Citrus Sinensis ID: 030172

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180--
Protein Sequence
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDG
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEEEEEEEEccccEEEEEcHHHHHHHHHcccccccEEEcEEccEEEEEcccccccccEEEEEEcccccccccccHHHcccccEEEEEEEEEEccccEEEEEccccccccHHHHHHHHccccccEEEEEEEEEcccccEEEEcccHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccEEEEccEEEEEEEEEccccccEEEEHHHHHHHHHHHHcccccEEEcccEEEEEEEccccccccEEEEEEcccccccccccccHEEEcccEEEEEEEEEcccccEEEEEEHcccccHHHHHHHHHcccccEEEEEEEEEccccEEEEEccccccHHHHHHHcccc
Coil and Loop (DISEMBL)
mspshsckepqKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWnkyssrvnvedifvgrdygafihlrfpdglyhlTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKqleedplletlekvipqdgsvisdsssmsssnsntieplpgLGAIFEELLQEDG
Flexible Loop (DISEMBL)
mspshsckepQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDilnegdevrvkvikidreksritlsikqleedplleTLEKVIPQDgsvisdsssmsssnsntieplpgLGAIFEELLQEDG
Low Complexity Region (SEG)
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGsvisdsssmsssnsNTIEPLPGLGAIFEELLQEDG
Disordered region (IsUnstruct)
***************EIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL****************************************************
Disordered Region (DISOPRED)
*SPS***KEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL*****
Disordered Region (DISEMBL)
***********KSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGS**************TIEPLPGLGAIFEELLQEDG
Disordered Region (DISPRO)
************SIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDG
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	182	2.2.26 [Sep-21-2011]
P73530	328	30S ribosomal protein S1	N/A	no	0.637	0.353	0.338	1e-12
Q89AJ3	566	30S ribosomal protein S1	yes	no	0.631	0.203	0.323	2e-12
Q83E09	551	30S ribosomal protein S1	yes	no	0.467	0.154	0.391	1e-11
P37985	557	30S ribosomal protein S1	yes	no	0.346	0.113	0.463	1e-11
P29344	411	30S ribosomal protein S1,	N/A	no	0.758	0.335	0.276	1e-11
P0AG70	557	30S ribosomal protein S1	yes	no	0.346	0.113	0.463	2e-11
P14128	378	30S ribosomal protein S1	N/A	no	0.346	0.166	0.463	2e-11
P0AG67	557	30S ribosomal protein S1	N/A	no	0.346	0.113	0.463	2e-11
P0AG68	557	30S ribosomal protein S1	yes	no	0.346	0.113	0.463	2e-11
P0AG69	557	30S ribosomal protein S1	N/A	no	0.346	0.113	0.463	2e-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 = 72.4 bits (176), 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 = 2e-12,   Method: Compositional matrix adjust.
 Identities = 43/133 (32%), Positives = 76/133 (57%), Gaps = 18/133 (13%)

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 QLEEDPLLETLEK 141
           QL +DP  +  E+
Sbjct: 261 QLSDDPWTKISER 273

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

 Score = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 58/92 (63%), Gaps = 7/92 (7%)

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 SIKQLEEDPLLETLEKVIPQDGSVISDSSSMS 157
            +KQL +DP  + +E+  P +  V    ++++
Sbjct: 254 GMKQLADDPWAK-IERRYPVNSRVFGKVTNIT 284

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)

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

 Score = 69.3 bits (168), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 48/69 (69%), Gaps = 6/69 (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 SIKQLEEDP 134
            +KQL EDP
Sbjct: 258 GLKQLGEDP 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.

Dickeya dadantii (strain 3937) (taxid: 198628)

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

 Score = 69.3 bits (168), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 44/159 (27%), Positives = 83/159 (52%), Gaps = 21/159 (13%)

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

Query: 81  HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP------ 134
            + GL+HVS++S D + DI  +L  GD ++V ++  DRE+ R++LS K+LE  P      
Sbjct: 282 GINGLLHVSQISHDRVSDIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRN 341

Query: 135 ---LLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGL 170
              + E  E++       I+ + +M+ ++    +P  GL
Sbjct: 342 PKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGL 380

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

 Score = 68.9 bits (167), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 48/69 (69%), Gaps = 6/69 (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 SIKQLEEDP 134
            +KQL EDP
Sbjct: 258 GLKQLGEDP 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.

Shigella flexneri (taxid: 623)

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

 Score = 68.9 bits (167), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 48/69 (69%), Gaps = 6/69 (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 SIKQLEEDP 134
            +KQL EDP
Sbjct: 153 GLKQLGEDP 161

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

 Score = 68.9 bits (167), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 48/69 (69%), Gaps = 6/69 (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 SIKQLEEDP 134
            +KQL EDP
Sbjct: 258 GLKQLGEDP 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.

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 = 68.9 bits (167), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 48/69 (69%), Gaps = 6/69 (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 SIKQLEEDP 134
            +KQL EDP
Sbjct: 258 GLKQLGEDP 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.

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 = 68.9 bits (167), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 48/69 (69%), Gaps = 6/69 (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 SIKQLEEDP 134
            +KQL EDP
Sbjct: 258 GLKQLGEDP 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.

Escherichia coli O157:H7 (taxid: 83334)

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	182
225433644	390	PREDICTED: 30S ribosomal protein S1 homo	0.989	0.461	0.737	6e-73
224131510	299	predicted protein [Populus trichocarpa]	0.989	0.602	0.734	1e-70
356569689	378	PREDICTED: 40S ribosomal protein S1-like	0.989	0.476	0.716	1e-68
356538073	383	PREDICTED: 30S ribosomal protein S1 homo	0.989	0.469	0.711	1e-67
147802809	418	hypothetical protein VITISV_006784 [Viti	0.989	0.430	0.641	4e-67
18403854	392	ribosomal protein S1-like RNA-binding do	0.989	0.459	0.700	4e-64
297835412	392	S1 RNA-binding domain-containing protein	0.989	0.459	0.700	1e-63
449484641	379	PREDICTED: 30S ribosomal protein S1-like	0.989	0.474	0.663	1e-62
449468800	378	PREDICTED: 30S ribosomal protein S1-like	0.989	0.476	0.657	4e-62
357462911	399	Polyribonucleotide nucleotidyltransferas	0.989	0.451	0.652	7e-59

>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 =  278 bits (711), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 138/187 (73%), Positives = 161/187 (86%), Gaps = 7/187 (3%)

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 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           +DR KSRITLSIKQLEEDPLLETL+KVIPQDGS   D  S+ +S+S  IEPLPGL  IFE
Sbjct: 256 VDRVKSRITLSIKQLEEDPLLETLDKVIPQDGSTGPD--SLRTSDSYDIEPLPGLETIFE 313

Query: 176 ELLQEDG 182
           ELLQE+G
Sbjct: 314 ELLQEEG 320

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 =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 138/188 (73%), Positives = 159/188 (84%), Gaps = 8/188 (4%)

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 KIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIF 174
            ID+ KSRITLSIKQLEEDPLLETL+KVIPQDGS+  D  SM   NS TIEPLPGL +IF
Sbjct: 164 DIDQGKSRITLSIKQLEEDPLLETLDKVIPQDGSIAPDPLSM--HNSITIEPLPGLESIF 221

Query: 175 EELLQEDG 182
           +EL +EDG
Sbjct: 222 QELTREDG 229

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  263 bits (673), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 134/187 (71%), Positives = 154/187 (82%), Gaps = 7/187 (3%)

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  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           IF  R     DYGAF+HLRFPDGLYHLTGL+HVSEVSWDLIQD+RDIL  GDEVR KV+ 
Sbjct: 184 IFEVRVGYVEDYGAFVHLRFPDGLYHLTGLIHVSEVSWDLIQDVRDILKVGDEVRAKVVG 243

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           ID  KSRI LSI+QLEEDPLLETL+KVIPQDGS  +D  SMS  +S +IEPLPGL  I E
Sbjct: 244 IDWGKSRINLSIRQLEEDPLLETLDKVIPQDGS--ADPDSMSGGDSGSIEPLPGLETILE 301

Query: 176 ELLQEDG 182
           ELLQEDG
Sbjct: 302 ELLQEDG 308

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  260 bits (665), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 133/187 (71%), Positives = 154/187 (82%), Gaps = 7/187 (3%)

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 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           ID  KSRI LSI+QLEEDPLLETL+KVIPQDGS  +D  SMS  +S +IEPLPGL  I E
Sbjct: 249 IDWGKSRINLSIRQLEEDPLLETLDKVIPQDGS--ADPDSMSGGDSGSIEPLPGLETILE 306

Query: 176 ELLQEDG 182
           ELLQEDG
Sbjct: 307 ELLQEDG 313

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  259 bits (662), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 138/215 (64%), Positives = 161/215 (74%), Gaps = 35/215 (16%)

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 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP------------------QDG 147
           GDEVRVK++K+DR KSRITLSIKQLEEDPLLETL+KVIP                  QDG
Sbjct: 256 GDEVRVKIVKVDRVKSRITLSIKQLEEDPLLETLDKVIPQIIFLLHRTKSSDVSHLLQDG 315

Query: 148 SVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDG 182
           S   D  S+ +S+S  IEPLPGL  IFEELLQE+G
Sbjct: 316 STGPD--SLRTSDSYDIEPLPGLETIFEELLQEEG 348

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  249 bits (635), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 131/187 (70%), Positives = 152/187 (81%), Gaps = 7/187 (3%)

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 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           ID+EKSRITLSIKQLE+DPLLETL+KVI +D    + S S+SS+N +TIEPLPGL  I E
Sbjct: 258 IDKEKSRITLSIKQLEDDPLLETLDKVILKD--SSTGSPSLSSNNGDTIEPLPGLETILE 315

Query: 176 ELLQEDG 182
           ELL+EDG
Sbjct: 316 ELLKEDG 322

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 =  247 bits (631), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 131/187 (70%), Positives = 152/187 (81%), Gaps = 7/187 (3%)

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 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           ID+EKSRITLSIKQLE+DPLLETL+KVI +D    S S S+SS+N +TIEPLPGL  I E
Sbjct: 258 IDKEKSRITLSIKQLEDDPLLETLDKVILKD--SSSGSPSLSSNNGDTIEPLPGLETILE 315

Query: 176 ELLQEDG 182
           ELL+EDG
Sbjct: 316 ELLKEDG 322

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 124/187 (66%), Positives = 149/187 (79%), Gaps = 7/187 (3%)

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 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           +++ KSRITLSI+QLEEDPLLETL+KVIPQD S   D  S      + I PLPGL  I E
Sbjct: 245 VNKNKSRITLSIRQLEEDPLLETLDKVIPQDSSAEPD--SFGPKGDSEIIPLPGLETIIE 302

Query: 176 ELLQEDG 182
           ELLQE+G
Sbjct: 303 ELLQEEG 309

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 =  242 bits (618), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 123/187 (65%), Positives = 149/187 (79%), Gaps = 7/187 (3%)

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 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           +++ KSRITLSI+QLEEDPLLETL+KVIPQ+ S   D  S      + I PLPGL  I E
Sbjct: 244 VNKNKSRITLSIRQLEEDPLLETLDKVIPQESSAEPD--SFGPKGDSEIIPLPGLETIIE 301

Query: 176 ELLQEDG 182
           ELLQE+G
Sbjct: 302 ELLQEEG 308

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  231 bits (590), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 122/187 (65%), Positives = 150/187 (80%), Gaps = 7/187 (3%)

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 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           ID  K R+TLSIKQLEEDPLLETL+KVI QDGS +   +S+SS+ S+ I+PLPGL  I E
Sbjct: 265 IDTVKMRLTLSIKQLEEDPLLETLDKVIRQDGSGV--PNSISSTTSSPIDPLPGLDTILE 322

Query: 176 ELLQEDG 182
           ELLQEDG
Sbjct: 323 ELLQEDG 329

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	182
TAIR|locus:2095203	392	AT3G23700 [Arabidopsis thalian	0.989	0.459	0.673	2.4e-60
TIGR_CMR|SO_2402	555	SO_2402 "ribosomal protein S1"	0.532	0.174	0.390	5.8e-13
TAIR|locus:2145860	416	RPS1 "ribosomal protein S1" [A	0.642	0.281	0.333	3.1e-12
UNIPROTKB|P0AG67	557	rpsA "30S ribosomal subunit pr	0.648	0.211	0.328	5.4e-12
TIGR_CMR|NSE_0408	553	NSE_0408 "ribosomal protein S1	0.587	0.193	0.348	6.9e-12
TIGR_CMR|CBU_0528	551	CBU_0528 "ribosomal protein S1	0.395	0.130	0.443	1.1e-11
TIGR_CMR|CPS_2335	553	CPS_2335 "ribosomal protein S1	0.593	0.195	0.341	1.1e-11
TIGR_CMR|ECH_0402	567	ECH_0402 "putative ribosomal p	0.593	0.190	0.339	1.9e-11
UNIPROTKB|Q9KQT3	556	VC_1915 "30S ribosomal protein	0.521	0.170	0.359	4e-11
TIGR_CMR|VC_1915	556	VC_1915 "ribosomal protein S1"	0.521	0.170	0.359	4e-11

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

 Score = 618 (222.6 bits), Expect = 2.4e-60, P = 2.4e-60
 Identities = 126/187 (67%), Positives = 144/187 (77%)

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 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGXXXXXXXXXXXXXXNTIEPLPGLGAIFE 175
             ID+EKSRITLSIKQLE+DPLLETL+KVI +D               +TIEPLPGL  I E
Sbjct:   258 IDKEKSRITLSIKQLEDDPLLETLDKVILKDSSTGSPSLSSNNG--DTIEPLPGLETILE 315

Query:   176 ELLQEDG 182
             ELL+EDG
Sbjct:   316 ELLKEDG 322

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

 Score = 180 (68.4 bits), Expect = 5.8e-13, P = 5.8e-13
 Identities = 41/105 (39%), Positives = 64/105 (60%)

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

Query:   102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQD 146
             I+N GDE+ VKV+K DRE++R++L +KQL EDP LE + K  P++
Sbjct:   234 IVNVGDEINVKVLKYDRERTRVSLGLKQLGEDPWLE-ISKRYPEN 277

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

GO:0006412 "translation" evidence=ISS

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

 Score = 171 (65.3 bits), Expect = 3.1e-12, P = 3.1e-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

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

 Score = 171 (65.3 bits), Expect = 5.4e-12, P = 5.4e-12
 Identities = 45/137 (32%), Positives = 74/137 (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 QLEEDPLLETLEKVIPQ 145
             QL EDP +  + K  P+
Sbjct:   261 QLGEDPWV-AIAKRYPE 276

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

 Score = 170 (64.9 bits), Expect = 6.9e-12, P = 6.9e-12
 Identities = 39/112 (34%), Positives = 63/112 (56%)

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

Query:    93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP 144
             W  +     I + G EVRVKVI +D EK RI+L +KQL E+P  +  +K  P
Sbjct:   255 WARVTHPSSIYSVGQEVRVKVIAVDPEKGRISLGVKQLTENPWKDVSKKYTP 306

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

TIGR_CMR|CBU_0528 CBU_0528 "ribosomal protein S1" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 168 (64.2 bits), Expect = 1.1e-11, P = 1.1e-11
 Identities = 35/79 (44%), Positives = 52/79 (65%)

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 SIKQLEEDPLLETLEKVIP 144
              +KQL +DP  + +E+  P
Sbjct:   254 GMKQLADDPWAK-IERRYP 271

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

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

 Score = 168 (64.2 bits), Expect = 1.1e-11, P = 1.1e-11
 Identities = 43/126 (34%), Positives = 70/126 (55%)

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 QLEEDP 134
             QL EDP
Sbjct:   261 QLGEDP 266

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

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

 Score = 166 (63.5 bits), Expect = 1.9e-11, P = 1.9e-11
 Identities = 39/115 (33%), Positives = 62/115 (53%)

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

Query:    92 SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQD 146
             SW  +     + + G  V+ K+IKIDRE  +I+L +KQLEE P    +EK  P D
Sbjct:   269 SWSRVSHPSAVFSCGQTVKTKIIKIDRENKKISLGVKQLEESPW-SNIEKKYPVD 322

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 = 163 (62.4 bits), Expect = 4.0e-11, P = 4.0e-11
 Identities = 37/103 (35%), Positives = 60/103 (58%)

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

Query:   103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ 145
             +N GDE+ VKV+K DR+++R++L +KQL EDP +  + K  P+
Sbjct:   235 VNVGDEILVKVLKFDRDRTRVSLGLKQLGEDPWV-AIAKRYPE 276

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 = 163 (62.4 bits), Expect = 4.0e-11, P = 4.0e-11
 Identities = 37/103 (35%), Positives = 60/103 (58%)

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

Query:   103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ 145
             +N GDE+ VKV+K DR+++R++L +KQL EDP +  + K  P+
Sbjct:   235 VNVGDEILVKVLKFDRDRTRVSLGLKQLGEDPWV-AIAKRYPE 276

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	182
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	5e-20
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-19
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	1e-18
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	4e-18
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	4e-18
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	5e-18
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	9e-18
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	2e-17
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	7e-17
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-16
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	3e-16
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-15
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	2e-15
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	2e-15
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	3e-15
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	4e-15
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	5e-15
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-14
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	1e-14
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	5e-14
pfam00575	74	pfam00575, S1, S1 RNA binding domain	2e-13
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	5e-13
PRK05807	136	PRK05807, PRK05807, hypothetical protein; Provisio	5e-13
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	6e-13
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	2e-12
PRK08582	139	PRK08582, PRK08582, hypothetical protein; Provisio	4e-12
cd05708	77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	7e-12
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	1e-11
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	2e-11
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	4e-11
PRK03987	262	PRK03987, PRK03987, translation initiation factor	2e-10
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	2e-10
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	4e-10
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	4e-10
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-09
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	1e-09
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	1e-09
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	2e-09
PRK07252	120	PRK07252, PRK07252, hypothetical protein; Provisio	2e-09
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	2e-09
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	3e-09
cd05691	73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	3e-09
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	8e-08
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	1e-07
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	8e-07
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	1e-06
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	3e-06
cd05698	70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	9e-06
cd05689	72	cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: R	1e-05
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	2e-05
cd05686	73	cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-b	2e-05
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	2e-04
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	5e-04
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	0.002

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

 Score = 86.0 bits (214), Expect = 5e-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 = 84.4 bits (210), Expect = 2e-19
 Identities = 46/135 (34%), Positives = 70/135 (51%), Gaps = 16/135 (11%)

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

Query: 78  GLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL 136
           G+    GLVHVSE+SW    +    +++ G EV V V++ID EK RI+L +KQ +E+P  
Sbjct: 309 GI---EGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWE 365

Query: 137 ETLEKVIPQDGSVIS 151
           E  EK     G V+ 
Sbjct: 366 EFAEKYPV--GDVVE 378

Length = 565

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

 Score = 82.3 bits (204), 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 = 80.4 bits (199), Expect = 4e-18
 Identities = 40/131 (30%), Positives = 73/131 (55%), Gaps = 18/131 (13%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAVWNKYS-------SRVNVEDIFVGR-----DYGAF 70
           G  +  K+++ +++   +V S +  +  + S       +++ V ++  G      DYGAF
Sbjct: 150 GKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAF 209

Query: 71  IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130
           + +        + GL+H+SE+SW  +    +++  GDEV+VKVI +D E+ R++LS+KQL
Sbjct: 210 VDI------GGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQL 263

Query: 131 EEDPLLETLEK 141
           EEDP     +K
Sbjct: 264 EEDPWEGIEKK 274

Length = 541

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

 Score = 79.9 bits (198), Expect = 4e-18
 Identities = 43/144 (29%), Positives = 74/144 (51%), Gaps = 28/144 (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 IKQLEEDPLLETLEKVIPQDGSVI 150
           +K     P  E +E+ +P+ G VI
Sbjct: 260 LKDTLPGP-WEGVEEKLPE-GDVI 281

Length = 390

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

 Score = 80.2 bits (199), Expect = 5e-18
 Identities = 47/139 (33%), Positives = 79/139 (56%), Gaps = 16/139 (11%)

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 DPLLETLEKVIPQDGSVIS 151
           DP  E  +K   + GS+++
Sbjct: 449 DPFEEFAKKH--KKGSIVT 465

Length = 565

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

 Score = 79.7 bits (197), Expect = 9e-18
 Identities = 44/120 (36%), Positives = 63/120 (52%), Gaps = 13/120 (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
                  + GLVHVSE+SW       +++  G EV VKV+ ID E+ RI+L +KQL+E+P
Sbjct: 299 EG-----VEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENP 353

Length = 541

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

 Score = 78.8 bits (195), 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 = 76.8 bits (190), Expect = 7e-17
 Identities = 44/143 (30%), Positives = 75/143 (52%), Gaps = 13/143 (9%)

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

Query: 135 LLETLEKVIPQDGSVISDSSSMS 157
             E   +   +   +  + +  S
Sbjct: 354 AEEEDRREEYRQYELPEEETGFS 376

Length = 390

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

 Score = 75.0 bits (185), Expect = 3e-16
 Identities = 49/138 (35%), Positives = 76/138 (55%), Gaps = 15/138 (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 PLLETLEKVIPQDGSVIS 151
           P  E  EK   + GSV+ 
Sbjct: 439 PWEEFSEK--YKKGSVVK 454

Length = 541

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

 Score = 74.5 bits (183), Expect = 3e-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 = 73.2 bits (180), 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|181215 PRK08059, PRK08059, general stress protein 13; Validated

 Score = 68.5 bits (168), 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|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 72.4 bits (179), Expect = 2e-15
 Identities = 31/81 (38%), Positives = 50/81 (61%), Gaps = 11/81 (13%)

Query: 56  VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVR 110
             V +I+ G+     D+GAF+      G     GLVH+SE++ + ++ + D+L EGDEV+
Sbjct: 619 PEVGEIYEGKVVRIVDFGAFVE--ILPGK---DGLVHISEIADERVEKVEDVLKEGDEVK 673

Query: 111 VKVIKIDREKSRITLSIKQLE 131
           VKV++ID ++ RI LS K + 
Sbjct: 674 VKVLEID-KRGRIRLSRKAVL 693

Length = 693

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

 Score = 72.1 bits (178), Expect = 3e-15
 Identities = 46/167 (27%), Positives = 78/167 (46%), Gaps = 31/167 (18%)

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

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
             DG+    GL+  SE+S D ++D  ++L  GDEV  KVI IDR+  RI+LSIK L+E  
Sbjct: 481 -EDGV---EGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEA- 535

Query: 135 LLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQED 181
                     ++   I++ +S S S +        LG + +  L+  
Sbjct: 536 ----------EEKEAIAEYNSASDSKTT-------LGDLLKAALKGK 565

Length = 565

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

 Score = 68.1 bits (167), Expect = 4e-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|240193 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

 Score = 65.7 bits (161), Expect = 5e-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|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 70.5 bits (173), Expect = 1e-14
 Identities = 34/81 (41%), Positives = 50/81 (61%), Gaps = 6/81 (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 SIKQLEEDPLLETLEKVIPQD 146
           S+KQL EDP     +K    D
Sbjct: 254 SLKQLGEDPWEAIEKKFPVGD 274

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

 Score = 70.1 bits (172), Expect = 1e-14
 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|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

 Score = 63.5 bits (155), Expect = 5e-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 = 61.9 bits (151), Expect = 2e-13
 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 = 66.1 bits (162), Expect = 5e-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|235614 PRK05807, PRK05807, hypothetical protein; Provisional

 Score = 62.5 bits (152), Expect = 5e-13
 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|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 65.5 bits (160), Expect = 6e-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 = 59.5 bits (145), Expect = 2e-12
 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|236305 PRK08582, PRK08582, hypothetical protein; Provisional

 Score = 60.4 bits (147), Expect = 4e-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|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 = 58.1 bits (141), 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|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 61.7 bits (150), Expect = 1e-11
 Identities = 43/135 (31%), Positives = 64/135 (47%), Gaps = 18/135 (13%)

Query: 23  GSIISVKVIQANEEMK----KLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAF 70
           G  + VKV+      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|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 61.4 bits (150), Expect = 2e-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 = 55.8 bits (135), Expect = 4e-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|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated

 Score = 57.9 bits (141), Expect = 2e-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|239918 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

 Score = 54.1 bits (131), Expect = 2e-10
 Identities = 29/73 (39%), Positives = 47/73 (64%), Gaps = 11/73 (15%)

Query: 60  DIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 114
            I+ G+     D+GAF+ +     L    GLVH+SE+S + ++ + D+L  GDEV+VKVI
Sbjct: 2   KIYEGKVVKIKDFGAFVEI-----LPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVI 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|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

 Score = 56.9 bits (138), Expect = 4e-10
 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 = 57.4 bits (139), 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|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 55.9 bits (135), 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|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 = 51.9 bits (125), Expect = 1e-09
 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 = 55.9 bits (134), Expect = 1e-09
 Identities = 39/124 (31%), Positives = 64/124 (51%), Gaps = 14/124 (11%)

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 PLLE 137
           P  E
Sbjct: 655 PWEE 658

Length = 863

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

 Score = 55.8 bits (135), 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|180908 PRK07252, PRK07252, hypothetical protein; Provisional

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

 Score = 51.4 bits (124), Expect = 2e-09
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 6/74 (8%)

Query: 56  VNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           V V+ I    D GA++ L     +    G++ +SE+S   I+ IR ++  G +  VKVI+
Sbjct: 9   VTVKSIA---DMGAYVSLLEYGNI---EGMILLSELSRRRIRSIRKLVKVGRKEVVKVIR 62

Query: 116 IDREKSRITLSIKQ 129
           +D+EK  I LS K+
Sbjct: 63  VDKEKGYIDLSKKR 76

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

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

 Score = 55.1 bits (132), Expect = 3e-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|240196 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain

 Score = 50.7 bits (122), Expect = 3e-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|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 = 47.2 bits (113), Expect = 8e-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|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 50.0 bits (120), Expect = 1e-07
 Identities = 41/138 (29%), Positives = 64/138 (46%), Gaps = 20/138 (14%)

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 LLETLEKVIPQDGSVISD 152
             E LE     D S + D
Sbjct: 519 EKEALESYNKDDDSSLGD 536

Length = 541

>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 = 46.4 bits (111), 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 = 44.4 bits (105), Expect = 8e-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|225094 COG2183, Tex, Transcriptional accessory protein [Transcription]

 Score = 47.3 bits (113), Expect = 1e-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 = 46.1 bits (110), Expect = 3e-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|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 = 9e-06
 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|240194 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain

 Score = 41.4 bits (97), Expect = 1e-05
 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|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 43.3 bits (103), 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|240191 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-binding domain

 Score = 40.9 bits (96), Expect = 2e-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|240192 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

 Score = 37.9 bits (89), Expect = 2e-04
 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 = 39.3 bits (92), Expect = 5e-04
 Identities = 28/112 (25%), Positives = 51/112 (45%), Gaps = 13/112 (11%)

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

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
            P     +TGL+  S +S        + L  GD V + V +ID  K +I+L+
Sbjct: 401 -PG----VTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447

Length = 491

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

 Score = 37.8 bits (87), Expect = 0.002
 Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 15/94 (15%)

Query: 49  WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDIL 103
           W +  +R  V   F  R     + GAFI +   +G+    G +HV ++SW  ++  R   
Sbjct: 656 WEEIEARYPVGARFTRRIVKVTNAGAFIEME--EGI---DGFLHVDDLSW--VKRTRPAD 708

Query: 104 NE---GDEVRVKVIKIDREKSRITLSIKQLEEDP 134
           +E   G E+   VI+ D +  RI L +KQL ++P
Sbjct: 709 HELEVGKEIECMVIECDPQARRIRLGVKQLSDNP 742

