIIGTFS-----------------------D------SYKVSLQNFSSSVSLSYMAFPNAS----------   45 (90)
T ss_dssp             CCTTCEEEEEEEEECS-----------------------S------EEEEESSTTSCCEEEETTSSTTCC----------
T ss_pred             CCCCCEEEEEEEEEeC-----------------------C------cEEEEcCCcchhhhhhhhccCccc----------
Confidence            3679999999988753                       2      779999888898874333222221          


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhc
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASK  216 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K  216 (234)
                            .+....+++||.|-|+|.++++   +.|+++
T Consensus        46 ------k~~r~~l~~GDlV~arV~~v~~~~~~~Lsc~   76 (90)
T d2ja9a1          46 ------KKNRPTLQVGDLVYARVCTAEKELEAEIECF   76 (90)
T ss_dssp             ------SSSCCCCCTTCEEEEEEEECCTTSCCEEESS
T ss_pred             ------cccCCccCCCCEEEEEEEEECCCCCEEEEEe
Confidence                  2233468999999999999986   777664

>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=95.83  E-value=0.0066  Score=41.74  Aligned_cols=44  Identities=30%  Similarity=0.534  Sum_probs=35.9

Q ss_pred             eEEEEEecCCCcceeEEEEEceecccccc---------cchhhhhCCCCEEEEEEEEE
Q 026737           68 GAFIHLRFPDGLYHLTGLVHVSEVSWDLI---------QDIRDILNEGDEVRVKVIKI  116 (234)
Q Consensus        68 G~fV~l~~~~g~~g~~glv~isels~~~~---------~~~~~~~~vGd~v~vkVl~i  116 (234)
                      ++||+++     .+-.||+|++++...+.         .+..+.+++||.+-|.|.+=
T Consensus        17 AAFVDiG-----~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke   69 (87)
T d1smxa_          17 AAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE   69 (87)
T ss_dssp             EEEEESS-----SSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEEC
T ss_pred             EEEEEeC-----CCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeec
Confidence            6899997     36899999999887654         24567799999999999764

>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=95.73  E-value=0.02  Score=37.77  Aligned_cols=54  Identities=13%  Similarity=-0.062  Sum_probs=41.3

Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEEE-ccccccccccccccccccc
Q 026737          104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRI-TRQGFEKRVVSQDLQLWLS  182 (234)
Q Consensus       104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~~-s~~~~~~~~~~~~~~~~~~  182 (234)
                      +.|+.|.+.|..++.                       .      .++|+|. +.+|+++ +++                
T Consensus         7 ~~geiv~G~V~r~~~-----------------------~------~~~Vdlg-~~eaiLp~~eq----------------   40 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMG-----------------------E------WADIRIG-KLETRLPKKEW----------------   40 (72)
T ss_dssp             CTTCEEEEEEEEECS-----------------------S------EEEEEET-TEEEEEEGGGS----------------
T ss_pred             ccCcEEEEEEEEEcC-----------------------C------CEEEEEC-CcEEECCHHHc----------------
Confidence            478999999988764                       1      5688985 8999994 443                


Q ss_pred             cCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          183 NAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                             -+.+.++.||+|+|.|.++++
T Consensus        41 -------ip~E~~~~Gdrik~~i~~V~~   61 (72)
T d1hh2p1          41 -------IPGEEIKAGDLVKVYIIDVVK   61 (72)
T ss_dssp             -------CTTCCCCTTCEEEEEEEEEEE
T ss_pred             -------CCCCCCCCCCEEEEEEEEEEE
Confidence                   124478999999999999975

>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=94.23  E-value=0.06  Score=39.11  Aligned_cols=78  Identities=13%  Similarity=-0.000  Sum_probs=46.9

Q ss_pred             hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL  181 (234)
Q Consensus       103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~  181 (234)
                      .++||.|.++|.++..  .+..+.+-.....                   .+...+.|++ .++.+...           
T Consensus         5 P~vGDiVig~V~~v~~--~~a~v~I~~v~~~-------------------~l~~~~~g~i~~~dvr~te-----------   52 (125)
T d2nn6i1           5 PDVGAIVTCKVSSINS--RFAKVHILYVGSM-------------------PLKNSFRGTIRKEDVRATE-----------   52 (125)
T ss_dssp             CCTTCEEEEEEEEECS--SEEEEEEEESSSS-------------------CCCCSSCSCEEEEGGGTCS-----------
T ss_pred             CCCCCEEEEEEEEecC--CEEEEEEeEecCc-------------------ccccCccccccHHHcccch-----------
Confidence            4689999999999964  3333433222111                   1223566777 44332111           


Q ss_pred             ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737          182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK  216 (234)
Q Consensus       182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K  216 (234)
                        .+  ..++.+.|++||-|+|+|+++..    +.||.+
T Consensus        53 --~d--~~~m~~~fr~GDiV~A~Vis~~~~~~~~~Lst~   87 (125)
T d2nn6i1          53 --KD--KVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTA   87 (125)
T ss_dssp             --SC--CCCGGGTCCSSSEEEEEEEEEETTTTEEEEECC
T ss_pred             --hh--hhhHHHhcCCCCEEEEEEEEccCCCccEEEEec
Confidence              11  13466799999999999999853    445544