Length = 863

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	182
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.97
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	99.97
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	99.97
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	99.96
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.96
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.96
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	99.96
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.94
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.94
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.94
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.94
PRK07400	318	30S ribosomal protein S1; Reviewed	99.9
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.9
PRK07400	318	30S ribosomal protein S1; Reviewed	99.9
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.88
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.86
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.83
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.72
PRK08582	139	hypothetical protein; Provisional	99.59
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.58
PHA02945	88	interferon resistance protein; Provisional	99.54
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.54
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.54
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.52
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.51
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.51
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.51
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.5
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.5
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.49
PRK07252	120	hypothetical protein; Provisional	99.49
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.47
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.47
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.46
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.46
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.45
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.44
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.43
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.43
PRK08059	123	general stress protein 13; Validated	99.43
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.42
PRK05807	136	hypothetical protein; Provisional	99.4
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.4
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.37
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.36
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.35
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.34
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.3
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.27
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.27
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.26
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.26
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.24
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.23
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	99.22
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.21
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.21
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.21
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.2
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.18
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	99.14
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.09
COG2183	780	Tex Transcriptional accessory protein [Transcripti	99.06
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	99.06
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.06
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.99
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.99
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.99
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.97
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.95
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	98.92
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.92
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.87
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.87
PRK11642	813	exoribonuclease R; Provisional	98.86
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.77
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.77
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.66
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.65
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.62
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.55
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	98.47
PRK05054	644	exoribonuclease II; Provisional	98.47
TIGR01953	341	NusA transcription termination factor NusA. This m	98.42
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.4
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	98.29
COG0557	706	VacB Exoribonuclease R [Transcription]	98.2
KOG2916	304	consensus Translation initiation factor 2, alpha s	98.2
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	98.18
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	98.18
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	98.15
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	98.13
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	98.0
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	97.88
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	97.87
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	97.87
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	97.86
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	97.85
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	97.8
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	97.8
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	97.78
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	97.75
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.74
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.72
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	97.71
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	97.67
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	97.65
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	97.62
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	97.49
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.49
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	97.47
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	97.45
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	97.44
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	97.43
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	97.43
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	97.41
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	97.39
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	97.38
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.34
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.33
PRK09202	470	nusA transcription elongation factor NusA; Validat	97.3
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.29
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	97.23
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.23
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	97.22
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	97.22
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	97.17
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	97.16
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	97.13
PRK08059	123	general stress protein 13; Validated	97.1
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.08
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	97.06
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	97.05
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	97.0
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.98
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	96.9
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	96.74
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	96.66
TIGR01953	341	NusA transcription termination factor NusA. This m	96.52
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	96.51
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.44
PHA02945	88	interferon resistance protein; Provisional	96.32
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.24
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	96.18
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.1
PRK10811	1068	rne ribonuclease E; Reviewed	96.04
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	95.9
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	95.89
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.74
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.71
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.68
PRK11712	489	ribonuclease G; Provisional	95.56
COG2183	780	Tex Transcriptional accessory protein [Transcripti	95.22
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	95.0
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	94.87
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	94.37
PRK11642	813	exoribonuclease R; Provisional	94.25
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	93.74
COG1098	129	VacB Predicted RNA binding protein (contains ribos	93.67
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	93.58
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	93.22
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	93.13
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	92.97
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	92.6
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	92.51
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	92.43
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	90.83
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	88.58
PRK12328	374	nusA transcription elongation factor NusA; Provisi	88.36
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	88.17
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	87.64
PRK07252	120	hypothetical protein; Provisional	87.04
PRK05054	644	exoribonuclease II; Provisional	86.99
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	86.98
PRK08582	139	hypothetical protein; Provisional	86.91
COG4044	247	Uncharacterized protein conserved in archaea [Func	86.91
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	84.88
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	84.75
PRK11712	489	ribonuclease G; Provisional	83.84
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	83.36
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	83.35
PRK03987	262	translation initiation factor IF-2 subunit alpha;	82.14
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	81.75
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	80.57
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	80.01

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

Probab=100.00  E-value=1.5e-35  Score=258.98  Aligned_cols=168  Identities=26%  Similarity=0.460  Sum_probs=157.5

Q ss_pred             CCCCCCCCccHH--HhhhhcCCCeEEEEEEEEeCCCCEEEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeE
Q 030172            4 SHSCKEPQKSIH--EIAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGA   69 (182)
Q Consensus         4 ~~~~p~~e~~~~--~~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~   69 (182)
                      +.|+|.|..+.+  +.+..++|.++.++|+++|.+++++.+|++..       ...++..++++|+++.|+     +|||
T Consensus       129 r~FlP~S~v~~r~v~d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~Ga  208 (541)
T COG0539         129 RAFLPGSLVDVRPVRDLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGA  208 (541)
T ss_pred             EEeccHHHhcccccccccccCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcE
Confidence            358999999998  77888999999999999999999999999963       344567899999999999     9999


Q ss_pred             EEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCce
Q 030172           70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSV  149 (182)
Q Consensus        70 fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~  149 (182)
                      ||+|+   |   ++||||++||||.++.+|.+.|++||.|+|+|+++|++++|++||+|++.++||.....+|++  |+.
T Consensus       209 fVdig---G---vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~--g~~  280 (541)
T COG0539         209 FVDIG---G---VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPV--GDK  280 (541)
T ss_pred             EEEec---C---eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCC--CCE
Confidence            99996   5   999999999999999999999999999999999999999999999999999999999999998  999


Q ss_pred             eEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          150 ISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       150 v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      +.|+|+++++|||||++.+|++||||-..+
T Consensus       281 v~G~Vt~i~~~GafVei~~GvEGlvhvSEi  310 (541)
T COG0539         281 VEGKVTNLTDYGAFVEIEEGVEGLVHVSEI  310 (541)
T ss_pred             EEEEEEEeecCcEEEEecCCccceeechhh
Confidence            999999999999999999999999998765

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

Probab=100.00  E-value=1.3e-33  Score=246.79  Aligned_cols=167  Identities=31%  Similarity=0.487  Sum_probs=155.7

Q ss_pred             CCCCCCCccHHHh--hhhc--CCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----eEeEEEE
Q 030172            5 HSCKEPQKSIHEI--AKGL--TGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFIH   72 (182)
Q Consensus         5 ~~~p~~e~~~~~~--~~~~--vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~~G~fV~   72 (182)
                      .|+|.+|++|.+.  ...+  +|++|+++|+++|+++++++||.|+   .||+....++.+|+.+.|+     +|||||+
T Consensus       217 GLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVe  296 (541)
T COG0539         217 GLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVE  296 (541)
T ss_pred             eEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEE
Confidence            3678899999852  3333  8999999999999999999999997   4999999999999999999     9999999


Q ss_pred             EecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCceeEe
Q 030172           73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISD  152 (182)
Q Consensus        73 l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v~G  152 (182)
                      +.  +|   ++||+|+|||||.+...|.+++++||.|.|+|+++|++++||+||+|++..+||..+..++++  |+.++|
T Consensus       297 i~--~G---vEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~--g~~v~g  369 (541)
T COG0539         297 IE--EG---VEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPV--GDVVEG  369 (541)
T ss_pred             ec--CC---ccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCC--CCeEEE
Confidence            97  56   999999999999998889999999999999999999999999999999999999999999888  999999


Q ss_pred             eEeeecCCeeEEecCCChhhhchhhh
Q 030172          153 SSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       153 ~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      .|.++++||+||.+++|++||+|..+
T Consensus       370 ~v~~~t~~g~fv~le~gidG~vh~~d  395 (541)
T COG0539         370 KVKSITDFGAFVELEGGIDGLVHLSD  395 (541)
T ss_pred             EEeeecccceEEccCCCccceEEHHh
Confidence            99999999999999999999998765

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.97  E-value=2.2e-31  Score=233.01  Aligned_cols=166  Identities=23%  Similarity=0.412  Sum_probs=152.9

Q ss_pred             CCCCCCCccHHH--hhhhcCCCeEEEEEEEEeCCCCEEEEEech-------hHHhhhhcCCCCCCEEEEE-----eEeEE
Q 030172            5 HSCKEPQKSIHE--IAKGLTGSIISVKVIQANEEMKKLVFSEKD-------AVWNKYSSRVNVEDIFVGR-----DYGAF   70 (182)
Q Consensus         5 ~~~p~~e~~~~~--~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~-------~~~~~~~~~~~~G~iv~g~-----~~G~f   70 (182)
                      .|+|.++++++.  .++.++|++++|+|+++|++++++.+|+|.       .+|+.+..++++|+++.|+     ++|+|
T Consensus       146 gflP~Sel~~~~~~~~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~F  225 (486)
T PRK07899        146 GFLPASLVEMRRVRDLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAF  225 (486)
T ss_pred             EEEEhhHhcccccCChhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEE
Confidence            478999988873  456789999999999999999999999884       3567777899999999999     99999


Q ss_pred             EEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172           71 IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI  150 (182)
Q Consensus        71 V~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v  150 (182)
                      |+|+   |   ++||||+++++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++..+||..+.+++..  |+++
T Consensus       226 Vdlg---g---v~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~v--G~vv  297 (486)
T PRK07899        226 VDLG---G---VDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAI--GQIV  297 (486)
T ss_pred             EEEC---C---EEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCC--CCEE
Confidence            9995   5   999999999999999999999999999999999999999999999999999999998888877  9999


Q ss_pred             EeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          151 SDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      .|+|+++.+||+||++.+|++||||...
T Consensus       298 ~G~V~~I~~fGvFVeL~~gieGLvh~Se  325 (486)
T PRK07899        298 PGKVTKLVPFGAFVRVEEGIEGLVHISE  325 (486)
T ss_pred             EEEEEEEeccEEEEEeCCCcEEEEEHHH
Confidence            9999999999999999999999999754

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=99.97  E-value=1.1e-30  Score=230.15  Aligned_cols=167  Identities=28%  Similarity=0.520  Sum_probs=150.6

Q ss_pred             CCCCCCCccHHHh--hhhc--CCCeEEEEEEEEeCCC----CEEEEEechh---HHhhhhcCCCCCCEEEEE-----eEe
Q 030172            5 HSCKEPQKSIHEI--AKGL--TGSIISVKVIQANEEM----KKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYG   68 (182)
Q Consensus         5 ~~~p~~e~~~~~~--~~~~--vG~~v~~~v~~~d~~~----~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G   68 (182)
                      .|+|.+++++...  +..+  +|++++|+|+++|.++    +++.+|+|..   +|.....++++|+++.|+     ++|
T Consensus       228 g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G  307 (491)
T PRK13806        228 GMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFG  307 (491)
T ss_pred             EEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCce
Confidence            4678888888642  2332  9999999999999876    4799999874   888888899999999999     999


Q ss_pred             EEEEEecCCCceeEEEEEEccCcCC-ccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCC
Q 030172           69 AFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDG  147 (182)
Q Consensus        69 ~fV~l~~~~g~~~~~glv~~sels~-~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g  147 (182)
                      +||+++  .|   ++||+|+++++| .++.++.+.|++||.|+|+|+++|++++++.||+|++..+||..+.+++++  |
T Consensus       308 ~fV~l~--~g---v~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~v--G  380 (491)
T PRK13806        308 AFVEIL--PG---IEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAP--G  380 (491)
T ss_pred             EEEEeC--CC---cEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCC--C
Confidence            999996  46   999999999999 467889999999999999999999999999999999999999999999988  9


Q ss_pred             ceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          148 SVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       148 ~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      ++++|+|+++++||+||++++|++||||...
T Consensus       381 ~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se  411 (491)
T PRK13806        381 TTVTGTVEKRAQFGLFVNLAPGVTGLLPASV  411 (491)
T ss_pred             CEEEEEEEEEecCceEEEcCCCcEEEEEHHH
Confidence            9999999999999999999999999999765

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=99.97  E-value=2.6e-30  Score=238.33  Aligned_cols=167  Identities=26%  Similarity=0.449  Sum_probs=152.5

Q ss_pred             CCCCCCCccHHHh--hhh--cCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----eEeEEEE
Q 030172            5 HSCKEPQKSIHEI--AKG--LTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFIH   72 (182)
Q Consensus         5 ~~~p~~e~~~~~~--~~~--~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~~G~fV~   72 (182)
                      .|+|.++++++..  +..  .+|++++|+|+.+|++++++.+|+|.   .+|..+..++++|+++.|+     +||+||+
T Consensus       518 Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVe  597 (863)
T PRK12269        518 GLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIE  597 (863)
T ss_pred             EEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEE
Confidence            4789999988642  222  38999999999999999999999996   5888888899999999999     9999999


Q ss_pred             EecCCCceeEEEEEEccCcCC-ccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCceeE
Q 030172           73 LRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVIS  151 (182)
Q Consensus        73 l~~~~g~~~~~glv~~sels~-~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v~  151 (182)
                      ++  +|   ++||+|++|++| .+..+|.+.|++||.|+|+|+++|++++++.||+|++.++||..+.++|++  |++++
T Consensus       598 L~--~g---veGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~v--G~~v~  670 (863)
T PRK12269        598 LA--EG---IEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPV--GARFT  670 (863)
T ss_pred             ec--CC---ceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCC--CCEEE
Confidence            96  46   999999999999 578899999999999999999999999999999999999999999889988  99999


Q ss_pred             eeEeeecCCeeEEecCCChhhhchhhh
Q 030172          152 DSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       152 G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |+|+++++||+||++.+|++||+|...
T Consensus       671 G~V~~i~~~G~fV~l~~gV~GlIh~se  697 (863)
T PRK12269        671 RRIVKVTNAGAFIEMEEGIDGFLHVDD  697 (863)
T ss_pred             EEEEEEecceEEEEeCCCcEEEEEhHH
Confidence            999999999999999999999999654

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=99.96  E-value=9.8e-30  Score=224.07  Aligned_cols=167  Identities=28%  Similarity=0.478  Sum_probs=150.8

Q ss_pred             CCCCCCCccHH--HhhhhcCCCeEEEEEEEEeCCCCEEEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeEE
Q 030172            5 HSCKEPQKSIH--EIAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAF   70 (182)
Q Consensus         5 ~~~p~~e~~~~--~~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~f   70 (182)
                      .|+|.++++++  +.+..++|++++|+|+.+|++++++.+|++..       .|+.+..++++|+++.|+     ++|+|
T Consensus       140 ~flP~s~~~~~~~~~~~~~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~f  219 (491)
T PRK13806        140 AFCPVSQIDLRYVEDPESYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAF  219 (491)
T ss_pred             EEEEHHHhccccCCChHHcCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEE
Confidence            47899998876  34556899999999999999999999999863       456667789999999999     99999


Q ss_pred             EEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC----CeEEEEEeeccCCchhHHHhhhcCCC
Q 030172           71 IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK----SRITLSIKQLEEDPLLETLEKVIPQD  146 (182)
Q Consensus        71 V~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~----~ki~lS~k~~~~~p~~~~~~~~~~~~  146 (182)
                      |+++  +|   ++||||+++++|.++.++.+.|++||.|+|+|+++|.++    .++.||+|++.++||....+++..  
T Consensus       220 V~l~--~g---v~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~--  292 (491)
T PRK13806        220 VELA--PG---VEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKA--  292 (491)
T ss_pred             EEcC--CC---cEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCC--
Confidence            9996  45   999999999999999999999999999999999999866    479999999999999999888887  


Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |+++.|+|+++.+||+||++.+|++||+|...
T Consensus       293 G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~se  324 (491)
T PRK13806        293 GDKVTGKVVRLAPFGAFVEILPGIEGLVHVSE  324 (491)
T ss_pred             CCEEEEEEEEEeCceEEEEeCCCcEEEEEHHH
Confidence            99999999999999999999999999999654

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.96  E-value=2.4e-28  Score=218.66  Aligned_cols=166  Identities=28%  Similarity=0.466  Sum_probs=151.8

Q ss_pred             CCCCCCCccHHH--hhhhcCCCeEEEEEEEEeCCCCEEEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeEE
Q 030172            5 HSCKEPQKSIHE--IAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAF   70 (182)
Q Consensus         5 ~~~p~~e~~~~~--~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~f   70 (182)
                      .|||.++++++.  .+..++|+++.|+|+.+|++++++.+|+|.+       .|.....++++|+++.|+     ++|+|
T Consensus       139 gfip~s~~~~~~~~~~~~~vG~~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~  218 (565)
T PRK06299        139 AFLPGSQVDVRPVRDTDPLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAF  218 (565)
T ss_pred             EEEEHHHccCcCCCChHHhCCCEEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEE
Confidence            478999998863  3556899999999999999999999999863       356667899999999999     99999


Q ss_pred             EEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172           71 IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI  150 (182)
Q Consensus        71 V~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v  150 (182)
                      |+++   |   ++||+|+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|.+..+||....+.+.+  |+++
T Consensus       219 V~i~---g---~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~--G~~v  290 (565)
T PRK06299        219 VDLG---G---VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPV--GSKV  290 (565)
T ss_pred             EEEC---C---EEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhCCC--CCEE
Confidence            9995   5   999999999999999999999999999999999999999999999999999999998888887  9999


Q ss_pred             EeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          151 SDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      .|+|+++.++|+||++.+|++||+|...
T Consensus       291 ~g~V~~i~~~G~fV~l~~~v~Glv~~se  318 (565)
T PRK06299        291 KGKVTNITDYGAFVELEEGIEGLVHVSE  318 (565)
T ss_pred             EEEEEEEeCCeEEEEeCCCCEEEEEHHH
Confidence            9999999999999999999999998643

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.96  E-value=3.3e-28  Score=208.96  Aligned_cols=167  Identities=28%  Similarity=0.420  Sum_probs=150.7

Q ss_pred             CCCCCCCccHHH--hhhhcCCCeEEEEEEEEeCCCCEEEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeEE
Q 030172            5 HSCKEPQKSIHE--IAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAF   70 (182)
Q Consensus         5 ~~~p~~e~~~~~--~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~f   70 (182)
                      .|+|.++++++.  .+..++|+++.|+|+++|++++++.+|++..       .|.....+++.|+++.|+     ++|+|
T Consensus       130 gflp~~el~~~~~~~~~~~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~f  209 (390)
T PRK06676        130 GFIPASLISTRFVEDFSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAF  209 (390)
T ss_pred             EEEEHHHcCCccCCChHHcCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEE
Confidence            478888888763  3556799999999999999999999999863       455566789999999999     99999


Q ss_pred             EEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172           71 IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI  150 (182)
Q Consensus        71 V~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v  150 (182)
                      |+++   |   ++||||+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++..+||....+.+.+  |+++
T Consensus       210 V~l~---~---v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~--G~~v  281 (390)
T PRK06676        210 VDIG---G---VDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPE--GDVI  281 (390)
T ss_pred             EEeC---C---eEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcC--CcEE
Confidence            9994   5   999999999999999999999999999999999999999999999999999999988888887  9999


Q ss_pred             EeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          151 SDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .|+|+++.++|+||++.+|+.||||....
T Consensus       282 ~g~V~~i~~~G~fV~l~~gi~Glv~~se~  310 (390)
T PRK06676        282 EGTVKRLTDFGAFVEVLPGVEGLVHISQI  310 (390)
T ss_pred             EEEEEEEeCceEEEEECCCCeEEEEhHHc
Confidence            99999999999999999999999996543

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=99.96  E-value=2.8e-28  Score=224.94  Aligned_cols=167  Identities=21%  Similarity=0.329  Sum_probs=148.3

Q ss_pred             CCCCCCCccH-HH--hh-h-hcCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----eEeEEE
Q 030172            5 HSCKEPQKSI-HE--IA-K-GLTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFI   71 (182)
Q Consensus         5 ~~~p~~e~~~-~~--~~-~-~~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~~G~fV   71 (182)
                      .|+|.+|++| ++  .. . ..+|++++|+|+.+|++++++.+|.|+   .+|+.+..++++|+++.|+     +||+||
T Consensus       604 GLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV  683 (863)
T PRK12269        604 GLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFI  683 (863)
T ss_pred             eeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEE
Confidence            4577788887 22  12 2 239999999999999999999999996   4899998899999999999     999999


Q ss_pred             EEecCCCceeEEEEEEccCcCCccc-cCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172           72 HLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI  150 (182)
Q Consensus        72 ~l~~~~g~~~~~glv~~sels~~~~-~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v  150 (182)
                      ++.  +|   ++||||.++++|.+. .++.+.|++||.|+|+|+++|+++++|.||+|++..+||..+.+.+++  |+++
T Consensus       684 ~l~--~g---V~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~v--G~iV  756 (863)
T PRK12269        684 EME--EG---IDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGV--GSTV  756 (863)
T ss_pred             EeC--CC---cEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCC--CCEE
Confidence            996  46   999999999999765 445568999999999999999999999999999999999998888877  9999


Q ss_pred             EeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          151 SDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      +|+|+++.++|+||+|.+|++||+|...
T Consensus       757 ~GkV~~v~~~GvFVeL~~gVeGlI~~s~  784 (863)
T PRK12269        757 EGEVSSVTDFGIFVRVPGGVEGLVRKQH  784 (863)
T ss_pred             EEEEEEEecCeEEEEcCCCeEEEEEHHH
Confidence            9999999999999999999999998764

>TIGR00717 rpsA ribosomal protein S1

Probab=99.94  E-value=1.3e-26  Score=205.39  Aligned_cols=166  Identities=28%  Similarity=0.459  Sum_probs=149.5

Q ss_pred             CCCCCCCccHH--HhhhhcCCCeEEEEEEEEeCCCCEEEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeEE
Q 030172            5 HSCKEPQKSIH--EIAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAF   70 (182)
Q Consensus         5 ~~~p~~e~~~~--~~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~f   70 (182)
                      .|||.++++.+  +....++|++++|+|+.+|+.++++.+|+|..       .+......+++|+++.|+     ++|+|
T Consensus       125 ~flP~s~~~~~~~~~~~~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~  204 (516)
T TIGR00717       125 AFLPGSQVDVKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAF  204 (516)
T ss_pred             EEEeHHHhcCcccCchhhhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEE
Confidence            47888888765  34556899999999999999999999999864       244556789999999999     99999


Q ss_pred             EEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172           71 IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI  150 (182)
Q Consensus        71 V~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v  150 (182)
                      |+++   |   ++||+|.++++|.+..++.+.|++||.+.|+|+++|++++++.+|+|.+..+||....+.+.+  |+++
T Consensus       205 V~l~---g---~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~--G~i~  276 (516)
T TIGR00717       205 VDLG---G---VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPV--GDKI  276 (516)
T ss_pred             EEEC---C---EEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccC--CCEE
Confidence            9994   5   999999999999999999999999999999999999999999999999999999998878877  9999


Q ss_pred             EeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          151 SDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      +|+|+++.++|+||++.+|++||+|...
T Consensus       277 ~g~V~~v~~~G~fV~l~~~v~g~v~~se  304 (516)
T TIGR00717       277 TGRVTNLTDYGVFVEIEEGIEGLVHVSE  304 (516)
T ss_pred             EEEEEEeeCCcEEEEeCCCCEEEEEHHH
Confidence            9999999999999999999999999654

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.

>TIGR00717 rpsA ribosomal protein S1

Probab=99.94  E-value=1.6e-26  Score=204.87  Aligned_cols=167  Identities=26%  Similarity=0.480  Sum_probs=147.1

Q ss_pred             CCCCCCCccHHH---hhh--hcCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----eEeEEE
Q 030172            5 HSCKEPQKSIHE---IAK--GLTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFI   71 (182)
Q Consensus         5 ~~~p~~e~~~~~---~~~--~~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~~G~fV   71 (182)
                      .|+|.+++++..   ...  ..+|+.++|+|+++|++++++.+|++.   .+|..+...+++|+++.|+     ++|+||
T Consensus       298 g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV  377 (516)
T TIGR00717       298 GLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFV  377 (516)
T ss_pred             EEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEE
Confidence            457777776531   111  249999999999999999999999986   4788887889999999999     999999


Q ss_pred             EEecCCCceeEEEEEEccCcCCccc-cCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172           72 HLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI  150 (182)
Q Consensus        72 ~l~~~~g~~~~~glv~~sels~~~~-~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v  150 (182)
                      +++  .|   ++||+|+++++|.+. .++.+.|++||.|.|+|+++|+++++|.||+|.+..+||..+.+.+.+  |+++
T Consensus       378 ~l~--~~---v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~--G~~v  450 (516)
T TIGR00717       378 ELE--GG---IDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKV--GSVV  450 (516)
T ss_pred             ECC--CC---CEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCc--ceEE
Confidence            996  45   999999999999764 567788999999999999999999999999999999999888877877  9999


Q ss_pred             EeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          151 SDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      +|+|++++++|+||++.+|+.||||...
T Consensus       451 ~g~V~~v~~~G~fV~l~~~~~Glv~~s~  478 (516)
T TIGR00717       451 KGKVTEIKDFGAFVELPGGVEGLIRNSE  478 (516)
T ss_pred             EEEEEEEecceEEEEcCCCeEEEEEHHH
Confidence            9999999999999999999999999865

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

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

Probab=99.94  E-value=1.9e-26  Score=209.10  Aligned_cols=167  Identities=28%  Similarity=0.447  Sum_probs=149.8

Q ss_pred             CCCCCCCccHHH--hhhhcCCCeEEEEEEEEeCCCCE-EEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeE
Q 030172            5 HSCKEPQKSIHE--IAKGLTGSIISVKVIQANEEMKK-LVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGA   69 (182)
Q Consensus         5 ~~~p~~e~~~~~--~~~~~vG~~v~~~v~~~d~~~~~-i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~   69 (182)
                      .|+|.++++++.  .+..++|+++.|+|+++|+++++ +.+|+|..       ++...+.++++|+++.|+     ++|+
T Consensus       414 gfiP~sel~~~~~~d~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~  493 (647)
T PRK00087        414 AFLPASHVELGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGA  493 (647)
T ss_pred             EEEEHHHhCccccCCHHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcE
Confidence            368888877652  45557999999999999999888 99999864       345566789999999999     9999


Q ss_pred             EEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCce
Q 030172           70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSV  149 (182)
Q Consensus        70 fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~  149 (182)
                      ||+++   |   ++||+|+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++..+||....+++.+  |+.
T Consensus       494 fV~l~---g---v~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~--G~~  565 (647)
T PRK00087        494 FVDIG---G---VDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPV--GSI  565 (647)
T ss_pred             EEEEC---C---EEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccC--CeE
Confidence            99993   5   999999999999999999999999999999999999999999999999999999998888877  999


Q ss_pred             eEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          150 ISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       150 v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      +.|+|+++.++|+||++.+|++||||....
T Consensus       566 v~g~V~~i~~~G~fV~l~~~i~Gli~~sel  595 (647)
T PRK00087        566 VLGKVVRIAPFGAFVELEPGVDGLVHISQI  595 (647)
T ss_pred             EEEEEEEEECCeEEEEECCCCEEEEEhhhc
Confidence            999999999999999999999999997654

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.94  E-value=2.9e-26  Score=205.23  Aligned_cols=168  Identities=31%  Similarity=0.542  Sum_probs=149.0

Q ss_pred             CCCCCCCccHHHh---h-h-hcCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----eEeEEE
Q 030172            5 HSCKEPQKSIHEI---A-K-GLTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFI   71 (182)
Q Consensus         5 ~~~p~~e~~~~~~---~-~-~~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~~G~fV   71 (182)
                      .|+|.+++++...   . . ..+|+++.|+|+++|++++++.+|.+.   ++|..+...+++|+++.|+     ++|+||
T Consensus       312 Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV  391 (565)
T PRK06299        312 GLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFV  391 (565)
T ss_pred             EEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceEEE
Confidence            3577777775321   1 1 138999999999999999999999986   4788777789999999999     999999


Q ss_pred             EEecCCCceeEEEEEEccCcCCccc-cCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172           72 HLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI  150 (182)
Q Consensus        72 ~l~~~~g~~~~~glv~~sels~~~~-~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v  150 (182)
                      +++  +|   ++||+|+++++|.+. .++.+.|++||.|+|+|+++|+++++|.||+|.+..+||....+.+..  |+++
T Consensus       392 ~l~--~~---v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~--G~vV  464 (565)
T PRK06299        392 GLE--GG---IDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKK--GSIV  464 (565)
T ss_pred             ECC--CC---CEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCC--CCEE
Confidence            996  45   999999999999886 889999999999999999999999999999999999999988888877  9999


Q ss_pred             EeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          151 SDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .|+|+++.++|+||++.+|+.||||....
T Consensus       465 ~G~V~~v~~~G~fV~l~~gi~g~i~~se~  493 (565)
T PRK06299        465 TGTVTEVKDKGAFVELEDGVEGLIRASEL  493 (565)
T ss_pred             EEEEEEEecCceEEecCCCcEEEEEHHHh
Confidence            99999999999999999999999998654

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.90  E-value=2.1e-23  Score=174.81  Aligned_cols=158  Identities=16%  Similarity=0.254  Sum_probs=132.2

Q ss_pred             CCCCCCCccHHH--hhhh--cCCCeEEEEEEEEeCCCCEEEEEech----hHHhhhhcCCCCCCEEEEE-----eEeEEE
Q 030172            5 HSCKEPQKSIHE--IAKG--LTGSIISVKVIQANEEMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR-----DYGAFI   71 (182)
Q Consensus         5 ~~~p~~e~~~~~--~~~~--~vG~~v~~~v~~~d~~~~~i~lS~k~----~~~~~~~~~~~~G~iv~g~-----~~G~fV   71 (182)
                      .|+|.+|+++..  .+..  -+|++++|+|++++++++++.+|+|.    .+|+.+......|+++.|+     ++|+||
T Consensus        57 g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V  136 (318)
T PRK07400         57 AFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALV  136 (318)
T ss_pred             EEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence            478888888763  1222  27999999999999999999999986    3677777777889999998     899999


Q ss_pred             EEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCceeE
Q 030172           72 HLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVIS  151 (182)
Q Consensus        72 ~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v~  151 (182)
                      +++   |   ++||||+++++|.+..   +.+ +|+.+.++|+++|++++++.||+|.+..+.   ..+++..  |+++.
T Consensus       137 ~l~---G---v~gfip~s~ls~~~~~---~~~-vG~~i~~kVl~id~~~~~i~lS~K~~~~~~---~~~~~k~--G~vv~  201 (318)
T PRK07400        137 RIE---G---LRGFIPGSHISTRKPK---EEL-VGEELPLKFLEVDEERNRLVLSHRRALVER---KMNRLEV--GEVVV  201 (318)
T ss_pred             EEC---C---EEEEEEHHHcCccCCc---ccc-CCCEEEEEEEEEEcccCEEEEEhhHhhhhh---hhccCCC--CCEEE
Confidence            994   5   9999999999986433   334 999999999999999999999999765432   3456666  99999


Q ss_pred             eeEeeecCCeeEEecCCChhhhchhhh
Q 030172          152 DSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       152 G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |+|+++.+||+||++ .|++||||...
T Consensus       202 G~V~~I~~~G~fV~i-~gv~Gllhise  227 (318)
T PRK07400        202 GTVRGIKPYGAFIDI-GGVSGLLHISE  227 (318)
T ss_pred             EEEEEEECCeEEEEE-CCEEEEEEHHH
Confidence            999999999999999 69999998654

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.90  E-value=3.8e-23  Score=181.22  Aligned_cols=162  Identities=19%  Similarity=0.293  Sum_probs=138.4

Q ss_pred             CCCCCCCccHHHh--hhh--cCCCeEEEEEEEEeCCCCEEEEEechh----HHhhhhcCCCCCCEEEEE-----eEeEEE
Q 030172            5 HSCKEPQKSIHEI--AKG--LTGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFI   71 (182)
Q Consensus         5 ~~~p~~e~~~~~~--~~~--~vG~~v~~~v~~~d~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV   71 (182)
                      .|+|..|+++...  +..  -+|++|+|+|+.+++.++++.+|++..    +|..+...++.|+++.|+     ++|+||
T Consensus        61 G~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~V  140 (486)
T PRK07899         61 GVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLIL  140 (486)
T ss_pred             EEEEHHHhcccccCChhhcCCCCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEE
Confidence            4678888877532  222  399999999999999999999999963    677766667789999999     889999


Q ss_pred             EEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeecc----CCchhHHHhhhcCCCC
Q 030172           72 HLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE----EDPLLETLEKVIPQDG  147 (182)
Q Consensus        72 ~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~----~~p~~~~~~~~~~~~g  147 (182)
                      +++       ++||||++++++.++.++..  .+||.|+|+|+++|++++++.||+|.+.    .++|..+...+.+  |
T Consensus       141 dlG-------i~gflP~Sel~~~~~~~~~~--~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~--G  209 (486)
T PRK07899        141 DIG-------LRGFLPASLVEMRRVRDLQP--YIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQK--G  209 (486)
T ss_pred             EEC-------CEEEEEhhHhcccccCChhh--cCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccC--C
Confidence            994       89999999999988888876  3899999999999999999999999643    3678888888877  9


Q ss_pred             ceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          148 SVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       148 ~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      ++++|+|+++.+||+||++ .|++||+|...
T Consensus       210 ~iv~G~V~~i~~~G~FVdl-ggv~Glv~~Se  239 (486)
T PRK07899        210 QVRKGVVSSIVNFGAFVDL-GGVDGLVHVSE  239 (486)
T ss_pred             CEEEEEEEEEECCeEEEEE-CCEEEEEEHHH
Confidence            9999999999999999999 58999999654

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.90  E-value=4.1e-23  Score=173.02  Aligned_cols=127  Identities=34%  Similarity=0.569  Sum_probs=118.3

Q ss_pred             CCCCCCCccHHHhhhhcCCCeEEEEEEEEeCCCCEEEEEechhHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCc
Q 030172            5 HSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGL   79 (182)
Q Consensus         5 ~~~p~~e~~~~~~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~   79 (182)
                      .|+|.++++++...+.++|+++.|+|+++|++++++.+|+|.+.++....++++|+++.|+     +||+||+++   | 
T Consensus       143 gfip~s~ls~~~~~~~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i~---g-  218 (318)
T PRK07400        143 GFIPGSHISTRKPKEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIG---G-  218 (318)
T ss_pred             EEEEHHHcCccCCccccCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEEC---C-
Confidence            4799999999866667899999999999999999999999988777778899999999999     999999994   5 


Q ss_pred             eeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhH
Q 030172           80 YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE  137 (182)
Q Consensus        80 ~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~  137 (182)
                        ++||+|+++++|.+..++.+.|++||.|+|+|+++|.+++++.||+|.+.++||+.
T Consensus       219 --v~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~  274 (318)
T PRK07400        219 --VSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDM  274 (318)
T ss_pred             --EEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhh
Confidence              99999999999999999999999999999999999999999999999999999954

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.88  E-value=2.3e-22  Score=172.80  Aligned_cols=163  Identities=19%  Similarity=0.318  Sum_probs=138.1

Q ss_pred             CCCCCCccHHH----hhhhcCCCeEEEEEEEEeCCCCEEEEEech----hHHhhhhcCCCCCCEEEEE-----eEeEEEE
Q 030172            6 SCKEPQKSIHE----IAKGLTGSIISVKVIQANEEMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR-----DYGAFIH   72 (182)
Q Consensus         6 ~~p~~e~~~~~----~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~----~~~~~~~~~~~~G~iv~g~-----~~G~fV~   72 (182)
                      |+|..+++...    .....+|++++|+|+.++.+++++.+|++.    ..|..+...++.|+++.|+     ++|+||+
T Consensus        45 ~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~  124 (390)
T PRK06676         45 VIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVD  124 (390)
T ss_pred             EEEHHHhccccccCcccccCCCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEE
Confidence            46666665521    112349999999999999999999999996    3577777788999999999     8999999


Q ss_pred             EecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccC----CchhHHHhhhcCCCCc
Q 030172           73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE----DPLLETLEKVIPQDGS  148 (182)
Q Consensus        73 l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~----~p~~~~~~~~~~~~g~  148 (182)
                      ++   |   ++||||++++++.+..++.++  +||.+.|+|+++|.+++++.||+|.+..    ++|......+..  |+
T Consensus       125 ~~---G---~~gflp~~el~~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~--G~  194 (390)
T PRK06676        125 VE---G---VRGFIPASLISTRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKE--GD  194 (390)
T ss_pred             EC---C---EEEEEEHHHcCCccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCC--CC
Confidence            94   5   899999999999988888764  8999999999999999999999998754    467777777776  99


Q ss_pred             eeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          149 VISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       149 ~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      +++|+|+++.++|+||++ +|++||+|....
T Consensus       195 ~v~g~V~~v~~~G~fV~l-~~v~g~v~~sel  224 (390)
T PRK06676        195 VVEGTVARLTDFGAFVDI-GGVDGLVHISEL  224 (390)
T ss_pred             EEEEEEEEEecceEEEEe-CCeEEEEEHHHc
Confidence            999999999999999999 689999997643

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.86  E-value=2.4e-21  Score=160.85  Aligned_cols=119  Identities=22%  Similarity=0.316  Sum_probs=108.1

Q ss_pred             cCCC-CCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           54 SRVN-VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        54 ~~~~-~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      .++. +|+++.|+     +||+||+|..++|   ++||||+||+||.++.++++.+++||.+.|+|+.+|+++++|.||+
T Consensus        12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~g---vEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~   88 (319)
T PTZ00248         12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYDD---IEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSK   88 (319)
T ss_pred             hhCCCCCCEEEEEEEEEeCCeEEEEecCCCC---cEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEe
Confidence            3455 89999998     9999999964445   9999999999999999999999999999999999999999999999


Q ss_pred             eeccCCchhHHHhhhcCCCCceeEeeEeeecC-CeeEEe------cCCChhhhchhh
Q 030172          128 KQLEEDPLLETLEKVIPQDGSVISDSSSMSSS-NSNTIE------PLPGLGAIFEEL  177 (182)
Q Consensus       128 k~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~-~G~fV~------l~~gv~gl~~~~  177 (182)
                      |++.++||....++|..  |+.++|+|.++.. +|+|++      ..++++++.|..
T Consensus        89 K~v~~~pw~~~~e~~~~--g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y  143 (319)
T PTZ00248         89 KRVSPEDIEACEEKFSK--SKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHAL  143 (319)
T ss_pred             eecccchHHHHHHhCcC--CCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHH
Confidence            99999999999999988  9999999999965 999998      578888777644

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

Probab=99.83  E-value=2.3e-20  Score=169.46  Aligned_cols=162  Identities=20%  Similarity=0.358  Sum_probs=137.3

Q ss_pred             CCCCCCccHHH---hhh-hcCCCeEEEEEEEEeCCCCEEEEEechh----HHhhhhcCCCCCCEEEEE-----eEeEEEE
Q 030172            6 SCKEPQKSIHE---IAK-GLTGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIH   72 (182)
Q Consensus         6 ~~p~~e~~~~~---~~~-~~vG~~v~~~v~~~d~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV~   72 (182)
                      |+|..++++..   ... ..+|++++|+|+.+|..++++.+|++..    .|+.+...++.|+++.|+     ++|+||+
T Consensus       329 ~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~  408 (647)
T PRK00087        329 VIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVD  408 (647)
T ss_pred             EEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEE
Confidence            45666665432   112 2499999999999999899999999863    577777778999999999     8899999


Q ss_pred             EecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCe-EEEEEeeccC----CchhHHHhhhcCCCC
Q 030172           73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR-ITLSIKQLEE----DPLLETLEKVIPQDG  147 (182)
Q Consensus        73 l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~k-i~lS~k~~~~----~p~~~~~~~~~~~~g  147 (182)
                      ++   |   ++||||.+++++.+..++.++  +||.++|+|+++|+++++ +.+|+|.+..    .++....+.+.+  |
T Consensus       409 lg---g---i~gfiP~sel~~~~~~d~~~~--vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~--G  478 (647)
T PRK00087        409 YG---G---VRAFLPASHVELGYVEDLSEY--KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEE--G  478 (647)
T ss_pred             EC---C---EEEEEEHHHhCccccCCHHHh--CCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCC--C
Confidence            95   4   999999999999988888764  899999999999998888 9999998753    567777777776  9


Q ss_pred             ceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          148 SVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       148 ~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      +++.|+|+++.++|+||++ +|++||+|...
T Consensus       479 ~iV~g~V~~v~~~G~fV~l-~gv~Gll~~se  508 (647)
T PRK00087        479 DVVEGEVKRLTDFGAFVDI-GGVDGLLHVSE  508 (647)
T ss_pred             CEEEEEEEEEeCCcEEEEE-CCEEEEEEHHH
Confidence            9999999999999999999 89999998754

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

Probab=99.72  E-value=5.5e-18  Score=121.34  Aligned_cols=77  Identities=45%  Similarity=0.787  Sum_probs=71.4

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      .+++|++++|+     +|||||+|.  +|   -.|||||||+.+.|+.++.+++++||.|+|+|+++|. ++++.||+|.
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~--~g---~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~   75 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELE--GG---KTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRK   75 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEec--CC---CcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHH
Confidence            57899999999     999999997  56   8999999999999999999999999999999999997 9999999999


Q ss_pred             ccCCchhH
Q 030172          130 LEEDPLLE  137 (182)
Q Consensus       130 ~~~~p~~~  137 (182)
                      ++..|-..
T Consensus        76 ~~e~pe~~   83 (129)
T COG1098          76 LEEEPEKQ   83 (129)
T ss_pred             hhhCcccc
Confidence            98877543

>PRK08582 hypothetical protein; Provisional

Probab=99.59  E-value=8.5e-15  Score=109.16  Aligned_cols=77  Identities=42%  Similarity=0.737  Sum_probs=71.5

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      .+++|++|.|+     ++|+||+|.  ++   ++||||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|+
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--EG---KTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKK   75 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEEC--CC---CEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence            47899999999     999999996  45   9999999999999999999999999999999999997 5999999999


Q ss_pred             ccCCchhH
Q 030172          130 LEEDPLLE  137 (182)
Q Consensus       130 ~~~~p~~~  137 (182)
                      +..+||..
T Consensus        76 ~~~~~~~~   83 (139)
T PRK08582         76 AKDRPKRQ   83 (139)
T ss_pred             cccCchhh
Confidence            99999965

>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=99.58  E-value=5.9e-15  Score=98.63  Aligned_cols=66  Identities=26%  Similarity=0.438  Sum_probs=59.9

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCc---cccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~---~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      +++|+++.|+     ++|+||+++  .|   ++|++|+++++|.++.++   .+.|++||.++|+|+++|++++++.||
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--SS---IVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeC--CC---CEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            5789999999     999999996  45   999999999999997765   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.

>PHA02945 interferon resistance protein; Provisional

Probab=99.54  E-value=5.1e-14  Score=95.34  Aligned_cols=74  Identities=30%  Similarity=0.366  Sum_probs=67.5

Q ss_pred             cCCCCCCEEEEE----eEeEEEEEecCCCceeEEEEEEccCc--CCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVSEV--SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        54 ~~~~~G~iv~g~----~~G~fV~l~~~~g~~~~~glv~~sel--s~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      .-+++|+++.|+    ++|+||.|..++|   .+||+|+|+.  +..|+++ ++++ .||.+.|+|+.+|+.++.|.||+
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 SLPNVGDVLKGKVYENGYALYIDLFDYPH---SEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNY   81 (88)
T ss_pred             cCCCCCcEEEEEEEecCceEEEEecccCC---cEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEe
Confidence            346899999999    9999999987666   9999999955  9999999 9999 99999999999999999999999


Q ss_pred             eeccC
Q 030172          128 KQLEE  132 (182)
Q Consensus       128 k~~~~  132 (182)
                      |....
T Consensus        82 K~V~~   86 (88)
T PHA02945         82 KRMCR   86 (88)
T ss_pred             eEccc
Confidence            98754

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

Probab=99.54  E-value=2.9e-14  Score=94.67  Aligned_cols=69  Identities=45%  Similarity=0.787  Sum_probs=64.5

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      +++.|+++.|+     ++|+||+++  +|   ++||||++++++.+..++.+.|++||.++|+|+++|++++++.||+|
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--NG---IEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEES--TS---SEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEEC--Cc---EEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            47899999999     899999997  45   99999999999999999999999999999999999999999999986

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 ....

>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=99.54  E-value=2.7e-14  Score=97.21  Aligned_cols=70  Identities=33%  Similarity=0.464  Sum_probs=65.5

Q ss_pred             hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      +.++++|+++.|+     ++|+||+++  +|   ++||+|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+
T Consensus         9 ~~~~~~G~i~~g~V~~v~~~G~fv~l~--~~---~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461           9 FSDLKPGMVVHGYVRNITPYGVFVEFL--GG---LTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             HHhCCCCCEEEEEEEEEeeceEEEEcC--CC---CEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence            4679999999999     999999996  45   9999999999999999999999999999999999999999999985

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.

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

Probab=99.52  E-value=1.1e-13  Score=92.27  Aligned_cols=71  Identities=34%  Similarity=0.504  Sum_probs=64.2

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      ++.|+++.|+     ++|+||++...+|   ++|++|++++++.+..++.+.|++||.|+|+|+++|.+++++.||+|+
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 PEEGELVVVTVKSIADMGAYVSLLEYGN---IEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCCCC---eEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            3579999999     9999999963334   999999999999999999999999999999999999989999999974

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

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.51  E-value=6.3e-14  Score=129.46  Aligned_cols=86  Identities=29%  Similarity=0.474  Sum_probs=77.3

Q ss_pred             HhhhhcCCCCCCEEE-EE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCe
Q 030172           49 WNKYSSRVNVEDIFV-GR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR  122 (182)
Q Consensus        49 ~~~~~~~~~~G~iv~-g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~k  122 (182)
                      ++.+....++|++|. |+     +||+||+|.  +|   ++||||+|+++|.++.++.+.|++||.|+|+|+++|+ ++|
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--PG---REGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQ  817 (891)
T ss_pred             HHHHhcCcCCCcEEECcEEEEEeccEEEEEeC--CC---CEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCc
Confidence            444556789999996 45     999999996  46   9999999999999999999999999999999999997 899


Q ss_pred             EEEEEeeccCCchhHHHh
Q 030172          123 ITLSIKQLEEDPLLETLE  140 (182)
Q Consensus       123 i~lS~k~~~~~p~~~~~~  140 (182)
                      |.||+|.+.++||.++.+
T Consensus       818 I~LSlK~l~~~Pw~~~~~  835 (891)
T PLN00207        818 LRLSRRALLPEANSEKSS  835 (891)
T ss_pred             EEEEEeccccCchhhhhh
Confidence            999999999999988765

>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=99.51  E-value=5.5e-14  Score=93.38  Aligned_cols=66  Identities=21%  Similarity=0.297  Sum_probs=60.2

Q ss_pred             CCCCCEEEEE-----e-EeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           56 VNVEDIFVGR-----D-YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        56 ~~~G~iv~g~-----~-~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      +++|+++.|+     + +|+|+++.  .|   .+|++|++++++.+..++.+.|++||.|+|+|+++|.  +++.||+|
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--FG---KTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR   72 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECC--CC---CEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence            4689999999     4 89999996  55   9999999999999999999999999999999999983  89999985

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

>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=99.51  E-value=6.9e-14  Score=93.18  Aligned_cols=65  Identities=17%  Similarity=0.315  Sum_probs=59.7

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcc--ccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~--~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      |+++.|+     ++|+||++.  ++   ++|+||++++++..  ..++.+.|++||.|+|+|+++|+++++|.||+|
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--PD---VKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeC--CC---cEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            6788888     999999996  45   99999999999864  889999999999999999999999999999987

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

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

Probab=99.50  E-value=8.5e-14  Score=91.51  Aligned_cols=65  Identities=29%  Similarity=0.410  Sum_probs=60.2

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      |+++.|+     ++|+||++.  ++   ++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||+|
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--NN---VKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEEC--CC---CEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            6778888     999999996  45   99999999999999999999999999999999999999999999986

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=99.50  E-value=2e-13  Score=90.86  Aligned_cols=66  Identities=33%  Similarity=0.538  Sum_probs=59.0

Q ss_pred             CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      +.|+++.|+     +||+||++... +   .+||+|++++++.++.++.+.|++||.|+|+|+++|.++ ++.||+
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~~-~---~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGC-R---KQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECCC-C---eEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence            579999999     99999999411 2   699999999999999999999999999999999999865 999886

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=99.49  E-value=2.2e-13  Score=90.35  Aligned_cols=68  Identities=26%  Similarity=0.428  Sum_probs=62.5

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      +++|+++.|+     ++|+||++.  ++   ++|++|++++++++..++.+.|++||.++|+|+++|++++++.||++
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--NK---VTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeC--CC---cEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            4689999999     999999996  45   99999999999998888889999999999999999998999999985

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=99.49  E-value=2.1e-13  Score=99.23  Aligned_cols=73  Identities=38%  Similarity=0.727  Sum_probs=67.3

Q ss_pred             CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (182)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~  131 (182)
                      ++|+++.|+     ++|+||+|.  ++   ++||+|++++++.++.++.+.|++||.|+|+|+++|++++++.||+|++.
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~--~~---~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~   76 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALE--NG---TTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE   76 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEEC--CC---CEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence            579999999     999999996  45   99999999999999999999999999999999999999999999999998


Q ss_pred             CCc
Q 030172          132 EDP  134 (182)
Q Consensus       132 ~~p  134 (182)
                      +++
T Consensus        77 ~~~   79 (120)
T PRK07252         77 EEK   79 (120)
T ss_pred             cCc
Confidence            643

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

Probab=99.47  E-value=4.3e-14  Score=113.34  Aligned_cols=78  Identities=36%  Similarity=0.640  Sum_probs=72.6

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      -+..|++|.|+     +||+||.|..++|   ++||+|+||++..|+.+.+++++.||.+-|+|+.+|+.++.|.||+|.
T Consensus         8 ~PeeGEiVv~tV~~V~~~GAyv~L~EY~g---~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkr   84 (269)
T COG1093           8 YPEEGEIVVGTVKQVADYGAYVELDEYPG---KEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKR   84 (269)
T ss_pred             CCCCCcEEEEEEEEeeccccEEEeeccCC---eeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhh
Confidence            36789999999     9999999987777   999999999999999999999999999999999999999999999999


Q ss_pred             ccCCch
Q 030172          130 LEEDPL  135 (182)
Q Consensus       130 ~~~~p~  135 (182)
                      +.++.-
T Consensus        85 V~~~q~   90 (269)
T COG1093          85 VTEHQR   90 (269)
T ss_pred             CCHHHH
Confidence            876553

>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=99.47  E-value=2.4e-13  Score=89.25  Aligned_cols=64  Identities=22%  Similarity=0.438  Sum_probs=59.2

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      |+++.|+     ++|+||++.  +|   ++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||+
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--DH---IKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEec--CC---cEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            6788888     999999996  45   9999999999999999999999999999999999999999999984

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.

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

Probab=99.46  E-value=1e-12  Score=123.76  Aligned_cols=151  Identities=19%  Similarity=0.189  Sum_probs=126.7

Q ss_pred             CCCeEEEEEEEEeCCCCEEEEEechh-----------HHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEE
Q 030172           22 TGSIISVKVIQANEEMKKLVFSEKDA-----------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL   85 (182)
Q Consensus        22 vG~~v~~~v~~~d~~~~~i~lS~k~~-----------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~gl   85 (182)
                      .++.+.+.++.++..++.+.+|.+..           .-....++++.|+++.|.     +.|+|+.+.  -+   ++++
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--RK---VEAF 1189 (1710)
T ss_pred             cccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEEc--cc---eEEE
Confidence            57899999999999888899998731           122335789999999999     999999996  23   9999


Q ss_pred             EEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcC-CCCceeEeeEeeecCCeeEE
Q 030172           86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP-QDGSVISDSSSMSSSNSNTI  164 (182)
Q Consensus        86 v~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~-~~g~~v~G~V~~v~~~G~fV  164 (182)
                      +++++++..+...+++.|++||.+.++|+++++..+++.||+|......-......+.. ..|+...|+|..+.++|.||
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            99999999999999999999999999999999999999999998764333233333321 34999999999999999999


Q ss_pred             ecCCCh--hhhchhh
Q 030172          165 EPLPGL--GAIFEEL  177 (182)
Q Consensus       165 ~l~~gv--~gl~~~~  177 (182)
                      ++++++  .|+||.-
T Consensus      1270 ~l~~tv~~~g~~~~~ 1284 (1710)
T KOG1070|consen 1270 KLDVTVNMVGLCHIS 1284 (1710)
T ss_pred             EecCcceecccccce
Confidence            999888  9999853

>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=99.46  E-value=2.7e-13  Score=89.78  Aligned_cols=57  Identities=30%  Similarity=0.493  Sum_probs=53.5

Q ss_pred             eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        66 ~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      ++|+||++.  +|   ++||+|++++++.+..++.+.|++||.++|+|+++|+.++++.||+
T Consensus        15 ~~G~~V~l~--~g---v~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696          15 DLGAVFELK--DG---LLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CceEEEEeC--CC---CEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            799999996  46   9999999999999999999999999999999999999999999985

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

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

Probab=99.45  E-value=9.3e-13  Score=87.99  Aligned_cols=68  Identities=18%  Similarity=0.199  Sum_probs=60.6

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      +++.|+++.|.     ++|+||+++ .+|   ++||+|.+++++.      +.+++||.+.|+|+++|++++++.||+|+
T Consensus         1 dl~~G~~v~g~V~si~d~G~~v~~g-~~g---v~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~   70 (74)
T cd05694           1 DLVEGMVLSGCVSSVEDHGYILDIG-IPG---TTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADP   70 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeC-CCC---cEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            46889999999     999999995 345   9999999999986      66899999999999999999999999997


Q ss_pred             ccC
Q 030172          130 LEE  132 (182)
Q Consensus       130 ~~~  132 (182)
                      ..+
T Consensus        71 ~~~   73 (74)
T cd05694          71 SKV   73 (74)
T ss_pred             ccc
Confidence            653

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.

>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=99.44  E-value=1.3e-12  Score=88.01  Aligned_cols=71  Identities=35%  Similarity=0.685  Sum_probs=62.0

Q ss_pred             CCEEEEE-----eEeEEEEEecC-CCceeEEEEEEccCcCCccc-cCccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172           59 EDIFVGR-----DYGAFIHLRFP-DGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~-~g~~~~~glv~~sels~~~~-~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~  131 (182)
                      |+++.|+     ++|+||+|... ++   .+||+|++++++.+. .++.+.|++||.|+|+|+++|  ++++.+|+|+++
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~---~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~   75 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGR---KEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVD   75 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCC---cEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEecc
Confidence            5677777     99999999622 24   899999999999986 899999999999999999999  899999999987


Q ss_pred             CCc
Q 030172          132 EDP  134 (182)
Q Consensus       132 ~~p  134 (182)
                      ++.
T Consensus        76 ~~~   78 (79)
T cd05684          76 QDT   78 (79)
T ss_pred             cCC
Confidence            653

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.

>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=99.43  E-value=1.2e-12  Score=87.27  Aligned_cols=70  Identities=41%  Similarity=0.648  Sum_probs=63.4

Q ss_pred             CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (182)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~  130 (182)
                      ++|+++.|+     ++|+||++.. .+   .+|++|++++++.+..++.+.|++||.|+|+|+++|++++++.+|+|.+
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-TN---VSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECC-CC---eEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            368899998     9999999962 24   9999999999999988999999999999999999999999999999974

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

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

Probab=99.43  E-value=9e-13  Score=87.03  Aligned_cols=67  Identities=36%  Similarity=0.630  Sum_probs=61.5

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~  130 (182)
                      |+++.|+     ++|+||++.  ++   ++|++|++++++.+..++.+.|++||.++|+|+++|++++++.||+|.+
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~--~~---~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~   72 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLG--DG---VEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK   72 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeC--CC---CEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence            6777777     999999996  44   9999999999999999999999999999999999999889999999975

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.

>PRK08059 general stress protein 13; Validated

Probab=99.43  E-value=1e-12  Score=96.08  Aligned_cols=76  Identities=46%  Similarity=0.831  Sum_probs=70.6

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      .++++|+++.|+     ++|+||++.  ++   ++|++|++++++.++.++.+.|++||.|+|+|+++|.+++++.+|+|
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--EE---TQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR   77 (123)
T ss_pred             ccCCCCCEEEEEEEEEecceEEEEEC--CC---CEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEE
Confidence            468899999999     999999996  45   99999999999999999999999999999999999999999999999


Q ss_pred             eccCCc
Q 030172          129 QLEEDP  134 (182)
Q Consensus       129 ~~~~~p  134 (182)
                      .+..+|
T Consensus        78 ~~~~~~   83 (123)
T PRK08059         78 ATEEAP   83 (123)
T ss_pred             EcccCc
Confidence            998877

>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=99.42  E-value=5.5e-13  Score=87.29  Aligned_cols=63  Identities=30%  Similarity=0.520  Sum_probs=57.9

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      |+++.|+     ++|+||++.  ++   ++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||
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--RG---VDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeC--CC---CEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            6777787     999999996  45   999999999999999999999999999999999999999999876

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=99.40  E-value=2.1e-12  Score=95.98  Aligned_cols=70  Identities=47%  Similarity=0.760  Sum_probs=65.3

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      .+++|+++.|+     ++|+||+|.   +   ..||||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|.
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L~---~---~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~   74 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEVE---G---KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQ   74 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEEC---C---EEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence            46789999999     999999993   4   8999999999999999999999999999999999998 7999999999


Q ss_pred             cc
Q 030172          130 LE  131 (182)
Q Consensus       130 ~~  131 (182)
                      +.
T Consensus        75 ~~   76 (136)
T PRK05807         75 AM   76 (136)
T ss_pred             cc
Confidence            86

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

Probab=99.40  E-value=1.2e-12  Score=85.67  Aligned_cols=63  Identities=38%  Similarity=0.811  Sum_probs=56.1

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCC-ccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~-~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      |+++.|+     ++|+||++.  ++   ++||+|+++++| .+..++.+.|++||.|+|+|+++|.+++++.|+
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--GG---IDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeC--CC---CEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            5677777     999999996  45   999999999997 567888999999999999999999999999874

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.