>d1jjga_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Myxoma virus, m156r [TaxId: 10273]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Myxoma virus, m156r [TaxId: 10273]

Probab=94.18  E-value=0.045  Score=37.58  Aligned_cols=62  Identities=13%  Similarity=0.116  Sum_probs=47.2

Q ss_pred             hcCCCCCcEEEEE----EeeEEEEEecCCCcceeEEEEE-ceecccccccchhhhhCCCCEEEEEEEEEeC
Q 026737           53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDR  118 (234)
Q Consensus        53 ~~~~~~G~iv~g~----~~G~fV~l~~~~g~~g~~glv~-isels~~~~~~~~~~~~vGd~v~vkVl~id~  118 (234)
                      .-++.+|++.+|.    ++-.+|.|.+.   +|.+|++- .-++-.++..+.++.+ +|.+|+++|+.+|.
T Consensus        27 ~~~~~~G~V~kGiVy~rd~~fyV~L~dY---~g~eail~dY~n~~~dr~~klkkkL-VGKTIkVqVIRvDk   93 (102)
T d1jjga_          27 AMDLSPGSVHEGIVYFKDGIFKVRLLGY---EGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG   93 (102)
T ss_dssp             CCCCCSSCEEEEEEEEETTEEEEECTTT---SSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS
T ss_pred             ecccCCCcEeeeEEEEeCCEEEEEecCC---CCceeeeeehhhhhHHHHHHHHHHh-cCceEEEEEEEecc
Confidence            3468999999999    55568898743   26888853 3355556677777777 79999999999983

>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=90.24  E-value=0.16  Score=33.54  Aligned_cols=38  Identities=11%  Similarity=-0.050  Sum_probs=29.3

Q ss_pred             eeeeec---CCceEEEE-ccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737          150 YLKSFY---KKMDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL  210 (234)
Q Consensus       150 ~fV~l~---~gi~Gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~  210 (234)
                      ++|+|.   ++++|+++ +++                       -+.+.++.||+|+|.|.+++.
T Consensus        24 v~vdlG~~~~~~EaiLp~~eq-----------------------ip~E~y~~Gdrik~~i~~V~~   65 (76)
T d2asba1          24 VVVRIGTETKASEGVIPAAEQ-----------------------VPGESYEHGNRLRCYVVGVTR   65 (76)
T ss_dssp             EEEEECSSSSCEEEEECGGGS-----------------------CTTCCCCTTCEEEEEEEEEEC
T ss_pred             EEEECCCCCCCEEEECCHHHc-----------------------CCCcccCCCCEEEEEEEEEEe
Confidence            588885   58999994 432                       134478999999999999975

>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=87.98  E-value=0.38  Score=32.39  Aligned_cols=52  Identities=8%  Similarity=-0.027  Sum_probs=35.1

Q ss_pred             ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeee
Q 026737          149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSH  208 (234)
Q Consensus       149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~  208 (234)
                      +|||++..+-.|++ .+++..+...        .........+++..+++||.+-|.|.+=
T Consensus        17 AAFVDiG~~k~gFL~~~di~~~~~~--------~~~~~~~~~~i~~~l~~G~~ilVQV~Ke   69 (87)
T d1smxa_          17 AAFVDYGAERHGFLPLKEIAREYFP--------ANYSAHGRPNIKDVLREGQEVIVQIDKE   69 (87)
T ss_dssp             EEEEESSSSSCEEEEGGGSCGGGCS--------SCCCSSSCCCGGGTCCTTCEEEEEEEEC
T ss_pred             EEEEEeCCCccceeEecccceeeec--------cccccccccchhhhccCCCeEEEEEeec
Confidence            89999999999999 5665322111        0011112256778999999998888764

>d1k3ra1 b.40.4.10 (A:93-163) Hypothetical protein MTH1 (MT0001), insert domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Hypothetical protein MTH1 (MT0001), insert domain
domain: Hypothetical protein MTH1 (MT0001), insert domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=83.66  E-value=0.54  Score=30.27  Aligned_cols=45  Identities=13%  Similarity=0.226  Sum_probs=35.6

Q ss_pred             cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEE
Q 026737           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI  116 (234)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~i  116 (234)
                      ..+++|++-+|.     ..|+||+++       ++-+..+..           .|++|+.+.++|.++
T Consensus         6 g~p~vGEiReG~~~rr~~~g~~vDiG-------lD~la~~k~-----------~~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           6 GKPVTGEYRQGLTVKRVKKGTLVDIG-------ADKLALCRE-----------KLTVNRIMSFRVVRL   55 (71)
T ss_dssp             SSCCTTCEEEEEEEEECSSSEEEESS-------SSCEEECSS-----------CCCSSCEEEEEEEEC
T ss_pred             CCCcccceeeEEEEEecCCcEEEEec-------CCceeeeec-----------ccccCcEEEEEEEEc
Confidence            457899999998     778999995       555555432           377899999999997