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

Probab=99.37  E-value=2.5e-12  Score=84.55  Aligned_cols=65  Identities=31%  Similarity=0.469  Sum_probs=59.8

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      |+++.|+     ++|+||+++  .+   .+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~--~~---~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIG--YK---SEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeC--CC---ceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            6788888     889999996  34   99999999999999999999999999999999999988899999985

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.

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

Probab=99.36  E-value=3.7e-12  Score=82.65  Aligned_cols=64  Identities=45%  Similarity=0.893  Sum_probs=58.5

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      |+++.|+     ++|+||++.  ++   .+||+|.+++++.++.++.+.|++||.++|+|+++|+ ++++.||+|
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--GG---ISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEEC--CC---CEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence            6777777     999999996  45   9999999999999999999999999999999999998 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.

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

Probab=99.35  E-value=4.4e-12  Score=103.72  Aligned_cols=85  Identities=35%  Similarity=0.597  Sum_probs=73.1

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      -+++|+++.|+     ++|+||+|..++|   ++||+|++++++.++.++++.|++||.+.|+|+++|++++++.||+|.
T Consensus         5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~g---ieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~   81 (262)
T PRK03987          5 WPEEGELVVGTVKEVKDFGAFVTLDEYPG---KEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR   81 (262)
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCCCC---cEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEe
Confidence            36789999999     9999999974445   999999999999999999999999999999999999999999999998


Q ss_pred             ccCCchhHHHhhh
Q 030172          130 LEEDPLLETLEKV  142 (182)
Q Consensus       130 ~~~~p~~~~~~~~  142 (182)
                      +.++.-....+.+
T Consensus        82 v~~~e~~~~~~~~   94 (262)
T PRK03987         82 VNEHQRREKIQEW   94 (262)
T ss_pred             cccchHHHHHHHH
Confidence            8765533333333

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

Probab=99.34  E-value=7.1e-12  Score=82.77  Aligned_cols=66  Identities=41%  Similarity=0.741  Sum_probs=57.8

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCc-cccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~-~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      +.+|+++.|+     ++|+||++.  +|   ++||+|+++++|. +..++.+.|++||.++|+|+++|.+++++.++
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~--~~---~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELE--EG---VEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcC--CC---CEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence            4678999998     999999996  45   9999999999875 45577788999999999999999988988764

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=99.30  E-value=4.4e-12  Score=89.47  Aligned_cols=70  Identities=31%  Similarity=0.541  Sum_probs=61.6

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc-------------------cCccccccCCCEEEE
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDEVRV  111 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~-------------------~~~~~~~~~Gd~v~v  111 (182)
                      +++|+++.|+     ++|+||.+.  +|   ++|++|++++++.+.                   .++.+.|++||.|+|
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--NG---LTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRC   75 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECC--CC---cEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEE
Confidence            5789999999     999999995  56   999999999998753                   347788999999999


Q ss_pred             EEEEEeCC---CCeEEEEEeec
Q 030172          112 KVIKIDRE---KSRITLSIKQL  130 (182)
Q Consensus       112 kV~~id~~---~~ki~lS~k~~  130 (182)
                      +|+++|++   +++|.||+|..
T Consensus        76 kVi~~d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          76 KVVSLDKSKSGKKRIELSLEPE   97 (100)
T ss_pred             EEEEccCCcCCCcEEEEEecHH
Confidence            99999987   78999999864

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

>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=99.27  E-value=1.4e-11  Score=79.76  Aligned_cols=63  Identities=38%  Similarity=0.652  Sum_probs=56.6

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      |+++.|+     ++|+||++.  ++   .+|++|.+++++.++.++.+.|++||.++|+|+++|++++++.||
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--VK---QDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcC--CC---CEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            5677777     999999996  44   999999999999988899999999999999999999988998875

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.

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

Probab=99.27  E-value=1.8e-11  Score=79.87  Aligned_cols=61  Identities=20%  Similarity=0.349  Sum_probs=53.2

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      |+++.|+     ++|+||++.  +|   ++|++|.++++..+..  .+.|++||.++|+|+++|++++++.||
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--SS---FTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEc--CC---ceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            6788888     999999996  45   9999999999765544  677999999999999999999998876

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.

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

Probab=99.26  E-value=3.1e-11  Score=78.30  Aligned_cols=63  Identities=46%  Similarity=0.907  Sum_probs=57.5

Q ss_pred             CCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        58 ~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      +|+++.|+     ++|+||+++   +   .+|++|.+++++.+..++.+.|++||.++|+|+++|.+++++.||
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---G---VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC---C---eEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            47888888     999999995   3   999999999999888899999999999999999999989999875

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.

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

Probab=99.26  E-value=3.2e-11  Score=78.32  Aligned_cols=63  Identities=46%  Similarity=0.838  Sum_probs=56.7

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      |+++.|+     ++|+||++.  ++   .+||+|++++++.+..++.+.|++||.++|+|.++|+ ++++.+|+
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--PG---KDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeC--CC---CEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence            5677777     999999996  44   8999999999999988888999999999999999998 89999884

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.

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

Probab=99.24  E-value=5.6e-11  Score=112.33  Aligned_cols=156  Identities=16%  Similarity=0.218  Sum_probs=131.3

Q ss_pred             CCCeEEEEEEEEeCCCCEEEEEechhHHhh---hhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCC
Q 030172           22 TGSIISVKVIQANEEMKKLVFSEKDAVWNK---YSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW   93 (182)
Q Consensus        22 vG~~v~~~v~~~d~~~~~i~lS~k~~~~~~---~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~   93 (182)
                      +|.++.+++..+-.....+.+|..++....   ...++++|++|.|+     +-|+-|.+.  +|  ++.|++|-+.+++
T Consensus       470 ~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~nDI~iG~~V~~~I~~vt~~Gv~v~v~--~~--ni~g~lp~~hlsd  545 (1710)
T KOG1070|consen  470 VGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVNDIEIGQLVPGVIRKVTPQGVEVLVT--FG--NIKGVLPKEHLSD  545 (1710)
T ss_pred             cCCcccCccceecccCcEEEEEEehHhhcccccccccccccceeeeEEEEecCCcEEEEEe--cC--ceeeecChHhhhh
Confidence            788999999999999899999988753221   24579999999999     889999986  34  5999999999999


Q ss_pred             ccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcC-CCCceeEeeEeeecCCeeEEecCCChhh
Q 030172           94 DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP-QDGSVISDSSSMSSSNSNTIEPLPGLGA  172 (182)
Q Consensus        94 ~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~-~~g~~v~G~V~~v~~~G~fV~l~~gv~g  172 (182)
                      ....-|...|.+|..++.||+.++.+++++.|++|....+...+..++|.. ..|..+.|++.++.++||||++..|++|
T Consensus       546 ~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsG  625 (1710)
T KOG1070|consen  546 HPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGAFVTFTGGLSG  625 (1710)
T ss_pred             cccccccceeeeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCeEEEecCcccc
Confidence            998889889999999999999999999999999997765554444444421 2399999999999999999999999999


Q ss_pred             hchhhhhcc
Q 030172          173 IFEELLQED  181 (182)
Q Consensus       173 l~~~~~~~~  181 (182)
                      |.|...+-|
T Consensus       626 f~p~s~~sd  634 (1710)
T KOG1070|consen  626 FAPVSEMSD  634 (1710)
T ss_pred             ccchhhhhh
Confidence            999987754

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

Probab=99.23  E-value=3.6e-11  Score=82.17  Aligned_cols=70  Identities=23%  Similarity=0.372  Sum_probs=61.4

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCC----ccccCccccccCCCEEEEEEEEEeCCCCeEEE
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW----DLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~----~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~l  125 (182)
                      .+++|++|.|+     ++|++|+++  .+   ++|++|++++++    .+..++.+.+++||.++|+|+++|++ +++.|
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--SP---YDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSL   76 (86)
T ss_pred             cCCCCCEEEEEEEEECCCEEEEECC--CC---eEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEE
Confidence            46899999999     999999996  34   999999999996    45577788899999999999999975 99999


Q ss_pred             EEeec
Q 030172          126 SIKQL  130 (182)
Q Consensus       126 S~k~~  130 (182)
                      |+|..
T Consensus        77 S~~~~   81 (86)
T cd05789          77 HTRSL   81 (86)
T ss_pred             EeCcc
Confidence            99864

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".

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=99.22  E-value=6.7e-11  Score=92.54  Aligned_cols=101  Identities=23%  Similarity=0.318  Sum_probs=80.9

Q ss_pred             CCCeEEEEEE---EEeCCCCEEEEEechhHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCC--C---ceeEEEEEEc
Q 030172           22 TGSIISVKVI---QANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPD--G---LYHLTGLVHV   88 (182)
Q Consensus        22 vG~~v~~~v~---~~d~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~--g---~~~~~glv~~   88 (182)
                      .+..+.+.+.   ++|.+++++.+    .+|......+++|++|.|+     ++|+||+|...+  +   ..+.+|++|+
T Consensus        29 ~~~~i~as~~G~~~id~~~~~Isv----~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~  104 (189)
T PRK09521         29 DNGEVYASVVGKVFIDDINRKISV----IPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHI  104 (189)
T ss_pred             eCCEEEEEeeEEEEEcCCCCEEEE----ecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEh
Confidence            4666666554   44667778877    4666656778999999999     999999996321  0   0028999999


Q ss_pred             cCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           89 SEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        89 sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      +++++.+..++.+.|++||.|.|+|++++   +++.||+|+
T Consensus       105 s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~  142 (189)
T PRK09521        105 SQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKG  142 (189)
T ss_pred             hHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEec
Confidence            99999988899999999999999999997   789999985

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

Probab=99.21  E-value=6.7e-11  Score=77.13  Aligned_cols=62  Identities=29%  Similarity=0.584  Sum_probs=55.0

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      |+++.|+     ++|+||+++   |   ++||+|.+++++.+..++.+  .+||.++|+|+++|.+++++.||+|
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---G---VRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEEC---C---EEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            6788887     999999993   5   99999999999988777766  3899999999999998999999975

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=99.21  E-value=9.8e-11  Score=107.42  Aligned_cols=91  Identities=35%  Similarity=0.647  Sum_probs=76.1

Q ss_pred             EeCCCCEEEEEech--------hHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCc
Q 030172           33 ANEEMKKLVFSEKD--------AVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI   99 (182)
Q Consensus        33 ~d~~~~~i~lS~k~--------~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~   99 (182)
                      +++ ++.+.++...        ...+.....+++|+++.|+     +||+||+|.  +|   .+||+|++++++.++.++
T Consensus       589 i~d-~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~--~~---~~GllhiSels~~~v~~~  662 (693)
T PRK11824        589 IED-DGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEIL--PG---KDGLVHISEIADERVEKV  662 (693)
T ss_pred             cCC-CceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEEC--CC---CEEEEEeeeccCccccCc
Confidence            443 4676666542        1233445678999999999     999999996  45   999999999999999999


Q ss_pred             cccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172          100 RDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (182)
Q Consensus       100 ~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~  130 (182)
                      .+.|++||.|+|+|+++|++ +++.||+|.+
T Consensus       663 ~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~  692 (693)
T PRK11824        663 EDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV  692 (693)
T ss_pred             cceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence            99999999999999999986 9999999975

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.21  E-value=8.5e-11  Score=106.92  Aligned_cols=89  Identities=25%  Similarity=0.545  Sum_probs=71.3

Q ss_pred             EEEeCCCCEEEEEechh--------HHhhhhc--CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcC---
Q 030172           31 IQANEEMKKLVFSEKDA--------VWNKYSS--RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS---   92 (182)
Q Consensus        31 ~~~d~~~~~i~lS~k~~--------~~~~~~~--~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels---   92 (182)
                      +++++ ++.+.++-...        ..+.+..  .+++|++|.|+     +||+||+|.  .|   ++||||+|+++   
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--PG---KDGLLHISQIRKLA  684 (719)
T ss_pred             EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEec--CC---ceEEEEhhhccccc
Confidence            35665 57777765431        2223333  47899999999     999999996  45   99999999996   


Q ss_pred             -CccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           93 -WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        93 -~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                       +.++.++.+.|++||.|+|+|+++|. ++|+.|+
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             45789999999999999999999995 8899886

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.

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

Probab=99.20  E-value=1.1e-10  Score=75.74  Aligned_cols=67  Identities=45%  Similarity=0.783  Sum_probs=60.6

Q ss_pred             CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      ++|+++.|+     ++|+||+++  ++   +.|++|.+++++.+..++.+.|++||.+.|+|++++++++++.+|++
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~--~~---~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLG--NG---VEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeC--CC---CEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            368999998     899999996  35   99999999999988888888999999999999999998899999975

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

Probab=99.18  E-value=1.2e-10  Score=80.34  Aligned_cols=70  Identities=27%  Similarity=0.423  Sum_probs=59.2

Q ss_pred             cCCCCCCEEEEE-----eE--eEEEEEecCCCceeEEEEEEccCcCC---ccccCccccccCCCEEEEEEEEEeCCCCeE
Q 030172           54 SRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSW---DLIQDIRDILNEGDEVRVKVIKIDREKSRI  123 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~--G~fV~l~~~~g~~~~~glv~~sels~---~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki  123 (182)
                      .+++.|++|.|+     ++  ||||+++  +|   .+||||+++++|   .++.++.+.+++||.|.|+|++.....+-.
T Consensus         3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~--~g---~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~   77 (88)
T cd04453           3 REPIVGNIYLGRVKKIVPGLQAAFVDIG--LG---KNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGP   77 (88)
T ss_pred             CcCCCCCEEEEEEEEeccCCcEEEEEeC--CC---CEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCc
Confidence            357899999999     64  9999997  46   999999999999   668888999999999999999987655555


Q ss_pred             EEEEe
Q 030172          124 TLSIK  128 (182)
Q Consensus       124 ~lS~k  128 (182)
                      .||.+
T Consensus        78 ~lt~~   82 (88)
T cd04453          78 RLTTN   82 (88)
T ss_pred             eEEEE
Confidence            55554

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

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

Probab=99.14  E-value=4.9e-10  Score=75.61  Aligned_cols=65  Identities=29%  Similarity=0.577  Sum_probs=54.8

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcccc-----------CccccccCCCEEEEEEEEEeCCCCe
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKSR  122 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~-----------~~~~~~~~Gd~v~vkV~~id~~~~k  122 (182)
                      |+++.|.     ++|+||++.. .|   ++|++|++++++.++.           +..+.|++||.|+|+|.++|.++++
T Consensus         2 g~~~~g~V~~v~~~G~fv~l~~-~~---~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~   77 (83)
T cd04471           2 GEEFDGVISGVTSFGLFVELDN-LT---VEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRK   77 (83)
T ss_pred             CCEEEEEEEeEEeeeEEEEecC-CC---EEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCE
Confidence            7788888     9999999962 15   9999999999876422           3457899999999999999998999


Q ss_pred             EEEEE
Q 030172          123 ITLSI  127 (182)
Q Consensus       123 i~lS~  127 (182)
                      +.+++
T Consensus        78 i~~~l   82 (83)
T cd04471          78 IDFEL   82 (83)
T ss_pred             EEEEE
Confidence            99986

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.

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

Probab=99.09  E-value=5e-10  Score=75.89  Aligned_cols=69  Identities=22%  Similarity=0.216  Sum_probs=62.7

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      .+++|+++.|+     +.+++|+++  .+   .+|++|.++++..+..++.+.|++||.+.|+|+++|.+ +++.||++.
T Consensus         3 ~p~~GdiV~G~V~~v~~~~~~V~i~--~~---~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~   76 (82)
T cd04454           3 LPDVGDIVIGIVTEVNSRFWKVDIL--SR---GTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD   76 (82)
T ss_pred             CCCCCCEEEEEEEEEcCCEEEEEeC--CC---ceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence            35899999999     899999996  33   99999999999888888999999999999999999985 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".

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=99.06  E-value=2.8e-10  Score=103.39  Aligned_cols=75  Identities=36%  Similarity=0.607  Sum_probs=69.4

Q ss_pred             hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      ..++++|.++.|+     +||+||+|+  -+   .+|+||+|+++..++.+|.+.+++||.|+|+|+++|..+++|.|||
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--VH---QDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSM  727 (780)
T ss_pred             HhhccCCCEEEEEEEEeeeccceEEec--cc---cceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEe
Confidence            3579999999999     999999997  23   8999999999999999999999999999999999999999999999


Q ss_pred             eeccC
Q 030172          128 KQLEE  132 (182)
Q Consensus       128 k~~~~  132 (182)
                      +....
T Consensus       728 r~~~~  732 (780)
T COG2183         728 RLDEE  732 (780)
T ss_pred             eccCC
Confidence            97644

>TIGR02063 RNase_R ribonuclease R

Probab=99.06  E-value=1e-10  Score=107.82  Aligned_cols=120  Identities=23%  Similarity=0.341  Sum_probs=80.7

Q ss_pred             CCCCCCCCCCccHHHhhhhcCCCe--EE-EEEEEEeCCC-CEE--EEEec--hh---------HHhhhhcCCCCCCEEEE
Q 030172            2 SPSHSCKEPQKSIHEIAKGLTGSI--IS-VKVIQANEEM-KKL--VFSEK--DA---------VWNKYSSRVNVEDIFVG   64 (182)
Q Consensus         2 ~p~~~~p~~e~~~~~~~~~~vG~~--v~-~~v~~~d~~~-~~i--~lS~k--~~---------~~~~~~~~~~~G~iv~g   64 (182)
                      ||+|  +|+|+-.|+.++.++...  .. ..-....... ..+  .++.+  .+         .|...+...++|+++.|
T Consensus       556 SPIR--RY~DLivHr~L~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g  633 (709)
T TIGR02063       556 SPIR--RYPDLIVHRLIKKALFGGENTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEG  633 (709)
T ss_pred             Cccc--cchHHHHHHHHHHHHcCCCCCCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCcEEEE
Confidence            8999  999999999888775322  11 0000000000 000  00000  00         12223445678999999


Q ss_pred             E-----eEeEEEEEecCCCceeEEEEEEccCcCCccc-----------cCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           65 R-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        65 ~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~-----------~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      +     +||+||++.. .|   ++|+||++++++.+.           .+..+.|++||.|+|+|.++|..+++|.+++
T Consensus       634 ~V~~v~~fGifV~L~~-~~---~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~I~~~l  708 (709)
T TIGR02063       634 VISGVTSFGLFVELEN-NT---IEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFEL  708 (709)
T ss_pred             EEEEEEeCCEEEEecC-Cc---eEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCeEEEEE
Confidence            9     9999999962 15   999999999987643           2345679999999999999999999999986

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.

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

Probab=99.06  E-value=6.4e-10  Score=99.72  Aligned_cols=93  Identities=37%  Similarity=0.659  Sum_probs=78.0

Q ss_pred             EEeCCCCEEEEEech--------hHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccC
Q 030172           32 QANEEMKKLVFSEKD--------AVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD   98 (182)
Q Consensus        32 ~~d~~~~~i~lS~k~--------~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~   98 (182)
                      +++ +++.+..+-..        .........+++|++|.|+     +||+||++.  +|   .+|+||+|++++.++.+
T Consensus       586 die-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~--~g---kdgl~hiS~~~~~rv~k  659 (692)
T COG1185         586 DIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELL--PG---KDGLVHISQLAKERVEK  659 (692)
T ss_pred             Eec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEec--CC---cceeEEehhhhhhhhhc
Confidence            455 45666555443        1344556789999999999     999999996  45   89999999999999999


Q ss_pred             ccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172           99 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (182)
Q Consensus        99 ~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~  131 (182)
                      ..+.+++||.+.||++.+|. .+++.||+|...
T Consensus       660 v~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~~  691 (692)
T COG1185         660 VEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAVL  691 (692)
T ss_pred             ccceeecCceEEEEEeeecc-cCCccceehhcc
Confidence            99999999999999999996 899999998653

>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=98.99  E-value=1.4e-09  Score=71.56  Aligned_cols=57  Identities=23%  Similarity=0.295  Sum_probs=50.5

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcc--ccCccccccCCCEEEEEEEEEeCCC
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREK  120 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~--~~~~~~~~~~Gd~v~vkV~~id~~~  120 (182)
                      |+++.|+     ++|+||+++  +|   ++|++|++++++.+  ..++.+.|++||.|+|+|+++|.++
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--DN---VHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK   64 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeC--CC---cEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence            6778888     889999996  55   99999999999885  7888899999999999999999743

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.99  E-value=1.7e-09  Score=99.13  Aligned_cols=87  Identities=34%  Similarity=0.679  Sum_probs=70.6

Q ss_pred             EEeCCCCEEEEEech-h-------HHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccC
Q 030172           32 QANEEMKKLVFSEKD-A-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD   98 (182)
Q Consensus        32 ~~d~~~~~i~lS~k~-~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~   98 (182)
                      +++. ++.+.++... +       ..+.....+++|++|.|+     +||+||++.  +|   .+||||+|++++.++.+
T Consensus       585 ~i~d-dG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~--~g---~~GllHiSei~~~~v~~  658 (684)
T TIGR03591       585 DIED-DGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEIL--PG---KDGLVHISEIANERVEK  658 (684)
T ss_pred             EEec-CeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEEC--CC---cEEEEEHHHcCCCcccC
Confidence            4554 4777666532 1       233345568999999999     999999996  45   99999999999999999


Q ss_pred             ccccccCCCEEEEEEEEEeCCCCeEEE
Q 030172           99 IRDILNEGDEVRVKVIKIDREKSRITL  125 (182)
Q Consensus        99 ~~~~~~~Gd~v~vkV~~id~~~~ki~l  125 (182)
                      +.+.|++||.|+|+|+++|. ++++.|
T Consensus       659 ~~~~~kvGD~V~VkVi~id~-~gki~L  684 (684)
T TIGR03591       659 VEDVLKEGDEVKVKVLEIDK-QGRIKL  684 (684)
T ss_pred             hhhccCCCCEEEEEEEEECC-CCCccC
Confidence            99999999999999999997 677754

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).

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

Probab=98.99  E-value=1.5e-09  Score=68.96  Aligned_cols=56  Identities=48%  Similarity=0.873  Sum_probs=51.3

Q ss_pred             eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        66 ~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      ++|+||+++  ++   .+|++|.+++++.+..++.+.|++||.|+|+|+++|++++++.||
T Consensus        10 ~~g~~v~l~--~~---~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164          10 KFGVFVELE--DG---VEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             eeeEEEEec--CC---CEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            899999996  45   999999999999988888999999999999999999988888875

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=98.97  E-value=5.6e-09  Score=70.02  Aligned_cols=61  Identities=34%  Similarity=0.579  Sum_probs=53.8

Q ss_pred             hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      .++++.|+.+.|+     ++|+||++.  ++   .+||+|.+++.        +.|++||.++++|.++ .+++++.+|+
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--DH---VRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP   76 (77)
T ss_pred             hhhCCCCCEEEEEEEeEecceEEEEEC--CC---cEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence            3568999999999     999999996  44   99999999964        4599999999999999 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=98.95  E-value=6.4e-09  Score=73.02  Aligned_cols=68  Identities=29%  Similarity=0.518  Sum_probs=57.7

Q ss_pred             eEeEEEEEecCCCceeEEEEEEccCcCCccccC-----------ccccccCCCEEEEEEEEEeCCC-----CeEEEEEee
Q 030172           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-----------IRDILNEGDEVRVKVIKIDREK-----SRITLSIKQ  129 (182)
Q Consensus        66 ~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~-----------~~~~~~~Gd~v~vkV~~id~~~-----~ki~lS~k~  129 (182)
                      ++|+||++.   +   ++|++|++++++.+...           ..+.|++||.|+|+|.++|.+.     .++.||+|+
T Consensus        12 ~~GifV~l~---~---v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~   85 (99)
T cd04460          12 DFGAFVRIG---P---VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMRQ   85 (99)
T ss_pred             eccEEEEEc---C---eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEec
Confidence            999999995   3   99999999999876543           3477999999999999999753     589999999


Q ss_pred             ccCCchhHHH
Q 030172          130 LEEDPLLETL  139 (182)
Q Consensus       130 ~~~~p~~~~~  139 (182)
                      ....||....
T Consensus        86 ~~~g~~~~~~   95 (99)
T cd04460          86 PGLGKLEWIE   95 (99)
T ss_pred             CCCCcHHHhh
Confidence            9888887654

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.

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

Probab=98.92  E-value=1.5e-08  Score=82.16  Aligned_cols=137  Identities=16%  Similarity=0.158  Sum_probs=102.7

Q ss_pred             CCCeEEEEEEEEeCCCCEEEEEechhHHhhhhcCCCCCCEEEEE------eEeEEEEEecCCCceeEEEEEEccCcCCcc
Q 030172           22 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL   95 (182)
Q Consensus        22 vG~~v~~~v~~~d~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~------~~G~fV~l~~~~g~~~~~glv~~sels~~~   95 (182)
                      +|++|++.|  +-..++++.+|.++       +..++|+.-.++      +-|+|++.+-+     .+.+||++++...+
T Consensus        46 vGdev~vFi--Y~D~~~rl~aTt~~-------p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~-----KDl~vp~~elp~~~  111 (287)
T COG2996          46 VGDEVTVFI--YVDSEDRLIATTRE-------PKATVGEYGWLKVVEVNKDLGAFLDWGLP-----KDLLVPLDELPTLK  111 (287)
T ss_pred             cCcEEEEEE--EECCCCceeheeec-------ceEeecceeEEEEEEEcCCcceEEecCCC-----cceeeehhhccccc
Confidence            899999999  65567889988877       566677765554      88999999743     79999999987531


Q ss_pred             ccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcC-CCCceeEeeEeeecCCeeEEecCCChhhhc
Q 030172           96 IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP-QDGSVISDSSSMSSSNSNTIEPLPGLGAIF  174 (182)
Q Consensus        96 ~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~-~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~  174 (182)
                          .--+++||.+-|.+ .+|. ++|+.-+++.  ....+..+..... -.++.+.|+|++....|.||-+++++-||+
T Consensus       112 ----~~wpq~Gd~l~v~l-~~Dk-k~Ri~g~~a~--~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfI  183 (287)
T COG2996         112 ----SLWPQKGDKLLVYL-YVDK-KGRIWGTLAI--EKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFI  183 (287)
T ss_pred             ----ccCCCCCCEEEEEE-EEcc-CCcEEEEecc--hhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEE
Confidence                00168999999997 8997 6688888763  2222222222111 128999999999999999999999999999


Q ss_pred             hhhhhc
Q 030172          175 EELLQE  180 (182)
Q Consensus       175 ~~~~~~  180 (182)
                      |..++.
T Consensus       184 h~sEr~  189 (287)
T COG2996         184 HKSERF  189 (287)
T ss_pred             cchhhc
Confidence            987753

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

Probab=98.92  E-value=1.7e-10  Score=105.40  Aligned_cols=119  Identities=22%  Similarity=0.353  Sum_probs=80.2

Q ss_pred             CCCCCCCCCCccHHHhhhhcC-CCeEEEEEEEEeCCC-CEE--EEEec--hh---------HHhhhhcCCCCCCEEEEE-
Q 030172            2 SPSHSCKEPQKSIHEIAKGLT-GSIISVKVIQANEEM-KKL--VFSEK--DA---------VWNKYSSRVNVEDIFVGR-   65 (182)
Q Consensus         2 ~p~~~~p~~e~~~~~~~~~~v-G~~v~~~v~~~d~~~-~~i--~lS~k--~~---------~~~~~~~~~~~G~iv~g~-   65 (182)
                      ||+|  +|+|+-.|+.++.++ |......- ..+.+. ..+  .+|.+  .+         .|...+..-++|+++.|+ 
T Consensus       504 SPIR--RY~DLivHr~L~a~l~~~~~~~~~-~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g~I  580 (654)
T TIGR00358       504 SPIR--RYPDLTNHRLIKAVLAKEQTDTER-YQPQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVGTEFSGEI  580 (654)
T ss_pred             Cccc--cchHHHHHHHHHHHHcCCCCcccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCcEEEEEE
Confidence            9999  999999999888775 33211000 000000 000  00000  00         122223445689999999 


Q ss_pred             ----eEeEEEEEecCCCceeEEEEEEccCcCCccc-----------cCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           66 ----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        66 ----~~G~fV~l~~~~g~~~~~glv~~sels~~~~-----------~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                          ++|+||+|.. .|   ++|+||++++.+.+.           .+....|++||.|+|+|.++|.++++|.+++
T Consensus       581 ~~v~~~GifV~L~~-~~---veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~f~l  653 (654)
T TIGR00358       581 SSVTRFGMFVRLDD-NG---IDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSIIFEL  653 (654)
T ss_pred             EeEEcCcEEEEecC-Cc---eEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEEEEE
Confidence                9999999963 24   999999999988742           2334679999999999999999999999986

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.

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

Probab=98.87  E-value=1.2e-08  Score=79.16  Aligned_cols=131  Identities=23%  Similarity=0.480  Sum_probs=85.9

Q ss_pred             CCCCCCCCCCCccHH-HhhhhcCCCe-----EEEEEEEEeC-CCCEEEEEec----hhHHhhhhcCCCCCCEEEEE----
Q 030172            1 MSPSHSCKEPQKSIH-EIAKGLTGSI-----ISVKVIQANE-EMKKLVFSEK----DAVWNKYSSRVNVEDIFVGR----   65 (182)
Q Consensus         1 ~~p~~~~p~~e~~~~-~~~~~~vG~~-----v~~~v~~~d~-~~~~i~lS~k----~~~~~~~~~~~~~G~iv~g~----   65 (182)
                      ++|+.|.+...-.+. ++.+.+.|..     +-..|.++.. ..+++.-..-    .........+...|+++.|+    
T Consensus        13 i~P~~~~~~~~~~i~~~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~~gEvv~G~V~~v   92 (179)
T TIGR00448        13 IPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPELGEIVEGEVIEI   92 (179)
T ss_pred             ECHHHhCccHHHHHHHHHHHHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEeccCCCEEEEEEEEE
Confidence            467777654444443 3444455543     2333333332 2344431111    11233344567889999999    


Q ss_pred             -eEeEEEEEecCCCceeEEEEEEccCcCCcccc-----------CccccccCCCEEEEEEEEEe-----CCCCeEEEEEe
Q 030172           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKID-----REKSRITLSIK  128 (182)
Q Consensus        66 -~~G~fV~l~~~~g~~~~~glv~~sels~~~~~-----------~~~~~~~~Gd~v~vkV~~id-----~~~~ki~lS~k  128 (182)
                       ++|+||+++ +     ++|++|.+++.+.+..           +....|+.||.|++||+++|     ++..++.+|+|
T Consensus        93 ~~~GifV~lg-~-----~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~~I~lt~k  166 (179)
T TIGR00448        93 VEFGAFVSLG-P-----FDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEGSKIGLTMR  166 (179)
T ss_pred             EeeEEEEEeC-C-----ceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCcceEEEEec
Confidence             999999995 2     8999999998865432           23467999999999999998     56789999999


Q ss_pred             eccCCchhH
Q 030172          129 QLEEDPLLE  137 (182)
Q Consensus       129 ~~~~~p~~~  137 (182)
                      +.-..+++.
T Consensus       167 ~~~LG~~~w  175 (179)
T TIGR00448       167 QPLLGKLEW  175 (179)
T ss_pred             cCcCCcccc
Confidence            876555443

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

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.87  E-value=4.8e-09  Score=92.23  Aligned_cols=108  Identities=19%  Similarity=0.271  Sum_probs=82.1

Q ss_pred             CCCCccHHHh----hhhcCCCeEEEEEEEEeCCCCEEEEEe-ch--------hHHhhhhcCCC--CCCEEEEE-----eE
Q 030172            8 KEPQKSIHEI----AKGLTGSIISVKVIQANEEMKKLVFSE-KD--------AVWNKYSSRVN--VEDIFVGR-----DY   67 (182)
Q Consensus         8 p~~e~~~~~~----~~~~vG~~v~~~v~~~d~~~~~i~lS~-k~--------~~~~~~~~~~~--~G~iv~g~-----~~   67 (182)
                      |..++++.+.    ....+|+.+.+.|...+  .+++.++. |+        +.++..+..++  .|+++.|+     ++
T Consensus        71 ~~~eI~L~eAk~~~~~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~  148 (470)
T PRK09202         71 PTKEISLEEARKIDPDAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERG  148 (470)
T ss_pred             CcceeeHHHHhhhCccccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecC
Confidence            3445555532    33459999999997776  34443332 22        12335566776  99999999     89


Q ss_pred             eEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCC--eEEEEEee
Q 030172           68 GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ  129 (182)
Q Consensus        68 G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~--ki~lS~k~  129 (182)
                      |+||+++   |   ++||+|.++++      |++.|++||.++|.|++++++++  +|.||++.
T Consensus       149 giiVDLg---g---vea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~  200 (470)
T PRK09202        149 NIIVDLG---R---AEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH  200 (470)
T ss_pred             CEEEEEC---C---eEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence            9999995   5   99999999986      77889999999999999998777  89999975

>PRK11642 exoribonuclease R; Provisional

Probab=98.86  E-value=5.8e-10  Score=103.77  Aligned_cols=73  Identities=29%  Similarity=0.432  Sum_probs=60.8

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcccc-----------CccccccCCCEEEEEEEEEeC
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDR  118 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~-----------~~~~~~~~Gd~v~vkV~~id~  118 (182)
                      .-++|+++.|+     +||+||+|.. .+   ++|+||++++++.|..           +..+.|++||.|+|+|.++|.
T Consensus       640 ~~~iGe~f~G~Is~V~~fGifVeL~~-~~---vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~  715 (813)
T PRK11642        640 LDQVGNVFKGVISSVTGFGFFVRLDD-LF---IDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNM  715 (813)
T ss_pred             hccCCcEEEEEEEEeecCceEEEECC-CC---eeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeec
Confidence            44789999999     9999999962 24   9999999999876432           234679999999999999999


Q ss_pred             CCCeEEEEEeecc
Q 030172          119 EKSRITLSIKQLE  131 (182)
Q Consensus       119 ~~~ki~lS~k~~~  131 (182)
                      ++++|.+++....
T Consensus       716 ~~rkI~f~l~~~~  728 (813)
T PRK11642        716 DERKIDFSLISSE  728 (813)
T ss_pred             CCCeEEEEEeccc
Confidence            9999999996443

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

Probab=98.77  E-value=3.2e-08  Score=76.13  Aligned_cols=126  Identities=25%  Similarity=0.433  Sum_probs=83.0

Q ss_pred             CCCCCC-CCCCCccHHHhhhhcCCCe-----EEEEEEEEeC-CCCEEEEEech----hHHhhhhcCCCCCCEEEEE----
Q 030172            1 MSPSHS-CKEPQKSIHEIAKGLTGSI-----ISVKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR----   65 (182)
Q Consensus         1 ~~p~~~-~p~~e~~~~~~~~~~vG~~-----v~~~v~~~d~-~~~~i~lS~k~----~~~~~~~~~~~~G~iv~g~----   65 (182)
                      ++|+.| -|..+.-.+.+.+.+.|.-     +-..|.++.. ..+++....-.    .....+..++..|+++.|.    
T Consensus        13 ipP~~fg~~~~~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~   92 (183)
T COG1095          13 IPPSYFGEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEV   92 (183)
T ss_pred             eCHHHcCccHHHHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEE
Confidence            467766 3344444444555565543     3334444433 23444432211    2334445678889999998    


Q ss_pred             -eEeEEEEEecCCCceeEEEEEEccCcCCccc----------cC-ccccccCCCEEEEEEEEEeCCC-----CeEEEEEe
Q 030172           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----------QD-IRDILNEGDEVRVKVIKIDREK-----SRITLSIK  128 (182)
Q Consensus        66 -~~G~fV~l~~~~g~~~~~glv~~sels~~~~----------~~-~~~~~~~Gd~v~vkV~~id~~~-----~ki~lS~k  128 (182)
                       ++|+||.++ |     .+||+|++++.+.++          .+ ....+++||.|++||++.+...     .+|.+|+|
T Consensus        93 ~~~G~fV~ig-p-----~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~~I~lTmr  166 (183)
T COG1095          93 VEFGAFVRIG-P-----LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMR  166 (183)
T ss_pred             eecceEEEec-c-----ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCccccceEEEEec
Confidence             999999997 3     899999999988743          22 3346999999999999998654     67899999


Q ss_pred             eccC
Q 030172          129 QLEE  132 (182)
Q Consensus       129 ~~~~  132 (182)
                      +.-.
T Consensus       167 q~~L  170 (183)
T COG1095         167 QPGL  170 (183)
T ss_pred             cccC
Confidence            8654

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.77  E-value=2.4e-08  Score=80.71  Aligned_cols=71  Identities=27%  Similarity=0.364  Sum_probs=62.7

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc----cCccccccCCCEEEEEEEEEeCCCCeEE
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRIT  124 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~----~~~~~~~~~Gd~v~vkV~~id~~~~ki~  124 (182)
                      ..+++||+|.|+     ++|+||+|+  .+   .+|++|++++++.++    .++++.|++||.|.|+|+++++ .+++.
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~--~~---~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~-~~~~~  132 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDIN--SP---YKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR-TRDVV  132 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeC--CC---ceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC-CCcEE
Confidence            457899999999     899999996  23   899999999999887    7889999999999999999996 55699


Q ss_pred             EEEeec
Q 030172          125 LSIKQL  130 (182)
Q Consensus       125 lS~k~~  130 (182)
                      ||+|+.
T Consensus       133 LS~k~~  138 (235)
T PRK04163        133 LTLKGK  138 (235)
T ss_pred             EEEcCC
Confidence            999863

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

Probab=98.66  E-value=1.6e-08  Score=88.91  Aligned_cols=82  Identities=27%  Similarity=0.423  Sum_probs=71.4

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      .++..|.+|.|+     ++|+||++.  .|   ..|++|+++|+..++.+|.+.+.+||.|.|+.++.|+ ++.+.+|.|
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--PM---QQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSSR  737 (760)
T ss_pred             cceEeeeEEEEEEeeecccceEEEec--CC---chhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehhh
Confidence            356777788888     999999996  36   9999999999999999999999999999999999998 888888889


Q ss_pred             eccCCchhHHHhh
Q 030172          129 QLEEDPLLETLEK  141 (182)
Q Consensus       129 ~~~~~p~~~~~~~  141 (182)
                      .+.++|.......
T Consensus       738 alLp~p~~~~~st  750 (760)
T KOG1067|consen  738 ALLPDPATKESST  750 (760)
T ss_pred             hhcCCcccCCccc
Confidence            8888886554433

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

Probab=98.65  E-value=2.2e-07  Score=72.48  Aligned_cols=128  Identities=23%  Similarity=0.465  Sum_probs=84.0

Q ss_pred             CCCCCCCCCCCccHHH-hhhhcCCCe-----EEEEEEEEeC-CCCEEEEEech----hHHhhhhcCCCCCCEEEEE----
Q 030172            1 MSPSHSCKEPQKSIHE-IAKGLTGSI-----ISVKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR----   65 (182)
Q Consensus         1 ~~p~~~~p~~e~~~~~-~~~~~vG~~-----v~~~v~~~d~-~~~~i~lS~k~----~~~~~~~~~~~~G~iv~g~----   65 (182)
                      ++|++|.+..+-.+.+ +.+.+.|..     +-..|.+++. ..+++.-....    +.......++..|+++.|+    
T Consensus        13 i~P~~~~~~~~~~i~~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~~GEVv~g~V~~v   92 (187)
T PRK08563         13 IPPEMFGEDLEEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEV   92 (187)
T ss_pred             ECHHHcCccHHHHHHHHHHHHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEeccCCCEEEEEEEEE
Confidence            3677776644444443 333344443     3444444443 33444322111    2233444568899999999    


Q ss_pred             -eEeEEEEEecCCCceeEEEEEEccCcCCcccc-----------CccccccCCCEEEEEEEEEeCCC-----CeEEEEEe
Q 030172           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK-----SRITLSIK  128 (182)
Q Consensus        66 -~~G~fV~l~~~~g~~~~~glv~~sels~~~~~-----------~~~~~~~~Gd~v~vkV~~id~~~-----~ki~lS~k  128 (182)
                       ++|+||+++ +     ++|++|.+++.+.+..           +....+++||.|+++|.+++.+.     .++.+|++
T Consensus        93 ~~~Gi~V~lg-~-----~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~~I~ls~~  166 (187)
T PRK08563         93 VEFGAFVRIG-P-----VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRGSKIGLTMR  166 (187)
T ss_pred             EccEEEEEEe-C-----ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCCEEEEEec
Confidence             999999996 2     8999999999876432           34567999999999999998754     38999999


Q ss_pred             eccCCc
Q 030172          129 QLEEDP  134 (182)
Q Consensus       129 ~~~~~p  134 (182)
                      +.-.-+
T Consensus       167 ~~~LG~  172 (187)
T PRK08563        167 QPGLGK  172 (187)
T ss_pred             CCCCCc
Confidence            765433

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

Probab=98.62  E-value=2.1e-07  Score=60.70  Aligned_cols=59  Identities=17%  Similarity=0.285  Sum_probs=48.8

Q ss_pred             CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC--CeEEEEE
Q 030172           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLSI  127 (182)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~--~ki~lS~  127 (182)
                      ..|+++.|+     +.|+||+++   +   .+|++|.+|++      +.+.|++||.++|.|.+++.++  .+|.+|.
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig---~---~eg~lp~~e~~------~~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr   67 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLG---K---VEAILPKKEQI------PGESYRPGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcC---C---eEEEeeHHHCC------CCCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence            468999999     889999995   4   89999999987      3456899999999999998643  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.

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

Probab=98.55  E-value=2.5e-07  Score=64.25  Aligned_cols=74  Identities=22%  Similarity=0.262  Sum_probs=57.9

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCC---ceeEEEEEEccCcCCcccc--CccccccCCCEEEEEEEEEeCCCCeEE
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRIT  124 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g---~~~~~glv~~sels~~~~~--~~~~~~~~Gd~v~vkV~~id~~~~ki~  124 (182)
                      .+++|++|.|+     ...+.|+|...++   .....|++|++++...+..  ++.+.|++||.|+|+|++++. .+.+.
T Consensus         3 ~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~~~   81 (92)
T cd05791           3 LPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASSYY   81 (92)
T ss_pred             CCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCCcE
Confidence            35899999999     5568888821111   0027899999999877766  788999999999999999985 56789


Q ss_pred             EEEee
Q 030172          125 LSIKQ  129 (182)
Q Consensus       125 lS~k~  129 (182)
                      ||+++
T Consensus        82 Lst~~   86 (92)
T cd05791          82 LSTAE   86 (92)
T ss_pred             EEecC
Confidence            99975

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".

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=98.47  E-value=4.4e-07  Score=61.08  Aligned_cols=69  Identities=23%  Similarity=0.288  Sum_probs=62.5

Q ss_pred             cCCCCCCEEEEE----eEeEEEEEecCCCceeEEEEEE-ccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        54 ~~~~~G~iv~g~----~~G~fV~l~~~~g~~~~~glv~-~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      .-+++|+++.|.    +.|+||.|...    +++|++. .+|++.+++.+..+.+ +|..+.|+|+.+|+++|.|.||.
T Consensus        12 ~~P~v~dvv~~Vv~i~d~~~YV~LleY----~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         12 VFPNINEVTKGIVFVKDNIFYVKLIDY----GLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             ecCCCCeEEEEEEEEeccEEEEEEecC----ccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence            457899999987    99999999744    3999998 9999999999999999 99999999999999999999985

>PRK05054 exoribonuclease II; Provisional

Probab=98.47  E-value=7.4e-08  Score=88.00  Aligned_cols=117  Identities=16%  Similarity=0.136  Sum_probs=75.4

Q ss_pred             CCCCCCCCCCccHHHhhhhcC-CCeEEEEEEEEeCCCCEEEEEechh---------HHhhhhcCCCCC--CEEEEE----
Q 030172            2 SPSHSCKEPQKSIHEIAKGLT-GSIISVKVIQANEEMKKLVFSEKDA---------VWNKYSSRVNVE--DIFVGR----   65 (182)
Q Consensus         2 ~p~~~~p~~e~~~~~~~~~~v-G~~v~~~v~~~d~~~~~i~lS~k~~---------~~~~~~~~~~~G--~iv~g~----   65 (182)
                      ||||  +|+|+-.|+.++.++ |+... .  ..+.-..++....+.+         .+...+.+-++|  +.+.|.    
T Consensus       498 SPIR--RY~DLivHR~L~a~l~~~~~~-~--~~~~~~~~~s~~er~a~~aer~~~~~~~~~y~~~~~G~~~~f~g~I~~v  572 (644)
T PRK05054        498 SPIR--KYGDMINHRLLKAVIKGETAE-R--PQDEITVQLAERRRLNRMAERDVGDWLYARYLKDKAGTDTRFAAEIIDI  572 (644)
T ss_pred             Chhh--hhHHHHHHHHHHHHHcCCCCC-c--cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEEEEEee
Confidence            8999  999999999887765 33211 0  0000000011000111         111112334565  488887    


Q ss_pred             -eEeEEEEEecCCCceeEEEEEEccCcCCcc--c---c-------CccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--I---Q-------DIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        66 -~~G~fV~l~~~~g~~~~~glv~~sels~~~--~---~-------~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                       ++|+||+|.. .|   ++||||++.+...+  .   .       .-+..|+.||.|+|+|.++|..+++|.+++
T Consensus       573 ~~~G~fV~l~~-~~---veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~~~  643 (644)
T PRK05054        573 SRGGMRVRLLE-NG---AVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIARP  643 (644)
T ss_pred             ecCcEEEEEeC-Cc---eEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEEEE
Confidence             9999999973 45   99999999986531  1   1       112469999999999999999999999875

>TIGR01953 NusA transcription termination factor NusA

Probab=98.42  E-value=8.3e-07  Score=75.29  Aligned_cols=109  Identities=16%  Similarity=0.237  Sum_probs=76.7

Q ss_pred             CCCCccHHH----hhhhcCCCeEEEEEEEEeCCCCEEEEEe-ch--------hHHhhhhcCC--CCCCEEEEE-----eE
Q 030172            8 KEPQKSIHE----IAKGLTGSIISVKVIQANEEMKKLVFSE-KD--------AVWNKYSSRV--NVEDIFVGR-----DY   67 (182)
Q Consensus         8 p~~e~~~~~----~~~~~vG~~v~~~v~~~d~~~~~i~lS~-k~--------~~~~~~~~~~--~~G~iv~g~-----~~   67 (182)
                      |..++++.+    .....+|+.+.+.+...+  -++..++. +.        +.++..+..+  +.|+++.|+     +.
T Consensus        68 ~~~ei~l~~A~~~d~~~~vGD~I~~~I~~~~--fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~  145 (341)
T TIGR01953        68 PSLEISLEDAREIDPDVQIGDEVKKEIPPEN--FGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRR  145 (341)
T ss_pred             CcccccHHHHHhhccccccCCEEEEEecccC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecC
Confidence            344566653    233459999998884333  23433332 22        2344455566  599999999     44


Q ss_pred             e-EEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCC--CCeEEEEEeec
Q 030172           68 G-AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE--KSRITLSIKQL  130 (182)
Q Consensus        68 G-~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~--~~ki~lS~k~~  130 (182)
                      | +||+++   |   ++|++|.++..      +.+.|++||.++|.|++++..  ..++.||++..
T Consensus       146 g~v~VdiG---~---~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~  199 (341)
T TIGR01953       146 GNLYVELG---K---TEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP  199 (341)
T ss_pred             CcEEEEEC---C---eEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence            6 699995   4   99999999987      456699999999999999954  36799999853

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.40  E-value=5.1e-07  Score=77.06  Aligned_cols=109  Identities=17%  Similarity=0.247  Sum_probs=76.2

Q ss_pred             CCCCccHHHh----hhhcCCCeEEEEEEEEeCCCCEEEEEech--------hHHhhhhcCC--CCCCEEEEE-----eEe
Q 030172            8 KEPQKSIHEI----AKGLTGSIISVKVIQANEEMKKLVFSEKD--------AVWNKYSSRV--NVEDIFVGR-----DYG   68 (182)
Q Consensus         8 p~~e~~~~~~----~~~~vG~~v~~~v~~~d~~~~~i~lS~k~--------~~~~~~~~~~--~~G~iv~g~-----~~G   68 (182)
                      |..++++.+.    ....+|+.+.+.+...+.. +....+.++        +..+..+..+  +.|+++.|+     +.|
T Consensus        71 ~~~eisL~eAk~i~~~~~vGD~i~~~I~~~~fg-R~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~  149 (362)
T PRK12327         71 SRLEISLEDALAINPAYELGDVIEIEVTPKDFG-RIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRF  149 (362)
T ss_pred             CcccccHHHHhhhCccccCCCEEEEecCcCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCc
Confidence            4455666532    3335899999988654432 222222222        2334455666  899999999     889


Q ss_pred             EEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCC--eEEEEEee
Q 030172           69 AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ  129 (182)
Q Consensus        69 ~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~--ki~lS~k~  129 (182)
                      +||+++   |   ++|++|.+++.      +++.|++||.++|.|++++.+++  +|.||+..
T Consensus       150 ~~Vdlg---~---vEa~LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~  200 (362)
T PRK12327        150 VYVNLG---K---IEAVLPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH  200 (362)
T ss_pred             EEEEeC---C---eEEEecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence            999995   4   99999988875      36779999999999999996443  57777753

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

Probab=98.29  E-value=9.5e-06  Score=66.04  Aligned_cols=94  Identities=15%  Similarity=0.269  Sum_probs=73.0

Q ss_pred             CCCeEEEEEEEEeCCCCEEEEEechh-HHhhhhcCCCC---CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcC
Q 030172           22 TGSIISVKVIQANEEMKKLVFSEKDA-VWNKYSSRVNV---EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (182)
Q Consensus        22 vG~~v~~~v~~~d~~~~~i~lS~k~~-~~~~~~~~~~~---G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels   92 (182)
                      +|+++-+.+ .+|+. +++..+.+.. ..+........   ++.+.|+     ..|.||-++  ++   .-||||-||..
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 KGDKLLVYL-YVDKK-GRIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITE--NG---YLGFIHKSERF  189 (287)
T ss_pred             CCCEEEEEE-EEccC-CcEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEc--CC---eEEEEcchhhc
Confidence            799999998 56664 5777777653 33344444444   7777777     889999885  55   99999999865


Q ss_pred             CccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (182)
Q Consensus        93 ~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~  131 (182)
                      -.        ++.|+.++++|+.+.+ +++|.||++...
T Consensus       190 ~~--------prlG~~l~~rVi~~re-Dg~lnLSl~p~~  219 (287)
T COG2996         190 AE--------PRLGERLTARVIGVRE-DGKLNLSLRPRA  219 (287)
T ss_pred             cc--------ccCCceEEEEEEEEcc-CCeeeccccccc
Confidence            33        6799999999999997 999999998654

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=98.20  E-value=7.5e-07  Score=82.32  Aligned_cols=121  Identities=28%  Similarity=0.415  Sum_probs=82.1

Q ss_pred             CCCCCCCCCCccHHHhhhhcCCC-eEEEEEE---EEeCCCCEEEEEechh---------HHhhhhcCCCCCCEEEEE---
Q 030172            2 SPSHSCKEPQKSIHEIAKGLTGS-IISVKVI---QANEEMKKLVFSEKDA---------VWNKYSSRVNVEDIFVGR---   65 (182)
Q Consensus         2 ~p~~~~p~~e~~~~~~~~~~vG~-~v~~~v~---~~d~~~~~i~lS~k~~---------~~~~~~~~~~~G~iv~g~---   65 (182)
                      ||+|  +|+|+-.|+.++.++.. .....-.   .++.....+.-..+.+         .|...+.+-.+|+.+.|.   
T Consensus       555 SPIR--RY~DLivHR~L~~~l~~~~~~~~~~~~~~l~~i~~~~s~~er~a~~aer~~~~~~~~~~m~~~vg~~f~g~V~~  632 (706)
T COG0557         555 SPIR--RYPDLIVHRQLKALLSGEPIPEKKTSEEELDELAAHISSAERRAQEAERDVIDLLKAEYMKKRVGEEFDGVVTG  632 (706)
T ss_pred             Cchh--hchHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEE
Confidence            8999  99999999988776543 3222211   1111111111111111         233334567789888888   


Q ss_pred             --eEeEEEEEecCCCceeEEEEEEccCcCCccc-----------cCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           66 --DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        66 --~~G~fV~l~~~~g~~~~~glv~~sels~~~~-----------~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                        .+|+||.+.. .+   ++|++|++.+...+.           ......|+.||.|+|++.+++...+++.+++.
T Consensus       633 v~~~g~~V~l~~-~~---ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i~~~~v  704 (706)
T COG0557         633 VTSFGFFVELPE-LG---LEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKIDFELV  704 (706)
T ss_pred             EEeccEEEEecc-cc---cccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccceEEEec
Confidence              8999999973 24   899999999996542           12344599999999999999999999998875

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

Probab=98.20  E-value=1.1e-06  Score=70.99  Aligned_cols=85  Identities=26%  Similarity=0.441  Sum_probs=74.5

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~  130 (182)
                      +.++++|.+.     +.|+||.|-.++   +++|++-++|||..++...++.+++|..=.|.|+.+|++++.|.||.+.+
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            5688888887     999999997665   49999999999999999999999999999999999999999999999998


Q ss_pred             cCCchhHHHhhhc
Q 030172          131 EEDPLLETLEKVI  143 (182)
Q Consensus       131 ~~~p~~~~~~~~~  143 (182)
                      .++.-....++|.
T Consensus        91 s~ed~~kC~Er~~  103 (304)
T KOG2916|consen   91 SPEDKEKCEERFA  103 (304)
T ss_pred             CHHHHHHHHHHHH
Confidence            8766655555553

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=98.18  E-value=2e-07  Score=78.06  Aligned_cols=108  Identities=11%  Similarity=0.096  Sum_probs=84.4

Q ss_pred             CCCCCCCccHHH--hhhh--cCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE------eEeEEE
Q 030172            5 HSCKEPQKSIHE--IAKG--LTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR------DYGAFI   71 (182)
Q Consensus         5 ~~~p~~e~~~~~--~~~~--~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~------~~G~fV   71 (182)
                      .|+|.||+++.+  ..+.  -+|+++.|+|+.+|++++++.||.|+   .+|......++.|+++.|+      ++|+++
T Consensus        45 GlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~  124 (319)
T PTZ00248         45 GMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSV  124 (319)
T ss_pred             EEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCH
Confidence            357888888874  2333  28999999999999999999999996   4899999999999999999      699999


Q ss_pred             E-----EecCCCceeEEEEEEccCcCCccccCcccccc---CCCEEEEEEEEE
Q 030172           72 H-----LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILN---EGDEVRVKVIKI  116 (182)
Q Consensus        72 ~-----l~~~~g~~~~~glv~~sels~~~~~~~~~~~~---~Gd~v~vkV~~i  116 (182)
                      +     +.-+ +   .++|.|+.+.....+.++.+.|.   +++.+...++.+
T Consensus       125 eely~~i~~p-l---~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~~~l~~~  173 (319)
T PTZ00248        125 EELYTKIIWP-L---YKKYGHALDALKEALTNPDNVFEGLDIPEEVKESLLQD  173 (319)
T ss_pred             HHHHHHHHHH-H---HHhcCCHHHHHHHHhcCchhhhccCCCCHHHHHHHHHH
Confidence            7     1112 2   78899999887777777776665   666665555443

>TIGR02062 RNase_B exoribonuclease II

Probab=98.18  E-value=5.9e-07  Score=82.09  Aligned_cols=116  Identities=15%  Similarity=0.145  Sum_probs=73.2

Q ss_pred             CCCCCCCCCCccHHHhhhhcC-CCeEEEEEEEEeCCCCEEEEEechh---------HHhhhhcCCCCC--CEEEEE----
Q 030172            2 SPSHSCKEPQKSIHEIAKGLT-GSIISVKVIQANEEMKKLVFSEKDA---------VWNKYSSRVNVE--DIFVGR----   65 (182)
Q Consensus         2 ~p~~~~p~~e~~~~~~~~~~v-G~~v~~~v~~~d~~~~~i~lS~k~~---------~~~~~~~~~~~G--~iv~g~----   65 (182)
                      ||||  +|+|+-.|+.++.++ |+....   ..+.-..+++-..+.+         .+...+.+-++|  +.+.|.    
T Consensus       494 SPIR--RY~DLivHR~L~~~l~~~~~~~---~~~~~~~~~s~~er~a~~aeR~~~~~~~~~yl~~~~g~~~~f~g~I~~v  568 (639)
T TIGR02062       494 SPIR--KYGDMINHRLLKAVIKGETATR---PQEDITVQLAERRRLNRIAERDVADWLYARFLADKAAKNTRFAAEIVDI  568 (639)
T ss_pred             Chhh--hhHHHHHHHHHHHHHcCCCCCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEee
Confidence            8999  999999999887775 332111   0110000011001111         111112333564  477777    


Q ss_pred             -eEeEEEEEecCCCceeEEEEEEccCcCC--ccc---cCc-------cccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI---QDI-------RDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        66 -~~G~fV~l~~~~g~~~~~glv~~sels~--~~~---~~~-------~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                       ++|+||+|. .+|   ++|+||++.+..  .+.   .+.       +..|+.||.|+|+|.++|.++++|.+.
T Consensus       569 ~~~g~~v~l~-~~~---~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~~  638 (639)
T TIGR02062       569 SRGGMRVRLL-ENG---AIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIAR  638 (639)
T ss_pred             eCCcEEEEEe-cCc---eEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEeee
Confidence             899999996 345   999999999965  211   111       226999999999999999999988764

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.

>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=98.15  E-value=2e-06  Score=57.19  Aligned_cols=34  Identities=6%  Similarity=-0.077  Sum_probs=31.3

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .|+.+.|+|+++.++|+||++.+|++|++|....
T Consensus         3 ~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~l   36 (74)
T cd05705           3 EGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNV   36 (74)
T ss_pred             CCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHc
Confidence            3999999999999999999999999999996654

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.

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

Probab=98.13  E-value=2e-05  Score=60.90  Aligned_cols=75  Identities=28%  Similarity=0.335  Sum_probs=58.6

Q ss_pred             hhcCCCCCCEEEEE-----eEeEEEEEecCCC-----ceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCC
Q 030172           52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDG-----LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS  121 (182)
Q Consensus        52 ~~~~~~~G~iv~g~-----~~G~fV~l~~~~g-----~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~  121 (182)
                      ..+.++.|++|.|+     ...+.|++...++     .....|-+|+|+.+..+..+..+.|++||.|+|+|++.-   .
T Consensus        58 ~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~  134 (188)
T COG1096          58 TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---D  134 (188)
T ss_pred             CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC---C
Confidence            45678999999999     5557777643222     002578899999999999999999999999999999983   4


Q ss_pred             eEEEEEee
Q 030172          122 RITLSIKQ  129 (182)
Q Consensus       122 ki~lS~k~  129 (182)
                      .+.||.+.
T Consensus       135 ~~~Lst~~  142 (188)
T COG1096         135 PIQLSTKG  142 (188)
T ss_pred             CeEEEecC
Confidence            56777764

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

Probab=98.00  E-value=4.7e-05  Score=61.12  Aligned_cols=99  Identities=24%  Similarity=0.332  Sum_probs=73.8

Q ss_pred             cCCCeEEEEEEEEe-CCCCEEEEEechhHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCc
Q 030172           21 LTGSIISVKVIQAN-EEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD   94 (182)
Q Consensus        21 ~vG~~v~~~v~~~d-~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~   94 (182)
                      +.|+++...+...= ..++.+.+    -+... ...++.||+|.|+     ..++.|+|+.+     ..+++|++++.+.
T Consensus        31 ~~~~~iyssv~G~~~~~~~~v~V----Ipl~g-~YiP~~gD~VIG~I~~v~~~~W~VDI~sp-----~~A~L~ls~~~~r  100 (239)
T COG1097          31 FEGGKIYSSVVGLLDVKGKLVRV----IPLEG-RYIPEVGDVVIGKIIEVGPSGWKVDIGSP-----YPALLSLSDFLRR  100 (239)
T ss_pred             ecCCEEEEEEEeEEEEeCCEEEE----EeCCC-cccCCCCCEEEEEEEEEcccceEEEcCCc-----cceEeehhhhhcc
Confidence            46777777764432 22223322    12323 3568899999999     88999999754     8999999999665


Q ss_pred             c----ccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172           95 L----IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (182)
Q Consensus        95 ~----~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~  130 (182)
                      .    ..+++.+|++||.|.|+|..+|+ .+.+.|++|..
T Consensus       101 ~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~k~~  139 (239)
T COG1097         101 KFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTLKDE  139 (239)
T ss_pred             cccccccccccccccCCEEEEEEEEccC-CCceEEEeecC
Confidence            5    35788899999999999999997 88999999754

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

Probab=97.88  E-value=1e-05  Score=53.00  Aligned_cols=31  Identities=10%  Similarity=0.088  Sum_probs=29.2

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEEL  177 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~  177 (182)
                      |+.+.|+|+++.++|+||++.+|++||+|--
T Consensus         4 g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~   34 (72)
T cd05689           4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVS   34 (72)
T ss_pred             CCEEEEEEEEEEeeEEEEEcCCCCEEEEEEE
Confidence            8999999999999999999999999999843

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.

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

Probab=97.87  E-value=1.3e-05  Score=52.23  Aligned_cols=32  Identities=6%  Similarity=0.094  Sum_probs=29.4

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |++++|+|+++.++|+||++.+|++||+|...
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~   32 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMH   32 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHH
Confidence            68899999999999999999999999998644

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.

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

Probab=97.87  E-value=1.3e-05  Score=53.12  Aligned_cols=32  Identities=13%  Similarity=0.007  Sum_probs=29.9

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |+++.|+|+++.++|+||+|.+|++|+||.+.
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~   32 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLD   32 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHH
Confidence            68899999999999999999999999998764

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

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

Probab=97.86  E-value=1.6e-05  Score=52.91  Aligned_cols=35  Identities=17%  Similarity=0.221  Sum_probs=31.1

Q ss_pred             CCceeEeeEeeecCCeeEEecC-CChhhhchhhhhc
Q 030172          146 DGSVISDSSSMSSSNSNTIEPL-PGLGAIFEELLQE  180 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~-~gv~gl~~~~~~~  180 (182)
                      .|++++|+|.+++++|+||++. +|++||+|.....
T Consensus         4 ~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~   39 (74)
T cd05694           4 EGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG   39 (74)
T ss_pred             CCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCC
Confidence            3899999999999999999996 6999999976543

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.

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

Probab=97.85  E-value=1.1e-05  Score=52.28  Aligned_cols=32  Identities=13%  Similarity=0.058  Sum_probs=29.4

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |+++.|+|+++.+||+||++.+|++||+|...
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~   32 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISD   32 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHH
Confidence            67899999999999999999999999998654

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.

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

Probab=97.80  E-value=1.6e-05  Score=51.69  Aligned_cols=33  Identities=6%  Similarity=-0.017  Sum_probs=30.2

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |+++.|+|+++.++|+||++.+++.||+|....
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l   33 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSEL   33 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHc
Confidence            688999999999999999999999999997653

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.

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

Probab=97.80  E-value=2.5e-05  Score=51.34  Aligned_cols=35  Identities=6%  Similarity=0.078  Sum_probs=31.9

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhhhc
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE  180 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~  180 (182)
                      .|+++.|+|+++.++|+||++..|++||||.-...
T Consensus         4 ~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~   38 (74)
T PF00575_consen    4 EGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELS   38 (74)
T ss_dssp             TTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSS
T ss_pred             CCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhc
Confidence            39999999999999999999999999999986543

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 ....

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

Probab=97.78  E-value=2.9e-05  Score=52.40  Aligned_cols=39  Identities=18%  Similarity=0.203  Sum_probs=33.8

Q ss_pred             HhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          139 LEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       139 ~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .+++..  |+++.|+|+++.++|+||++.+|++||+|....
T Consensus         9 ~~~~~~--G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el   47 (83)
T cd04461           9 FSDLKP--GMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYI   47 (83)
T ss_pred             HHhCCC--CCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHC
Confidence            344555  999999999999999999999999999997543

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.

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

Probab=97.75  E-value=2.5e-05  Score=50.69  Aligned_cols=32  Identities=16%  Similarity=0.171  Sum_probs=29.6

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |+.++|+|+++.++|+||++.++++||+|...
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~   32 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLH   32 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHH
Confidence            68899999999999999999999999998764

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.

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

Probab=97.74  E-value=0.00019  Score=49.10  Aligned_cols=69  Identities=19%  Similarity=0.065  Sum_probs=55.3

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      .+++||+|.|+     ....+|+|+.+     ..|++|..++... .++.+..+++||.|.|+|..+|+ .....||...
T Consensus         3 ~P~~gD~VIG~V~~~~~~~~~VdI~s~-----~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~-~~~~eLtc~~   75 (86)
T cd05790           3 VPAKGDHVIGIVVAKAGDFFKVDIGGS-----EPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANR-DMEPELSCVD   75 (86)
T ss_pred             cCCCCCEEEEEEEEEcCCeEEEEcCCC-----cceEechHHcccc-cccccccCCCCCEEEEEEEecCC-CCCeEEEEeC
Confidence            46789999999     55689999743     7899999876543 44456779999999999999997 5678999986


Q ss_pred             c
Q 030172          130 L  130 (182)
Q Consensus       130 ~  130 (182)
                      .
T Consensus        76 ~   76 (86)
T cd05790          76 S   76 (86)
T ss_pred             C
Confidence            3

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".

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

Probab=97.72  E-value=0.00016  Score=55.94  Aligned_cols=123  Identities=17%  Similarity=0.211  Sum_probs=74.8

Q ss_pred             CCCCCCCCCCCccHHH-hhhhcCCCe-----EEEEEEEEeC-CCCEEEEEech----hHHhhhhcCCCCCCEEEEE----
Q 030172            1 MSPSHSCKEPQKSIHE-IAKGLTGSI-----ISVKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR----   65 (182)
Q Consensus         1 ~~p~~~~p~~e~~~~~-~~~~~vG~~-----v~~~v~~~d~-~~~~i~lS~k~----~~~~~~~~~~~~G~iv~g~----   65 (182)
                      +.|+.|.+..+-.+.+ +.+.+.|..     +-..|.+++. ..+++.-..-.    ........++-.|+++.|.    
T Consensus        13 i~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf~gEVv~g~V~~v   92 (176)
T PTZ00162         13 LKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDV   92 (176)
T ss_pred             ECHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecCCCCEEEEEEEEE
Confidence            3577775544444443 333455542     2233333332 22444321111    1233445678899999999    


Q ss_pred             -eEeEEEEEecCCCceeEEEEEEccCcCCcc-----------c-cCccccccCCCEEEEEEEEEeCCC--CeEEEEEee
Q 030172           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-----------I-QDIRDILNEGDEVRVKVIKIDREK--SRITLSIKQ  129 (182)
Q Consensus        66 -~~G~fV~l~~~~g~~~~~glv~~sels~~~-----------~-~~~~~~~~~Gd~v~vkV~~id~~~--~ki~lS~k~  129 (182)
                       ++|+|+.++ +     .++|+|.+.|....           . .+.+..++.|+.|++||.++..+.  .++..|+|+
T Consensus        93 ~~~G~~v~~G-p-----~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i~T~~~  165 (176)
T PTZ00162         93 NKLGFFAQAG-P-----LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAIATINS  165 (176)
T ss_pred             ecceEEEEee-C-----eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEEEEecC
Confidence             999999996 3     78999999986431           1 122456899999999998886533  345567765

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

Probab=97.71  E-value=2.8e-05  Score=50.40  Aligned_cols=32  Identities=16%  Similarity=0.057  Sum_probs=29.5

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |+++.|+|+++.++|+||++.++++||+|-..
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~   32 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSE   32 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHH
Confidence            67899999999999999999999999998654

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.

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

Probab=97.67  E-value=3.6e-05  Score=52.88  Aligned_cols=33  Identities=6%  Similarity=-0.043  Sum_probs=30.3

Q ss_pred             CCceeEeeEeeecCC--eeEEecCCChhhhchhhh
Q 030172          146 DGSVISDSSSMSSSN--SNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~--G~fV~l~~gv~gl~~~~~  178 (182)
                      .|+++.|+|+++.++  |+||++.+|.+||+|-..
T Consensus         7 ~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~se   41 (88)
T cd04453           7 VGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSD   41 (88)
T ss_pred             CCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHH
Confidence            399999999999996  999999999999999654

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

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

Probab=97.65  E-value=4.2e-05  Score=50.28  Aligned_cols=32  Identities=16%  Similarity=0.096  Sum_probs=28.5

Q ss_pred             CceeE-eeEeee-cCCeeEEecCCChhhhchhhh
Q 030172          147 GSVIS-DSSSMS-SSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       147 g~~v~-G~V~~v-~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |+++. |+|+++ .++|+||++.+|++||+|...
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~   34 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISH   34 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHH
Confidence            57788 899999 699999999999999999754

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

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

Probab=97.62  E-value=5.5e-05  Score=49.63  Aligned_cols=33  Identities=3%  Similarity=-0.150  Sum_probs=30.6

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      .|+++.|+|+++.++|+||+|+++++|++|...
T Consensus         3 ~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~   35 (73)
T cd05706           3 VGDILPGRVTKVNDRYVLVQLGNKVTGPSFITD   35 (73)
T ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhh
Confidence            499999999999999999999999999998654

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=97.49  E-value=0.00012  Score=48.19  Aligned_cols=35  Identities=11%  Similarity=0.066  Sum_probs=31.2

Q ss_pred             CCceeEeeEeeecC-CeeEEecCCChhhhchhhhhc
Q 030172          146 DGSVISDSSSMSSS-NSNTIEPLPGLGAIFEELLQE  180 (182)
Q Consensus       146 ~g~~v~G~V~~v~~-~G~fV~l~~gv~gl~~~~~~~  180 (182)
                      .|+++.|+|+++.+ +|+||++.+|.+|++|-....
T Consensus         3 ~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s   38 (72)
T cd05704           3 EGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLS   38 (72)
T ss_pred             CCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhc
Confidence            39999999999986 899999999999999976553

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.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.49  E-value=0.00034  Score=61.01  Aligned_cols=58  Identities=29%  Similarity=0.447  Sum_probs=46.9

Q ss_pred             cCCCCCCEEEEE-----eE--eEEEEEecCCCceeEEEEEEccCcCCc------------cccCccccccCCCEEEEEEE
Q 030172           54 SRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI  114 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~--G~fV~l~~~~g~~~~~glv~~sels~~------------~~~~~~~~~~~Gd~v~vkV~  114 (182)
                      ....+|++|.|+     ++  ||||+|+  .|   ..||+|++|+.+.            ...++.+.+++||.|.|.|.
T Consensus        21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG--~~---k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~   95 (414)
T TIGR00757        21 SRQLKGNIYKGRVTRILPSLQAAFVDIG--LE---KNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVV   95 (414)
T ss_pred             CcCCCCCEEEEEEeeecCCCceEEEEcC--CC---ceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEe
Confidence            456799999999     65  8999997  45   8999999998753            23345667999999999998


Q ss_pred             EE
Q 030172          115 KI  116 (182)
Q Consensus       115 ~i  116 (182)
                      +-
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.

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

Probab=97.47  E-value=0.00011  Score=49.04  Aligned_cols=35  Identities=3%  Similarity=-0.004  Sum_probs=31.4

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL  177 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~  177 (182)
                      +++.  |+.+.|+|+++.++|+||++.++++||+|..
T Consensus        13 ~~~~--G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~s   47 (77)
T cd04473          13 DLEV--GKLYKGKVNGVAKYGVFVDLNDHVRGLIHRS   47 (77)
T ss_pred             hCCC--CCEEEEEEEeEecceEEEEECCCcEEEEEch
Confidence            4555  9999999999999999999999999999854

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.

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

Probab=97.45  E-value=0.00011  Score=47.44  Aligned_cols=32  Identities=9%  Similarity=0.191  Sum_probs=29.3

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |++++|+|+++.++|+||++ +|++||+|....
T Consensus         1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~   32 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQV   32 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHC
Confidence            67899999999999999999 899999997654

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.

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

Probab=97.44  E-value=0.00011  Score=48.52  Aligned_cols=33  Identities=6%  Similarity=0.057  Sum_probs=28.7

Q ss_pred             CCceeEeeEeeecCCeeEEecCCC--hhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPG--LGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~g--v~gl~~~~~~  179 (182)
                      .|+++.|+|+++.+||+||++ +|  .+||||....
T Consensus         3 ~g~~~~g~V~~i~~fG~fv~l-~~~~~eGlvh~sel   37 (73)
T cd05686           3 LYQIFKGEVASVTEYGAFVKI-PGCRKQGLVHKSHM   37 (73)
T ss_pred             CCCEEEEEEEEEEeeeEEEEE-CCCCeEEEEEchhh
Confidence            499999999999999999999 56  6999996543

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.

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=97.43  E-value=0.00039  Score=54.36  Aligned_cols=67  Identities=13%  Similarity=0.130  Sum_probs=49.4

Q ss_pred             ccCCCEEEEEEEEE---eCCCCeEEEEEeeccCCchhHHHhhhcCCCCceeEeeEeeecCCeeEEecC----------CC
Q 030172          103 LNEGDEVRVKVIKI---DREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL----------PG  169 (182)
Q Consensus       103 ~~~Gd~v~vkV~~i---d~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~----------~g  169 (182)
                      |..++.+.+.+.+.   |.+++++.+       +||......+.  .|+++.|+|+++.++|+||++.          ++
T Consensus        27 y~~~~~i~as~~G~~~id~~~~~Isv-------~P~~~~~~~~~--~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~   97 (189)
T PRK09521         27 YEDNGEVYASVVGKVFIDDINRKISV-------IPFKKTPPLLK--KGDIVYGRVVDVKEQRALVRIVSIEGSERELATS   97 (189)
T ss_pred             EeeCCEEEEEeeEEEEEcCCCCEEEE-------ecCcCCCCCCC--CCCEEEEEEEEEcCCeEEEEEEEecccccccCCC
Confidence            55667777766555   666667766       47765433334  4999999999999999999984          47


Q ss_pred             hhhhchhhh
Q 030172          170 LGAIFEELL  178 (182)
Q Consensus       170 v~gl~~~~~  178 (182)
                      +.|++|...
T Consensus        98 ~~G~l~~s~  106 (189)
T PRK09521         98 KLAYIHISQ  106 (189)
T ss_pred             ceeeEEhhH
Confidence            889998654

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

Probab=97.43  E-value=0.00012  Score=46.76  Aligned_cols=33  Identities=15%  Similarity=0.131  Sum_probs=29.8

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |+++.|+|+++.++|+||++.+++.||+|....
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l   33 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQI   33 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHc
Confidence            678999999999999999999999999996543

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.

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

Probab=97.41  E-value=0.00015  Score=47.23  Aligned_cols=33  Identities=12%  Similarity=0.224  Sum_probs=30.1

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |+++.|+|+++.++|+||++.++++|+||....
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~   33 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAEL   33 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHC
Confidence            678999999999999999999999999987653

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.

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

Probab=97.39  E-value=0.00017  Score=48.87  Aligned_cols=37  Identities=14%  Similarity=0.107  Sum_probs=32.8

Q ss_pred             hcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          142 VIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       142 ~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |.+..|+++.|+|+++.++|++|++.++++|++|...
T Consensus         2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se   38 (86)
T cd05789           2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSE   38 (86)
T ss_pred             CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHH
Confidence            3445699999999999999999999999999999754

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".

>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=97.38  E-value=0.00016  Score=46.12  Aligned_cols=33  Identities=6%  Similarity=-0.038  Sum_probs=29.7

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |+.+.|+|+++.++|+||++.++..||||--..
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l   33 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKM   33 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHC
Confidence            578999999999999999999999999986544

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.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.34  E-value=0.00085  Score=42.83  Aligned_cols=48  Identities=35%  Similarity=0.515  Sum_probs=32.0

Q ss_pred             eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        66 ~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      ++|+|++.+  .+   -+.++|.+++...        +++||.|.|-| ..|. ++++..|+|
T Consensus        14 ~~g~fL~~~--~~---~~vlLp~~e~~~~--------~~~Gd~v~VFv-Y~D~-~~rl~AT~k   61 (61)
T PF13509_consen   14 EFGYFLDDG--EG---KEVLLPKSEVPEP--------LKVGDEVEVFV-YLDK-EGRLVATTK   61 (61)
T ss_dssp             SSEEEEEET--T----EEEEEEGGG--------------TTSEEEEEE-EE-T-TS-EEEE--
T ss_pred             CCEEEEECC--CC---CEEEechHHcCCC--------CCCCCEEEEEE-EECC-CCCEEEecC
Confidence            899999975  33   8999999987643        88999999887 7786 668888875

>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=97.33  E-value=0.00089  Score=44.19  Aligned_cols=64  Identities=19%  Similarity=0.240  Sum_probs=49.0

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcccc--CccccccCCCEE-EEEEEEEeCCCCeEEEEEe
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEV-RVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~--~~~~~~~~Gd~v-~vkV~~id~~~~ki~lS~k  128 (182)
                      |+++.|+     +-+++|++.. .|   +.|++|..++++..-+  ..-..+++||.+ .+.|+  +...+.+.+|.|
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-EE---IRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecC-CC---cEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence            5677777     6679999973 34   9999999999993322  234458999999 99998  777788888865

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=97.30  E-value=4.1e-05  Score=67.64  Aligned_cols=75  Identities=15%  Similarity=0.123  Sum_probs=56.1

Q ss_pred             ccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchh-----HHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172          103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL-----ETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL  177 (182)
Q Consensus       103 ~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~-----~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~  177 (182)
                      +.+||.+.+.|...+. .+....+.|+.....|.     .....|....|++++|+|.++.++|+||++ .|++||+|+.
T Consensus        87 ~~vGD~ie~~I~~~~f-gRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDL-ggvea~LP~s  164 (470)
T PRK09202         87 AEVGDYIEEEIESVDF-GRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDL-GRAEAILPRK  164 (470)
T ss_pred             ccCCCeEEEEEccccC-ChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEE-CCeEEEecHH
Confidence            7899999999988773 22223333444333343     566777644599999999999999999999 6999999986


Q ss_pred             hh
Q 030172          178 LQ  179 (182)
Q Consensus       178 ~~  179 (182)
                      .+
T Consensus       165 E~  166 (470)
T PRK09202        165 EQ  166 (470)
T ss_pred             Hc
Confidence            54

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

Probab=97.29  E-value=0.0021  Score=44.09  Aligned_cols=58  Identities=19%  Similarity=0.285  Sum_probs=44.0

Q ss_pred             CCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCc-----------cccccCCCEEEEEEEEEeCCCC
Q 030172           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----------RDILNEGDEVRVKVIKIDREKS  121 (182)
Q Consensus        58 ~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~-----------~~~~~~Gd~v~vkV~~id~~~~  121 (182)
                      .|+++.|+     +.|+|+.++ |     +++|+|...+......++           ...+..|+.|++||+++..+.+
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G-p-----l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~   74 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG-P-----LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT   74 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc-C-----ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence            47888888     999999996 2     889999888755433222           3458899999999999876443

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.

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

Probab=97.23  E-value=0.00023  Score=45.59  Aligned_cols=32  Identities=16%  Similarity=0.171  Sum_probs=28.8

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |+++.|+|+++.++|+||++.++.+||+|-..
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~   32 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISE   32 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHH
Confidence            57899999999999999999999999998543

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=97.23  E-value=0.00042  Score=63.91  Aligned_cols=63  Identities=11%  Similarity=0.195  Sum_probs=42.7

Q ss_pred             EEEeCCCCeEEEEEeeccC-CchhH----HHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172          114 IKIDREKSRITLSIKQLEE-DPLLE----TLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL  177 (182)
Q Consensus       114 ~~id~~~~ki~lS~k~~~~-~p~~~----~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~  177 (182)
                      ++++. ++++.++-..... +....    ....+.+..|+++.|+|+++.+||+||++.+|++||+|-.
T Consensus       611 Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHIS  678 (719)
T TIGR02696       611 ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHIS  678 (719)
T ss_pred             EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhh
Confidence            36664 6777776643211 00111    1111123469999999999999999999999999999965

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.

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

Probab=97.22  E-value=0.00022  Score=47.61  Aligned_cols=32  Identities=13%  Similarity=-0.048  Sum_probs=29.1

Q ss_pred             CceeEeeEeeecCCeeEEecCC-Chhhhchhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLP-GLGAIFEELL  178 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~-gv~gl~~~~~  178 (182)
                      |+++.|+|+++.++|+||++.+ |++|++|-..
T Consensus         2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~   34 (83)
T cd04471           2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVST   34 (83)
T ss_pred             CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEe
Confidence            7899999999999999999998 8999997543

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.

>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=97.22  E-value=0.00028  Score=47.03  Aligned_cols=33  Identities=3%  Similarity=-0.107  Sum_probs=28.9

Q ss_pred             CceeEeeEeeecCCeeEEecC---CChhhhchhhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPL---PGLGAIFEELLQ  179 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~---~gv~gl~~~~~~  179 (182)
                      |+++.|+|+++.+||+||+++   ++++||+|-...
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l   36 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQL   36 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhc
Confidence            578999999999999999998   479999986544

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.

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

Probab=97.17  E-value=0.00043  Score=45.48  Aligned_cols=34  Identities=6%  Similarity=0.034  Sum_probs=29.9

Q ss_pred             CCceeEeeEeeecCCeeEEecC--CChhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPL--PGLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~--~gv~gl~~~~~~  179 (182)
                      .|+++.|+|+++.++|+||++.  +|++||+|....
T Consensus         3 ~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l   38 (76)
T cd04452           3 EGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSEL   38 (76)
T ss_pred             CCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHc
Confidence            3899999999999999999997  469999997643

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

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

Probab=97.16  E-value=0.0004  Score=45.25  Aligned_cols=33  Identities=3%  Similarity=0.002  Sum_probs=30.1

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |+++.|+|+++.++|+||++.+|++|++|....
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i   33 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEV   33 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHh
Confidence            688999999999999999999999999987643

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.

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

Probab=97.13  E-value=0.00049  Score=44.62  Aligned_cols=33  Identities=6%  Similarity=-0.028  Sum_probs=30.3

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |+++.|+|.++.++|+||++..+++|++|....
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~   33 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEF   33 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHh
Confidence            688999999999999999999999999997654

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.

>PRK08059 general stress protein 13; Validated

Probab=97.10  E-value=0.0004  Score=50.58  Aligned_cols=36  Identities=8%  Similarity=-0.047  Sum_probs=32.1

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      ++.+  |+++.|+|+++.++|+||++.++++||+|...
T Consensus         4 ~~k~--G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~se   39 (123)
T PRK08059          4 QYEV--GSVVTGKVTGIQPYGAFVALDEETQGLVHISE   39 (123)
T ss_pred             cCCC--CCEEEEEEEEEecceEEEEECCCCEEEEEHHH
Confidence            3455  99999999999999999999999999998654

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.08  E-value=0.0023  Score=54.88  Aligned_cols=63  Identities=21%  Similarity=0.343  Sum_probs=51.7

Q ss_pred             CCCCCCEEEEE----e--EeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCC---eEEE
Q 030172           55 RVNVEDIFVGR----D--YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS---RITL  125 (182)
Q Consensus        55 ~~~~G~iv~g~----~--~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~---ki~l  125 (182)
                      .-+.|+++.|+    +  .++||+++   +   .+|++|.++..      |++.|++||.++|.|.+++...+   +|.|
T Consensus       135 ~~~~Geiv~g~V~r~~~~~~i~vdlg---~---~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~Iil  202 (374)
T PRK12328        135 KKKVGKIVFGTVVRVDNEENTFIEID---E---IRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIEL  202 (374)
T ss_pred             HHhcCcEEEEEEEEEecCCCEEEEcC---C---eEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEE
Confidence            35799999999    3  34899995   4   99999988765      66889999999999999987654   7888


Q ss_pred             EEee
Q 030172          126 SIKQ  129 (182)
Q Consensus       126 S~k~  129 (182)
                      |+..
T Consensus       203 SRt~  206 (374)
T PRK12328        203 SRTS  206 (374)
T ss_pred             EcCC
Confidence            8854

>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=97.06  E-value=0.00063  Score=44.65  Aligned_cols=34  Identities=9%  Similarity=-0.016  Sum_probs=29.9

Q ss_pred             CCceeEeeEeeecCCeeEEecCC-Chhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLP-GLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~-gv~gl~~~~~~  179 (182)
                      .|+++.|+|+++.++|+||++.+ +++|++|....
T Consensus         2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l   36 (77)
T cd05708           2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEI   36 (77)
T ss_pred             CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHC
Confidence            38999999999999999999985 89999986543

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.

>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=97.05  E-value=0.00052  Score=48.23  Aligned_cols=33  Identities=12%  Similarity=0.033  Sum_probs=30.3

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      .|+++.|+|+++.++|+||+|.+|+.|++|-..
T Consensus         3 ~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~se   35 (100)
T cd05693           3 EGMLVLGQVKEITKLDLVISLPNGLTGYVPITN   35 (100)
T ss_pred             CCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHH
Confidence            499999999999999999999999999998644

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.

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

Probab=97.00  E-value=0.00079  Score=42.86  Aligned_cols=33  Identities=9%  Similarity=0.095  Sum_probs=30.5

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |+++.|+|+++.++|+||++.+++.|++|....
T Consensus         3 G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~   35 (72)
T smart00316        3 GDVVEGTVTEITPFGAFVDLGNGVEGLIPISEL   35 (72)
T ss_pred             CCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHC
Confidence            899999999999999999999999999987654

>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=96.98  E-value=0.0018  Score=43.90  Aligned_cols=35  Identities=26%  Similarity=0.461  Sum_probs=23.7

Q ss_pred             EEEEEEccCcCCcccc--CccccccCCCEEEEEEEEE
Q 030172           82 LTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKI  116 (182)
Q Consensus        82 ~~glv~~sels~~~~~--~~~~~~~~Gd~v~vkV~~i  116 (182)
                      ..|.+|.+++......  ++.+-|++||.|+|+|++.
T Consensus        46 f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl   82 (82)
T PF10447_consen   46 FQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL   82 (82)
T ss_dssp             S-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred             cEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence            7899999998766544  4578899999999999974

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=96.90  E-value=0.00079  Score=64.08  Aligned_cols=75  Identities=24%  Similarity=0.328  Sum_probs=60.5

Q ss_pred             cCCCCCCEEEEE------eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           54 SRVNVEDIFVGR------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        54 ~~~~~G~iv~g~------~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      +.+..|.+|.++      ..|+-|.+-..+|   ++|+|+.+++|...+.+|.+.+++||.|.+||+++|.++-.+.||.
T Consensus       981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G---~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~ 1057 (1299)
T KOG1856|consen  981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCG---VTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSC 1057 (1299)
T ss_pred             hHhccCceEEEeeeEEEecccceeEEEecCC---CceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhh
Confidence            347788888866      3343333332367   9999999999999999999999999999999999999888888888


Q ss_pred             eecc
Q 030172          128 KQLE  131 (182)
Q Consensus       128 k~~~  131 (182)
                      |...
T Consensus      1058 r~sd 1061 (1299)
T KOG1856|consen 1058 RTSD 1061 (1299)
T ss_pred             hhHH
Confidence            7553

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

Probab=96.74  E-value=0.0018  Score=43.43  Aligned_cols=37  Identities=16%  Similarity=0.154  Sum_probs=33.2

Q ss_pred             hcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          142 VIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       142 ~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |.|..|+++.|+|+++.+.+++|++..+++|++|...
T Consensus         2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~   38 (82)
T cd04454           2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSS   38 (82)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechh
Confidence            4456799999999999999999999999999998764

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".

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

Probab=96.66  E-value=0.0042  Score=55.74  Aligned_cols=68  Identities=29%  Similarity=0.508  Sum_probs=57.1

Q ss_pred             hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      .++++.|.+|.|+     .||+||++.  .   .+.|++|-++++..      .-|.+|+.+-|++..+.+.++.+.+..
T Consensus       117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln--~---~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~  185 (715)
T COG1107         117 MEDVEAGKYYKGIVSRVEKYGVFVELN--S---HVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEP  185 (715)
T ss_pred             hhhcccceeeeccccchhhhcceeecC--h---hhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceee
Confidence            4678999999999     999999996  3   39999999998862      227899999999999998878888877


Q ss_pred             eecc
Q 030172          128 KQLE  131 (182)
Q Consensus       128 k~~~  131 (182)
                      ..+.
T Consensus       186 ~~~~  189 (715)
T COG1107         186 VGLD  189 (715)
T ss_pred             cCCc
Confidence            6554

>TIGR01953 NusA transcription termination factor NusA

Probab=96.52  E-value=0.0004  Score=59.09  Aligned_cols=78  Identities=17%  Similarity=0.139  Sum_probs=54.8

Q ss_pred             cccccCCCEEEEEEEEEeCCCCeEEEEEeecc-----CCchhHHHhhhcCCCCceeEeeEeeecCCe-eEEecCCChhhh
Q 030172          100 RDILNEGDEVRVKVIKIDREKSRITLSIKQLE-----EDPLLETLEKVIPQDGSVISDSSSMSSSNS-NTIEPLPGLGAI  173 (182)
Q Consensus       100 ~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~-----~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G-~fV~l~~gv~gl  173 (182)
                      ...+++||.+.+.+...+. .+....+.|+..     ...++...+.|....|++++|+|.++.+.| +||++ +|++|+
T Consensus        81 d~~~~vGD~I~~~I~~~~f-gR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~Vdi-G~~ea~  158 (341)
T TIGR01953        81 DPDVQIGDEVKKEIPPENF-GRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVEL-GKTEGI  158 (341)
T ss_pred             ccccccCCEEEEEecccCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEE-CCeEEE
Confidence            3448899999988854443 232333334421     234556667775445999999999999988 69999 699999


Q ss_pred             chhhhh
Q 030172          174 FEELLQ  179 (182)
Q Consensus       174 ~~~~~~  179 (182)
                      +|...+
T Consensus       159 LP~~E~  164 (341)
T TIGR01953       159 LPKKEQ  164 (341)
T ss_pred             ecHHHc
Confidence            998654

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.

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

Probab=96.51  E-value=0.0021  Score=40.92  Aligned_cols=31  Identities=10%  Similarity=0.138  Sum_probs=27.9

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      |+.+.|+|+++.++|+||++. +++|++|...
T Consensus         2 g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e   32 (68)
T cd05688           2 GDVVEGTVKSITDFGAFVDLG-GVDGLLHISD   32 (68)
T ss_pred             CCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHH
Confidence            889999999999999999996 7999998643

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.

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

Probab=96.44  E-value=0.0036  Score=57.11  Aligned_cols=61  Identities=15%  Similarity=0.183  Sum_probs=43.1

Q ss_pred             EEeCCCCeEEEEEeeccC--Cc--h-hHHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          115 KIDREKSRITLSIKQLEE--DP--L-LETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       115 ~id~~~~ki~lS~k~~~~--~p--~-~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      .++ +++.+.++-.....  .+  | ......+  .+|+++.|+|+++.+||+||++.+|-+||||-..
T Consensus       586 die-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~--evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~  651 (692)
T COG1185         586 DIE-DDGTVKIAASDGESAKKAKERIEAITREV--EVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQ  651 (692)
T ss_pred             Eec-CCCcEEEEecchHHHHHHHHHHHHHHhhc--ccccEEEEEEEEEeecceEEEecCCcceeEEehh
Confidence            555 57777776654321  11  1 1112233  4599999999999999999999999999998643

>PHA02945 interferon resistance protein; Provisional

Probab=96.32  E-value=0.0039  Score=42.51  Aligned_cols=34  Identities=24%  Similarity=0.263  Sum_probs=30.1

Q ss_pred             CCCceeEeeEeeecCCeeEEecC--CChhhhchhhhh
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPL--PGLGAIFEELLQ  179 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~--~gv~gl~~~~~~  179 (182)
                      ..|+.+-|+|.. .+||+||.|+  +|.+||+|....
T Consensus        10 ~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~sev   45 (88)
T PHA02945         10 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQ   45 (88)
T ss_pred             CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehh
Confidence            359999999999 9999999995  799999998743

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.24  E-value=0.0026  Score=60.05  Aligned_cols=34  Identities=12%  Similarity=0.060  Sum_probs=30.5

Q ss_pred             CCCceeE-eeEeeecCCeeEEecCCChhhhchhhh
Q 030172          145 QDGSVIS-DSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       145 ~~g~~v~-G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      ..|+++. |+|++|.+||+||++.+|++||||-..
T Consensus       752 ~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISe  786 (891)
T PLN00207        752 TVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISE  786 (891)
T ss_pred             CCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhh
Confidence            4699995 699999999999999999999999654

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

Probab=96.18  E-value=0.0051  Score=39.74  Aligned_cols=33  Identities=12%  Similarity=0.170  Sum_probs=29.0

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .|++++|+|.++.++|+||++. +++|++|.-..
T Consensus         3 ~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~   35 (67)
T cd04455           3 EGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQ   35 (67)
T ss_pred             CCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHC
Confidence            3899999999999999999995 59999997543

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.10  E-value=0.025  Score=45.77  Aligned_cols=38  Identities=11%  Similarity=0.047  Sum_probs=34.1

Q ss_pred             hcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          142 VIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       142 ~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |.|..|++|.|+|+++.++|+||++..+++|++|-...
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i   96 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEV   96 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHc
Confidence            66667999999999999999999999999999997653

>PRK10811 rne ribonuclease E; Reviewed

Probab=96.04  E-value=0.021  Score=54.30  Aligned_cols=57  Identities=26%  Similarity=0.490  Sum_probs=44.6

Q ss_pred             CCCCCEEEEE-------eEeEEEEEecCCCceeEEEEEEccCcCCcccc---------CccccccCCCEEEEEEEEEe
Q 030172           56 VNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKID  117 (182)
Q Consensus        56 ~~~G~iv~g~-------~~G~fV~l~~~~g~~~~~glv~~sels~~~~~---------~~~~~~~~Gd~v~vkV~~id  117 (182)
                      ..+|.||.|+       =.++||+|+  .|   ..||+|+++....+..         +....+++||.|.|.|.+-.
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDIG--~g---knGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa  108 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYG--AE---RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE  108 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEec--CC---cceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecc
Confidence            3589999999       557999998  55   8999999999644322         23456899999999998754

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=95.90  E-value=0.006  Score=56.54  Aligned_cols=35  Identities=14%  Similarity=0.110  Sum_probs=31.9

Q ss_pred             CCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      ..|+++.|+|+++.+||+||++.+|++||+|-...
T Consensus       617 ~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei  651 (684)
T TIGR03591       617 EVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEI  651 (684)
T ss_pred             ccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHc
Confidence            45999999999999999999999999999997643

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).

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

Probab=95.89  E-value=0.0061  Score=37.85  Aligned_cols=30  Identities=7%  Similarity=-0.028  Sum_probs=26.5

Q ss_pred             eEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          150 ISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       150 v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      +.|+|+++.++|+||++.++++|++|....
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~   30 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISEL   30 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHC
Confidence            368999999999999999999999987554

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

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.74  E-value=0.0076  Score=55.95  Aligned_cols=34  Identities=15%  Similarity=0.137  Sum_probs=31.0

Q ss_pred             CCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      ..|+++.|+|+++.+||+||++.+|.+||+|-..
T Consensus       620 ~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSe  653 (693)
T PRK11824        620 EVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISE  653 (693)
T ss_pred             cCCeEEEEEEEEEECCeEEEEECCCCEEEEEeee
Confidence            3599999999999999999999999999998543

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.71  E-value=0.0016  Score=55.80  Aligned_cols=76  Identities=12%  Similarity=0.098  Sum_probs=51.1

Q ss_pred             cccCCCEEEEEEEEEeCCCCeEEEEEeeccC-----CchhHHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchh
Q 030172          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEE-----DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEE  176 (182)
Q Consensus       102 ~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~-----~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~  176 (182)
                      ..++||.+...+...+.. +....+.|+...     -..+.....|....|++++|+|.++.++|+||++ +|++|++|+
T Consensus        86 ~~~vGD~i~~~I~~~~fg-R~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdl-g~vEa~LP~  163 (362)
T PRK12327         86 AYELGDVIEIEVTPKDFG-RIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNL-GKIEAVLPP  163 (362)
T ss_pred             cccCCCEEEEecCcCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEe-CCeEEEecH
Confidence            378999999887655432 222222222211     1123445566444599999999999999999999 579999997


Q ss_pred             hhh
Q 030172          177 LLQ  179 (182)
Q Consensus       177 ~~~  179 (182)
                      ..+
T Consensus       164 ~E~  166 (362)
T PRK12327        164 AEQ  166 (362)
T ss_pred             HHc
Confidence            544

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.68  E-value=0.057  Score=47.38  Aligned_cols=69  Identities=9%  Similarity=0.059  Sum_probs=51.3

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC---CeEEEE
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK---SRITLS  126 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~---~ki~lS  126 (182)
                      .-+.|+++.|+     ..+++|+++..-|-.+++|++|.++..      |++.|++||.++|.|.++....   -+|.||
T Consensus       149 ~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilS  222 (449)
T PRK12329        149 QDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVS  222 (449)
T ss_pred             HHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEE
Confidence            35689999999     557899983100100289999988755      5688999999999999997642   468888


Q ss_pred             Eee
Q 030172          127 IKQ  129 (182)
Q Consensus       127 ~k~  129 (182)
                      +..
T Consensus       223 Rt~  225 (449)
T PRK12329        223 RAN  225 (449)
T ss_pred             cCC
Confidence            753

>PRK11712 ribonuclease G; Provisional

Probab=95.56  E-value=0.064  Score=47.87  Aligned_cols=59  Identities=25%  Similarity=0.487  Sum_probs=43.9

Q ss_pred             cCCCCCCEEEEE-------eEeEEEEEecCCCceeEEEEEEccCcCCc------------cccCccccccCCCEEEEEEE
Q 030172           54 SRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI  114 (182)
Q Consensus        54 ~~~~~G~iv~g~-------~~G~fV~l~~~~g~~~~~glv~~sels~~------------~~~~~~~~~~~Gd~v~vkV~  114 (182)
                      ....+|.+|.|+       =.+|||+|+  .+   ..||+|++|+...            ...+..+.+++||.|-|.|.
T Consensus        34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG--~~---k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~  108 (489)
T PRK11712         34 KRGIVGNIYKGRVSRVLPGMQAAFVDIG--LD---KAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVV  108 (489)
T ss_pred             cccccccEEEEEEeecCCCCceeEEeeC--CC---ccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEE
Confidence            345689999999       446999998  44   8999999997321            01123456899999999997


Q ss_pred             EEe
Q 030172          115 KID  117 (182)
Q Consensus       115 ~id  117 (182)
                      +-.
T Consensus       109 Ke~  111 (489)
T PRK11712        109 KDP  111 (489)
T ss_pred             eCC
Confidence            753

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=95.22  E-value=0.016  Score=53.80  Aligned_cols=40  Identities=8%  Similarity=0.047  Sum_probs=34.5

Q ss_pred             hhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhhcc
Q 030172          140 EKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQED  181 (182)
Q Consensus       140 ~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~~  181 (182)
                      ..+++  |++..|+|+++.+||+||.+.-..+||+|-.-..|
T Consensus       654 ~dLk~--Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~  693 (780)
T COG2183         654 TDLKP--GMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSD  693 (780)
T ss_pred             hhccC--CCEEEEEEEEeeeccceEEeccccceeeeHHHhhh
Confidence            34455  99999999999999999999999999999766543

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

Probab=95.00  E-value=0.016  Score=40.25  Aligned_cols=28  Identities=4%  Similarity=-0.041  Sum_probs=24.7

Q ss_pred             ceeEeeEeeecCCeeEEecCCChhhhchh
Q 030172          148 SVISDSSSMSSSNSNTIEPLPGLGAIFEE  176 (182)
Q Consensus       148 ~~v~G~V~~v~~~G~fV~l~~gv~gl~~~  176 (182)
                      +++.|+|+++.++|+||++. +++|++|-
T Consensus         1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~   28 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHI   28 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEc-CeEEEEEE
Confidence            36889999999999999997 59999973

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.

>TIGR02063 RNase_R ribonuclease R

Probab=94.87  E-value=0.021  Score=53.21  Aligned_cols=32  Identities=13%  Similarity=-0.025  Sum_probs=29.4

Q ss_pred             CCCceeEeeEeeecCCeeEEecCC-Chhhhchh
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPLP-GLGAIFEE  176 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~~-gv~gl~~~  176 (182)
                      ..|+++.|+|+++.+||+||++.+ |++||+|-
T Consensus       626 ~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhi  658 (709)
T TIGR02063       626 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHI  658 (709)
T ss_pred             cCCcEEEEEEEEEEeCCEEEEecCCceEEEEEe
Confidence            359999999999999999999988 89999974

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.

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

Probab=94.37  E-value=0.035  Score=42.91  Aligned_cols=31  Identities=6%  Similarity=0.010  Sum_probs=26.9

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL  177 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~  177 (182)
                      .|+++.|+|+++.++|+||++. .++|+++-.
T Consensus        81 ~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~  111 (179)
T TIGR00448        81 LGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVS  111 (179)
T ss_pred             CCCEEEEEEEEEEeeEEEEEeC-CceEEEEcH
Confidence            3999999999999999999995 489887643

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

>PRK11642 exoribonuclease R; Provisional

Probab=94.25  E-value=0.034  Score=52.57  Aligned_cols=33  Identities=12%  Similarity=-0.022  Sum_probs=29.4

Q ss_pred             CCCceeEeeEeeecCCeeEEecCCC-hhhhchhh
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPLPG-LGAIFEEL  177 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~~g-v~gl~~~~  177 (182)
                      ..|+++.|+|+++.+||+||+|.++ ++||+|-.
T Consensus       642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs  675 (813)
T PRK11642        642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVS  675 (813)
T ss_pred             cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEe
Confidence            3599999999999999999999875 99999854

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

Probab=93.74  E-value=0.066  Score=41.54  Aligned_cols=37  Identities=14%  Similarity=0.052  Sum_probs=31.3

Q ss_pred             CCCCceeEeeEeeecCCeeEEecCCChhhhchhhhhcc
Q 030172          144 PQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQED  181 (182)
Q Consensus       144 ~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~~  181 (182)
                      |-.|.++.|.|+++.++|+||.+. =++||+|..+.-|
T Consensus        79 P~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~d  115 (183)
T COG1095          79 PFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMD  115 (183)
T ss_pred             eccccEEEEEEEEEeecceEEEec-cccccccHhhccC
Confidence            334899999999999999999996 7999999876433

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

Probab=93.67  E-value=0.08  Score=38.51  Aligned_cols=25  Identities=28%  Similarity=0.417  Sum_probs=23.3

Q ss_pred             CCCeEEEEEEEEeCCCCEEEEEechh
Q 030172           22 TGSIISVKVIQANEEMKKLVFSEKDA   47 (182)
Q Consensus        22 vG~~v~~~v~~~d~~~~~i~lS~k~~   47 (182)
                      +|++|.++|+.+|+ ++++.||.|.+
T Consensus        52 vG~eV~vKVl~ide-~GKisLSIr~~   76 (129)
T COG1098          52 VGQEVKVKVLDIDE-NGKISLSIRKL   76 (129)
T ss_pred             CCCEEEEEEEeecc-CCCcceehHHh
Confidence            89999999999998 89999998863

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

Probab=93.58  E-value=0.064  Score=49.58  Aligned_cols=32  Identities=13%  Similarity=0.051  Sum_probs=29.3

Q ss_pred             CCceeEeeEeeecCCeeEEecC-CChhhhchhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPL-PGLGAIFEEL  177 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~-~gv~gl~~~~  177 (182)
                      .|+++.|+|+++.++|+||+|+ .|++||+|-.
T Consensus       572 iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s  604 (654)
T TIGR00358       572 VGTEFSGEISSVTRFGMFVRLDDNGIDGLIHIS  604 (654)
T ss_pred             CCcEEEEEEEeEEcCcEEEEecCCceEEEEEeE
Confidence            5999999999999999999997 8899998753

This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=93.22  E-value=0.073  Score=46.58  Aligned_cols=32  Identities=3%  Similarity=-0.034  Sum_probs=29.9

Q ss_pred             CceeEeeEeeecCC--eeEEecCCChhhhchhhh
Q 030172          147 GSVISDSSSMSSSN--SNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       147 g~~v~G~V~~v~~~--G~fV~l~~gv~gl~~~~~  178 (182)
                      |+++.|+|.++.++  ||||++..|-+||+|-..
T Consensus        26 GnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d   59 (414)
T TIGR00757        26 GNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASD   59 (414)
T ss_pred             CCEEEEEEeeecCCCceEEEEcCCCceEEEEHHH
Confidence            99999999999997  999999999999998664

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.

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

Probab=93.13  E-value=0.078  Score=41.14  Aligned_cols=31  Identities=3%  Similarity=-0.116  Sum_probs=27.4

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL  177 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~  177 (182)
                      .|+++.|+|+++.++|+||++. .++|+++..
T Consensus        81 ~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~  111 (187)
T PRK08563         81 LQEVVEGEVVEVVEFGAFVRIG-PVDGLLHIS  111 (187)
T ss_pred             CCCEEEEEEEEEEccEEEEEEe-CceEEEEcH
Confidence            3999999999999999999996 499988754

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

Probab=92.97  E-value=0.099  Score=35.77  Aligned_cols=32  Identities=16%  Similarity=0.113  Sum_probs=27.3

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |+++.|+|+++.++|+||.+ ..+++|+++...
T Consensus         2 gEVi~g~V~~v~~~G~~v~~-Gpl~~f~~~~~i   33 (88)
T cd04462           2 GEVVDAIVTSVNKTGFFAEV-GPLSIFISRHLI   33 (88)
T ss_pred             CcEEEEEEEEEeccEEEEEE-cCceEEEEeeec
Confidence            78999999999999999999 567888776543

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.

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

Probab=92.60  E-value=0.11  Score=46.95  Aligned_cols=32  Identities=13%  Similarity=0.133  Sum_probs=29.2

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL  177 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~  177 (182)
                      .|-+++++|+.+.++|+||+++|+-.||||..
T Consensus       668 ~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~s  699 (760)
T KOG1067|consen  668 FGGVYTATITEIRDTGVMVELYPMQQGLLHNS  699 (760)
T ss_pred             eeeEEEEEEeeecccceEEEecCCchhhccch
Confidence            37788999999999999999999999999864

>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=92.51  E-value=0.13  Score=34.00  Aligned_cols=30  Identities=17%  Similarity=0.286  Sum_probs=27.2

Q ss_pred             CceeEeeEeeecCCeeEEecCC-Chhhhchh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLP-GLGAIFEE  176 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~-gv~gl~~~  176 (182)
                      |+.++|+|...++.+++|++.+ |+.|++|.
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~   31 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPT   31 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEc
Confidence            5789999999999999999987 99998874

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.

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

Probab=92.43  E-value=1  Score=34.35  Aligned_cols=61  Identities=20%  Similarity=0.288  Sum_probs=41.5

Q ss_pred             hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcC----CccccC-------ccccccCCCEEEEEEEEE
Q 030172           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS----WDLIQD-------IRDILNEGDEVRVKVIKI  116 (182)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels----~~~~~~-------~~~~~~~Gd~v~vkV~~i  116 (182)
                      ..+.-.|+++.|+     ..|+|++++ |     ++.++.---+.    ...-++       -...+++|..|+++|++.
T Consensus        76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~G-P-----l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigt  149 (170)
T KOG3298|consen   76 TFKPFKGEVVDGVVTKVNKMGVFARSG-P-----LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGT  149 (170)
T ss_pred             EEeecCCcEEEEEEEEEeeeeEEEecc-c-----eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEE
Confidence            3466789999999     899999996 2     77776432222    221122       122589999999999988


Q ss_pred             eCC
Q 030172          117 DRE  119 (182)
Q Consensus       117 d~~  119 (182)
                      .-+
T Consensus       150 r~~  152 (170)
T KOG3298|consen  150 RVD  152 (170)
T ss_pred             EEe
Confidence            543

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

Probab=90.83  E-value=0.1  Score=47.18  Aligned_cols=38  Identities=13%  Similarity=0.005  Sum_probs=33.4

Q ss_pred             hhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          140 EKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       140 ~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      ..+..  |..+.|+|.++..||+||+|..-+.||+++..+
T Consensus       118 ~Dve~--g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~  155 (715)
T COG1107         118 EDVEA--GKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDL  155 (715)
T ss_pred             hhccc--ceeeeccccchhhhcceeecChhhhcccccccc
Confidence            34555  999999999999999999999999999998743

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

Probab=88.58  E-value=0.51  Score=36.51  Aligned_cols=34  Identities=9%  Similarity=-0.080  Sum_probs=29.0

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhhhc
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE  180 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~  180 (182)
                      .|+++.|.|+++.++|+||.+. =+++|+|.....
T Consensus        81 ~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~  114 (176)
T PTZ00162         81 KDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIP  114 (176)
T ss_pred             CCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCC
Confidence            4999999999999999999995 455898887654

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=88.36  E-value=0.064  Score=46.16  Aligned_cols=77  Identities=13%  Similarity=0.055  Sum_probs=49.0

Q ss_pred             ccccCCCEEEEEEEEEeCCCCeEEEEEeeccC-----CchhHHHhhhcCCCCceeEeeEeeecCC-eeEEecCCChhhhc
Q 030172          101 DILNEGDEVRVKVIKIDREKSRITLSIKQLEE-----DPLLETLEKVIPQDGSVISDSSSMSSSN-SNTIEPLPGLGAIF  174 (182)
Q Consensus       101 ~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~-----~p~~~~~~~~~~~~g~~v~G~V~~v~~~-G~fV~l~~gv~gl~  174 (182)
                      ..+++||.+...+--.+. .+...-+.|+...     -..+.....|....|++++|+|.++... ++||++ +++.|++
T Consensus        89 ~~~~vGd~i~~~i~~~~f-gRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdl-g~~ea~L  166 (374)
T PRK12328         89 PSVEIGDELTYELSLENM-GRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEI-DEIRAVL  166 (374)
T ss_pred             CCCCCCCEEEEecChhhC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEc-CCeEEEe
Confidence            348899999876533322 2212222232221     0112344566556799999999999874 599999 4899999


Q ss_pred             hhhhh
Q 030172          175 EELLQ  179 (182)
Q Consensus       175 ~~~~~  179 (182)
                      |+-.+
T Consensus       167 P~~eq  171 (374)
T PRK12328        167 PMKNR  171 (374)
T ss_pred             CHHHc
Confidence            98765

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

Probab=88.17  E-value=1  Score=40.30  Aligned_cols=59  Identities=27%  Similarity=0.432  Sum_probs=46.1

Q ss_pred             cCCCCCCEEEEE-------eEeEEEEEecCCCceeEEEEEEccCcCCccccCc-----cccccCCCEEEEEEEEEeC
Q 030172           54 SRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----RDILNEGDEVRVKVIKIDR  118 (182)
Q Consensus        54 ~~~~~G~iv~g~-------~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~-----~~~~~~Gd~v~vkV~~id~  118 (182)
                      ....+|.+|.|+       =-.+||+++.  +   -.||+|++++.+ +...+     ...++.||.+-|.|+.-..
T Consensus        33 ~~~~~gniy~grv~~i~p~~~aafvdig~--~---r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~  103 (487)
T COG1530          33 KEQIVGNIYKGRVTRVLPSLEAAFVDIGL--E---RNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPR  103 (487)
T ss_pred             cEeeecCceEEEecccCccchhheeeccC--C---ccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecC
Confidence            456689999999       2348999983  3   789999999998 54433     3479999999999987654

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

Probab=87.64  E-value=0.5  Score=38.69  Aligned_cols=41  Identities=12%  Similarity=0.127  Sum_probs=31.8

Q ss_pred             CCCCCCccHH--Hhhhhc--CCCeEEEEEEEEeCCCCEEEEEech
Q 030172            6 SCKEPQKSIH--EIAKGL--TGSIISVKVIQANEEMKKLVFSEKD   46 (182)
Q Consensus         6 ~~p~~e~~~~--~~~~~~--vG~~v~~~v~~~d~~~~~i~lS~k~   46 (182)
                      |++.||++-.  ++.+.+  +|+++=|+|+.+|+..+.+.+|+|+
T Consensus        40 ~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkr   84 (269)
T COG1093          40 FIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKR   84 (269)
T ss_pred             eEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhh
Confidence            4555665544  334444  8999999999999999999999874

>PRK07252 hypothetical protein; Provisional

Probab=87.04  E-value=1.2  Score=32.17  Aligned_cols=42  Identities=14%  Similarity=0.008  Sum_probs=30.9

Q ss_pred             CCCCCCccHHH--hh-h-hcCCCeEEEEEEEEeCCCCEEEEEechh
Q 030172            6 SCKEPQKSIHE--IA-K-GLTGSIISVKVIQANEEMKKLVFSEKDA   47 (182)
Q Consensus         6 ~~p~~e~~~~~--~~-~-~~vG~~v~~~v~~~d~~~~~i~lS~k~~   47 (182)
                      |+|.++++...  .. . ..+||.|.++|+++|.+.+++.+|.++.
T Consensus        30 llhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~   75 (120)
T PRK07252         30 LIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTL   75 (120)
T ss_pred             EEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence            45555555331  11 1 2489999999999999999999999874

>PRK05054 exoribonuclease II; Provisional

Probab=86.99  E-value=0.45  Score=44.02  Aligned_cols=31  Identities=13%  Similarity=0.022  Sum_probs=26.5

Q ss_pred             CceeEeeEeeecCCeeEEecC-CChhhhchhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPL-PGLGAIFEEL  177 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~-~gv~gl~~~~  177 (182)
                      |+.+.|.|+++.+||.||+|. .|+.||+|-.
T Consensus       562 ~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~  593 (644)
T PRK05054        562 DTRFAAEIIDISRGGMRVRLLENGAVAFIPAS  593 (644)
T ss_pred             CeEEEEEEEeeecCcEEEEEeCCceEEEEEcc
Confidence            459999999999999999995 5799997754

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

Probab=86.98  E-value=3.8  Score=31.62  Aligned_cols=72  Identities=21%  Similarity=0.201  Sum_probs=45.5

Q ss_pred             CCCCCCEEEEE------eEeEEEEEecCCC-c--eeEEEEEEccCcCCcc--ccCccccccCCCEEEEEEEEEeCCCCeE
Q 030172           55 RVNVEDIFVGR------DYGAFIHLRFPDG-L--YHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRI  123 (182)
Q Consensus        55 ~~~~G~iv~g~------~~G~fV~l~~~~g-~--~~~~glv~~sels~~~--~~~~~~~~~~Gd~v~vkV~~id~~~~ki  123 (182)
                      -+..|+||.++      .| +-|+|...+. .  ....|++|..++....  .-++-+-|++||.|.|+|++.+. ....
T Consensus        65 LP~~G~IVtarV~~i~~rf-Akv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~-~~~y  142 (193)
T KOG3409|consen   65 LPFVGAIVTARVSRINLRF-AKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD-GSNY  142 (193)
T ss_pred             CCccCcEEEEEEEeeccce-eeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC-CCcE
Confidence            35789999999      22 3333321110 0  0378999988875431  23455669999999999999654 4555


Q ss_pred             EEEEe
Q 030172          124 TLSIK  128 (182)
Q Consensus       124 ~lS~k  128 (182)
                      .||.-
T Consensus       143 ~LTtA  147 (193)
T KOG3409|consen  143 LLTTA  147 (193)
T ss_pred             EEEEe
Confidence            55553

>PRK08582 hypothetical protein; Provisional

Probab=86.91  E-value=0.67  Score=34.42  Aligned_cols=41  Identities=22%  Similarity=0.171  Sum_probs=29.6

Q ss_pred             CCCCCCccHHH---hhh-hcCCCeEEEEEEEEeCCCCEEEEEechh
Q 030172            6 SCKEPQKSIHE---IAK-GLTGSIISVKVIQANEEMKKLVFSEKDA   47 (182)
Q Consensus         6 ~~p~~e~~~~~---~~~-~~vG~~v~~~v~~~d~~~~~i~lS~k~~   47 (182)
                      |++.++++...   ... ..+|+.|+|+|+.+|. .+++.+|.++.
T Consensus        32 lVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~   76 (139)
T PRK08582         32 LVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKA   76 (139)
T ss_pred             EEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEec
Confidence            45666665432   111 2389999999999997 48999999874

>COG4044 Uncharacterized protein conserved in archaea [Function unknown]

Probab=86.91  E-value=0.3  Score=38.73  Aligned_cols=73  Identities=23%  Similarity=0.352  Sum_probs=50.8

Q ss_pred             cCCCCCCEEEEE-------eEeEEEEEecCCCceeEEEEEEccCcCCccccCc----cccc--cCCCEEEEEEEEEeCCC
Q 030172           54 SRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----RDIL--NEGDEVRVKVIKIDREK  120 (182)
Q Consensus        54 ~~~~~G~iv~g~-------~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~----~~~~--~~Gd~v~vkV~~id~~~  120 (182)
                      .+++.|+++.|+       -||+||+++- .|.-..++++|.-+|....-..|    ...|  -.-..++|-|.+++...
T Consensus        71 ~~~~~Gdv~vGrl~~l~~vgyg~yvdigV-~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~~  149 (247)
T COG4044          71 SKVEEGDVYVGRLIDLGKVGYGAYVDIGV-LGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKLA  149 (247)
T ss_pred             ccCCCCcEEEEEEeeeccceeEEEccccc-cCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccchh
Confidence            688999999999       8899999852 22223789999988876654444    2223  23456777888888766


Q ss_pred             CeEEEEE
Q 030172          121 SRITLSI  127 (182)
Q Consensus       121 ~ki~lS~  127 (182)
                      +.|...+
T Consensus       150 ~EIea~l  156 (247)
T COG4044         150 QEIEARL  156 (247)
T ss_pred             hhhhhhh
Confidence            6665444

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

Probab=84.88  E-value=1.7  Score=29.68  Aligned_cols=39  Identities=13%  Similarity=0.062  Sum_probs=33.4

Q ss_pred             hcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhhc
Q 030172          142 VIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE  180 (182)
Q Consensus       142 ~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~  180 (182)
                      |.|..||.|=|+|+.+.....+|++..-..|++|-+.-|
T Consensus         2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~   40 (86)
T cd05790           2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFE   40 (86)
T ss_pred             CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcc
Confidence            556679999999999999999999988888998876544

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".

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

Probab=84.75  E-value=1.5  Score=30.12  Aligned_cols=34  Identities=9%  Similarity=0.197  Sum_probs=29.2

Q ss_pred             CCCCceeEeeEeeecCCeeEEec--------CCChhhhchhh
Q 030172          144 PQDGSVISDSSSMSSSNSNTIEP--------LPGLGAIFEEL  177 (182)
Q Consensus       144 ~~~g~~v~G~V~~v~~~G~fV~l--------~~gv~gl~~~~  177 (182)
                      |..|++|-|+|+++....+.|++        .....|++|-.
T Consensus         4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~   45 (92)
T cd05791           4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKE   45 (92)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHH
Confidence            45699999999999999999999        77788888743

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".

>PRK11712 ribonuclease G; Provisional

Probab=83.84  E-value=0.87  Score=40.77  Aligned_cols=32  Identities=9%  Similarity=0.021  Sum_probs=29.2

Q ss_pred             CCceeEeeEeeecC--CeeEEecCCChhhhchhh
Q 030172          146 DGSVISDSSSMSSS--NSNTIEPLPGLGAIFEEL  177 (182)
Q Consensus       146 ~g~~v~G~V~~v~~--~G~fV~l~~gv~gl~~~~  177 (182)
                      +|.++.|+|.++.|  .+|||++..+-.||+|--
T Consensus        38 vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~   71 (489)
T PRK11712         38 VGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHAS   71 (489)
T ss_pred             cccEEEEEEeecCCCCceeEEeeCCCccEEEEhh
Confidence            49999999999998  789999999999999754

>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit

Probab=83.36  E-value=4.4  Score=29.43  Aligned_cols=56  Identities=18%  Similarity=0.192  Sum_probs=37.3

Q ss_pred             CCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcc------------c-cCccccccCCCEEEEEEEEEeC
Q 030172           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL------------I-QDIRDILNEGDEVRVKVIKIDR  118 (182)
Q Consensus        58 ~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~------------~-~~~~~~~~~Gd~v~vkV~~id~  118 (182)
                      +|+++.|+     ..|+.|.|+..     -+.+||.+.|...-            . .+.+-++..|+.|+.||.++..
T Consensus         3 ~gEvl~g~I~~~~~~Gi~vslgFF-----ddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f   76 (122)
T PF08292_consen    3 VGEVLTGKIKSSTAEGIRVSLGFF-----DDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF   76 (122)
T ss_dssp             TT-EEEEEEEEEETTEEEEEECCE-----EEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred             CCCEEEEEEEecCCCcEEEEeccc-----ccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence            68888888     77899988632     57888888775321            1 3334457899999999998864

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

>TIGR02062 RNase_B exoribonuclease II

Probab=83.35  E-value=0.99  Score=41.77  Aligned_cols=32  Identities=9%  Similarity=-0.020  Sum_probs=26.9

Q ss_pred             CceeEeeEeeecCCeeEEec-CCChhhhchhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEP-LPGLGAIFEELL  178 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l-~~gv~gl~~~~~  178 (182)
                      ++.+.|.|+.+..+|+||+| ..|++||+|..-
T Consensus       558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~  590 (639)
T TIGR02062       558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAF  590 (639)
T ss_pred             CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhh
Confidence            45899999999999999999 577999987543

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.

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

Probab=82.14  E-value=0.97  Score=37.18  Aligned_cols=40  Identities=15%  Similarity=0.062  Sum_probs=29.6

Q ss_pred             CCCCCCccHHH--hhh-h-cCCCeEEEEEEEEeCCCCEEEEEec
Q 030172            6 SCKEPQKSIHE--IAK-G-LTGSIISVKVIQANEEMKKLVFSEK   45 (182)
Q Consensus         6 ~~p~~e~~~~~--~~~-~-~vG~~v~~~v~~~d~~~~~i~lS~k   45 (182)
                      |+|.++++...  .+. . -+|+.+.|+|+.+|..++++.+|.+
T Consensus        37 lI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK   80 (262)
T PRK03987         37 FIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK   80 (262)
T ss_pred             EEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEE
Confidence            45556655331  111 2 3899999999999999999999987

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=81.75  E-value=2.6  Score=28.59  Aligned_cols=37  Identities=19%  Similarity=0.239  Sum_probs=29.0

Q ss_pred             CCCCccHHH---hhhhcCCCeEEEEEEEEeCCCCEEEEEe
Q 030172            8 KEPQKSIHE---IAKGLTGSIISVKVIQANEEMKKLVFSE   44 (182)
Q Consensus         8 p~~e~~~~~---~~~~~vG~~v~~~v~~~d~~~~~i~lS~   44 (182)
                      +++|++-++   .-+.++|....+.|+.+|+.+|-+.+|.
T Consensus        46 ~~selsr~rirsi~kllVGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         46 NYVNVNADRAEKLKKKLVGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             cHHHHhHHHHHhhhhhhcCCeeEEEEEEECCCCCEEEeEc
Confidence            466666664   2334599999999999999999999874

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=80.57  E-value=1.3  Score=27.93  Aligned_cols=33  Identities=6%  Similarity=-0.024  Sum_probs=20.2

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |++...+|..+.++|+|++-..+-+-|+|....
T Consensus         2 G~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~   34 (61)
T PF13509_consen    2 GQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEV   34 (61)
T ss_dssp             -------EEEE-SSEEEEEETT-EEEEEEGGG-
T ss_pred             CCCcceEEEEEeCCEEEEECCCCCEEEechHHc
Confidence            778889999999999999977778888887654

>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=80.01  E-value=16  Score=24.66  Aligned_cols=25  Identities=20%  Similarity=0.340  Sum_probs=16.9

Q ss_pred             cCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172          104 NEGDEVRVKVIKIDREKSRITLSIKQL  130 (182)
Q Consensus       104 ~~Gd~v~vkV~~id~~~~ki~lS~k~~  130 (182)
                      ++|+.|.++|..+.  .++..+.+-.+
T Consensus         3 ~vGdiV~~rVtrv~--~~~a~v~Il~v   27 (82)
T PF10447_consen    3 KVGDIVIARVTRVN--PRQAKVEILCV   27 (82)
T ss_dssp             -TT-EEEEEEEEE---SSEEEEEEEES
T ss_pred             CCCCEEEEEEEEEe--ccEEEEEEEEE
Confidence            58999999999996  56666666555

The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	182
2k4k_A	130	Solution Structure Of Gsp13 From Bacillus Subtilis		6e-10
2aho_B	266	Structure Of The Archaeal Initiation Factor Eif2 Al		2e-06
3aev_A	275	Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex		3e-06
1yz6_A	274	Crystal Structure Of Intact Alpha Subunit Of Aif2 F		3e-06
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		1e-05
3bzc_A	785	Crystal Structure Of The Tex Protein From Pseudomon		5e-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 =		7e-05
4am3_A	717	Crystal Structure Of C. Crescentus Pnpase Bound To		5e-04
4aim_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		5e-04
4aid_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		5e-04

>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis Length = 130

Iteration: 1
 Score = 60.1 bits (144), Expect = 6e-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 = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 6/77 (7%)
Query: 57  NVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116
            V+ +F   DYG+++ L   D    L   +  SEVS   +++IRD+L E  +V VKVI++
Sbjct: 18  TVKQVF---DYGSYVSL---DEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRV 71
Query: 117 DREKSRITLSIKQLEED 133
           DR K  + +S+K++ +D
Sbjct: 72  DRRKGTVDVSLKKVTDD 88

>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From Pyrococcus Horikoshii Ot3 Length = 275

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-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 = 47.8 bits (112), Expect = 3e-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 = 1e-05,   Method: Compositional matrix adjust.
 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 = 43.9 bits (102), 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: 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 = 43.9 bits (102), 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 = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 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

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 6/68 (8%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           D+GAF++           GLVHVS++S + +    D+L EG  V+VK++  D ++ +  L
Sbjct: 641 DFGAFVNF-----FGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD-DRGKTKL 694
Query: 126 SIKQLEED 133
           S+K ++++
Sbjct: 695 SMKVVDQE 702

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 6/68 (8%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           D+GAF++           GLVHVS++S + +    D+L EG  V+VK++  D ++ +  L
Sbjct: 650 DFGAFVNF-----FGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD-DRGKTKL 703
Query: 126 SIKQLEED 133
           S+K ++++
Sbjct: 704 SMKVVDQE 711

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 6/68 (8%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           D+GAF++           GLVHVS++S + +    D+L EG  V+VK++  D ++ +  L
Sbjct: 650 DFGAFVNF-----FGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD-DRGKTKL 703
Query: 126 SIKQLEED 133
           S+K ++++
Sbjct: 704 SMKVVDQE 711

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	182
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	7e-22
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	9e-22
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	4e-21
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	3e-04
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	5e-21
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	2e-05
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	4e-19
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	2e-18
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	3e-18
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	2e-17
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	1e-16
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	8e-16
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	1e-15
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	3e-15
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	2e-14
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	6e-13
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	2e-12
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	1e-07
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	1e-07
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	4e-07
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	1e-06
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	3e-06
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	5e-05
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	1e-04

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130

 Score = 84.8 bits (210), Expect = 7e-22
 Identities = 35/108 (32%), Positives = 61/108 (56%), Gaps = 10/108 (9%)

Query: 53  SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGD 107
           +++  V  ++ G+      YGAF+ L          GLVH+SEV+   ++DI + L+ GD
Sbjct: 2   AAKFEVGSVYTGKVTGLQAYGAFVAL-----DEETQGLVHISEVTHGFVKDINEHLSVGD 56

Query: 108 EVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSS 155
           EV+VKV+ +D EK +I+LSI+  +  P  +  +   P+   V  ++S+
Sbjct: 57  EVQVKVLAVDEEKGKISLSIRATQAAPEKKESKPRKPKAAQVSEEAST 104

>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 = 86.0 bits (213), Expect = 9e-22
 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

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 82.2 bits (204), Expect = 4e-21
 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 = 37.6 bits (88), Expect = 3e-04
 Identities = 0/29 (0%), Positives = 4/29 (13%)

Query: 114 IKIDREKSRITLSIKQLEEDPLLETLEKV 142
           +         +  +           +   
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMFNNWVALN 29

>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 = 84.0 bits (208), Expect = 5e-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 = 42.4 bits (100), Expect = 2e-05
 Identities = 13/122 (10%), Positives = 32/122 (26%), Gaps = 11/122 (9%)

Query: 12  KSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-DY 67
           +SI ++ +   G      V++ ++E   +  S++        K   +            Y
Sbjct: 56  RSIQKLIR--VGKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRY 113

Query: 68  GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127
            A       + LY       ++           +              I+     +   +
Sbjct: 114 CAEKFQIPLEELYK-----TIAWPLSRKFGHAYEAFKLSIIDETVWEGIEPPSKDVLDEL 168

Query: 128 KQ 129
           K 
Sbjct: 169 KN 170

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 77.3 bits (191), 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

>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 = 79.6 bits (196), 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

>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 = 78.5 bits (193), Expect = 3e-18
 Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 8/90 (8%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
           +  +I +       DYG+++ L    GL      +  SEVS   +++IRD+L E  +V V
Sbjct: 10  SEGEILIATVKQVFDYGSYVSLDEYGGL---QAFLPWSEVSSKWVKNIRDVLKENRKVIV 66

Query: 112 KVIKIDREKSRITLSIKQLEEDPLLETLEK 141
           KVI++DR K  + +S+K++ +D   +   +
Sbjct: 67  KVIRVDRRKGTVDVSLKKVTDDERRKKNLQ 96

>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 = 73.2 bits (180), Expect = 2e-17
 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 = 70.4 bits (173), Expect = 1e-16
 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 = 73.3 bits (181), Expect = 8e-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 = 72.9 bits (180), Expect = 1e-15
 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 = 66.1 bits (162), 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 = 68.5 bits (167), Expect = 2e-14
 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 = 64.9 bits (159), Expect = 6e-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 = 2e-12
 Identities = 27/114 (23%), Positives = 55/114 (48%), Gaps = 5/114 (4%)

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 SIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179
           S++  +        ++     GS        +    +       + A+F    Q
Sbjct: 722 SMRMSDTPGEKVEGQRGGRPTGSGQPRQERGAPRGQSAPPANNAMAALFANAKQ 775

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030

 Score = 49.9 bits (119), Expect = 1e-07
 Identities = 9/65 (13%), Positives = 18/65 (27%), Gaps = 6/65 (9%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-IRDILNEGDEVRVKVIKIDREKSRIT 124
                           +  +V+    +   ++    +I   G     KVI ID       
Sbjct: 918 HNDIICTTNS-----EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAE 972

Query: 125 LSIKQ 129
           +S+  
Sbjct: 973 VSLLD 977

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219

 Score = 49.5 bits (118), Expect = 1e-07
 Identities = 9/50 (18%), Positives = 18/50 (36%), Gaps = 1/50 (2%)

Query: 81  HLTGLVHVSEVSWDLIQD-IRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129
            +  +V+    +   ++    +I   G     KVI ID       +S+  
Sbjct: 925 EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLD 974

>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 = 46.8 bits (111), Expect = 4e-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 = 45.7 bits (108), Expect = 1e-06
 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 = 45.3 bits (107), 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

>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 = 41.2 bits (96), Expect = 5e-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

>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 = 39.2 bits (91), Expect = 1e-04
 Identities = 11/82 (13%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           D+G  + +    G+      + + +    +  ++    L  G  +   V K+      ++
Sbjct: 34  DHGYLVDI----GVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVS 89

Query: 125 LSIKQLEEDPLLETLEKVIPQD 146
           LS+   E    + T ++    +
Sbjct: 90  LSVGHSEVSTAIATEQQSWNLN 111

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	182
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.9
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.89
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.82
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.79
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.76
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.76
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.76
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.67
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.66
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.65
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.64
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.64
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.61
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.58
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.41
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.36
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.34
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.32
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	99.29
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.26
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.23
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	99.15
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.15
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	99.12
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	99.09
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	99.04
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	99.01
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	98.96
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.93
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.93
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.92
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.88
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.83
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	98.8
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.79
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.77
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.63
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	98.54
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	98.49
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.39
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	98.31
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	98.18
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.17
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	98.17
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	98.13
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	98.04
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	98.0
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.97
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	97.94
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	97.93
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	97.87
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	97.85
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	97.82
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.66
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	97.65
2r7d_A	469	Ribonuclease II family protein; structural genomic	97.56
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	97.45
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	97.37
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	97.3
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	97.09
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	96.98
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	96.97
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.94
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	96.89
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	96.81
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	96.78
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	96.73
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	96.71
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	96.68
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	96.65
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	96.5
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	96.37
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	96.36
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	95.88
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	95.85
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	95.82
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	95.56
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	94.85
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	94.33
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	94.16
1jjg_A	102	M156R; beta barrel, S1 motif, OB fold, MYXV156R, N	93.52
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	92.0
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	91.14
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	90.58
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	89.98
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	89.0
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	87.95
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	86.17

>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=99.90  E-value=3.1e-25  Score=171.14  Aligned_cols=116  Identities=22%  Similarity=0.336  Sum_probs=96.6

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~  130 (182)
                      +++|+++.|+     +||+||+|...+|   ++||||+|+++|.++.++++.|++||.|+|+|+++|+++++|.||+|++
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 PEVEDVVMVNVRSIAEMGAYVSLLEYNN---IEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRV   89 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTT---EEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTTC
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCCC---cEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence            4899999999     9999999942245   9999999999999999999999999999999999999999999999999


Q ss_pred             cCCchhHHHhhhcCCCCceeEeeEeeecC-CeeEEecCCChhhhchhhh
Q 030172          131 EEDPLLETLEKVIPQDGSVISDSSSMSSS-NSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       131 ~~~p~~~~~~~~~~~~g~~v~G~V~~v~~-~G~fV~l~~gv~gl~~~~~  178 (182)
                      .++||....++|+.  |+.++|.|+++++ ||  |++.+|++||+|.+.
T Consensus        90 ~~~p~~~~~~~~~~--g~~v~g~v~~i~~~~g--v~l~~giegl~h~s~  134 (182)
T 1kl9_A           90 SPEEAIKCEDKFTK--SKTVYSILRHVAEVLE--YTKDEQLESLFQRTA  134 (182)
T ss_dssp             CHHHHHHHHHHHHH--HHHHHHHHHHHHHHTT--CCSHHHHHHHHHHTH
T ss_pred             CcChHHHHHHhccC--CCEEEEEEEEchhhcC--CcccCChhheEEeee
Confidence            99999999999988  9999999999998 99  899999999999863

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

Probab=99.89  E-value=4.7e-23  Score=169.10  Aligned_cols=138  Identities=13%  Similarity=0.127  Sum_probs=116.3

Q ss_pred             cCCCeEEEEEEEEeCCCCEEEEEechhHHhhhhcCCCCCCEEEEE------eEeEEEEEecCCCceeEEEEEEccCcCCc
Q 030172           21 LTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD   94 (182)
Q Consensus        21 ~vG~~v~~~v~~~d~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~------~~G~fV~l~~~~g~~~~~glv~~sels~~   94 (182)
                      .+|+++++.|. .|. ++++.+|.+.       +.+++|+++.|+      ++||||+++.+ |   .++|||+||++|.
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-KQKLRLTTLE-------VTATQDQFGWGRVTEVRKDLGVFVDTGLP-D---KEIVVSLDILPEL  107 (285)
T ss_dssp             CTTSEEEEEEE-ECT-TSCEEEECSC-------CCSCSSSCEEEEEEEEETTTEEEEECSCT-T---CCEEEEGGGSCSS
T ss_pred             ccCCEEEEEEE-ECC-CCCEEEeccc-------ccccCCCEEEEEEEEEccCceEEEEECCC-C---cEEEEEHHHCCcc
Confidence            68999999995 354 5677777664       568999999998      38999999721 3   7999999999986


Q ss_pred             cccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec-cCCchhHHHhhhcCCCCceeEeeEeeecCCeeEE-ecCCChhh
Q 030172           95 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL-EEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTI-EPLPGLGA  172 (182)
Q Consensus        95 ~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~-~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV-~l~~gv~g  172 (182)
                      +..    .+++||.+.|+ +.+|+ ++||.+|+|+. ..+||....+++.+  |+.++|+|+++++||+|| .+++|++|
T Consensus       108 ~~~----~~~~Gd~v~v~-l~iD~-~~Ri~ls~k~~~~~~~~~~~~~~~~~--G~~V~g~V~~i~~~G~fV~~i~~g~~G  179 (285)
T 3go5_A          108 KEL----WPKKGDQLYIR-LEVDK-KDRIWGLLAYQEDFQRLARPAYNNMQ--NQNWPAIVYRLKLSGTFVYLPENNMLG  179 (285)
T ss_dssp             GGG----SCCTTCEEEEE-EEECT-TSCEEEEECCHHHHHHHCCCCCSCCT--TCEEEEEEEEEETTEEEEEETTTTEEE
T ss_pred             ccc----ccCCCCEEEEE-EEECC-CCcEEEEehhhhhcchhhhhhhhCCC--CCEEEEEEEEEeCCcEEEEEeCCCeEE
Confidence            532    36899999766 59998 79999999976 46899887788887  999999999999999999 99999999


Q ss_pred             hchhhhh
Q 030172          173 IFEELLQ  179 (182)
Q Consensus       173 l~~~~~~  179 (182)
                      |||....
T Consensus       180 lih~SEl  186 (285)
T 3go5_A          180 FIHPSER  186 (285)
T ss_dssp             EECGGGC
T ss_pred             EEEHHHc
Confidence            9998754

>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=99.82  E-value=6.4e-22  Score=151.76  Aligned_cols=117  Identities=21%  Similarity=0.304  Sum_probs=93.7

Q ss_pred             CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (182)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~  131 (182)
                      ++|+++.|+     +||+||+|...+|   ++||||+|++++.++.++++.|++||.|+|+|+++|+++++|.||+|++.
T Consensus        14 ~~G~iv~G~V~~i~~fGaFV~L~e~~g---veGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~   90 (175)
T 2a19_A           14 EIDDIVMVNVQQIAEMGAYVKLLEYDN---IEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVS   90 (175)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTTTT---CEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTTCC
T ss_pred             CCCCEEEEEEEEEecceEEEEEcCCCC---cEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEecC
Confidence            489999999     9999999942235   99999999999999999999999999999999999999999999999999


Q ss_pred             CCchhHHHhhhcCCCCceeEeeEeeec-CCeeEEecCCChhhhchhhhhc
Q 030172          132 EDPLLETLEKVIPQDGSVISDSSSMSS-SNSNTIEPLPGLGAIFEELLQE  180 (182)
Q Consensus       132 ~~p~~~~~~~~~~~~g~~v~G~V~~v~-~~G~fV~l~~gv~gl~~~~~~~  180 (182)
                      ++||....++|+.  |+.+.|+|++++ ++|+  .+.+.+..+...|.++
T Consensus        91 ~~~~~~~~~~~~~--g~~v~g~V~~i~~~~G~--~~e~~~~~~~~~l~~~  136 (175)
T 2a19_A           91 SEDIIKCEEKYQK--SKTVHSILRYCAEKFQI--PLEELYKTIAWPLSRK  136 (175)
T ss_dssp             HHHHHHHHHHHHH--HHHHHHHHHHHHHHTTC--CHHHHHHHTHHHHHHH
T ss_pred             cChHHHHHHhccC--CCcceEEEEEchhhcCC--CHHHHHHHHHHHHHHH
Confidence            9999999999988  999999999999 6997  3434555554444443

>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=99.79  E-value=8.5e-21  Score=156.87  Aligned_cols=113  Identities=25%  Similarity=0.410  Sum_probs=101.5

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~  130 (182)
                      +++|+++.|+     +||+||+|+.++|   ++||||+|+++|.++.++.+.|++||.|.|+|+++|+++++|.||+|++
T Consensus        11 ~~vG~iv~G~V~~I~~fGaFV~L~ey~g---veGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~   87 (308)
T 1q8k_A           11 PEVEDVVMVNVRSIQEMGAYVSLLEYNN---IEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRV   87 (308)
T ss_dssp             CSSCCEEEEEEEEEETTEEEEESCTTTS---CCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSC
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEECCCCC---eEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEec
Confidence            4689999999     9999999952234   9999999999999999999999999999999999999999999999999


Q ss_pred             cCCchhHHHhhhcCCCCceeEeeEeeecC-CeeEEecCCChhhhch
Q 030172          131 EEDPLLETLEKVIPQDGSVISDSSSMSSS-NSNTIEPLPGLGAIFE  175 (182)
Q Consensus       131 ~~~p~~~~~~~~~~~~g~~v~G~V~~v~~-~G~fV~l~~gv~gl~~  175 (182)
                      .++||....+++..  |+.+.|+|+++.+ ||+|++  ++...|..
T Consensus        88 ~~~p~~~~~~~~~~--G~~v~G~V~~v~~~~G~fi~--~~~e~l~~  129 (308)
T 1q8k_A           88 SPEEAIKCEDKFTK--SKTVYSILRHVAEVLEYTKD--EQLESLFQ  129 (308)
T ss_dssp             CHHHHHHHHHHHHH--HHHHHHHHHHHHHHTTCCSS--HHHHHHHH
T ss_pred             ccChHHHHHHHccC--CCeeEEEEEEcccccCCccC--CCHHHHHH
Confidence            99999999999988  9999999999999 799986  45554443

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

Probab=99.76  E-value=3.5e-20  Score=151.21  Aligned_cols=119  Identities=25%  Similarity=0.419  Sum_probs=105.8

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      .+++|+++.|+     +||+||+|+..+|   ++||||+|++++.++.++.+.|++||.|.|+|+++|++++++.||+|+
T Consensus         8 ~p~~Gdiv~G~V~~I~~fGaFV~L~e~~g---ieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~   84 (275)
T 3aev_A            8 YPEEGEFVVATVKRIHNYGAFLELDEYPG---KEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRR   84 (275)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTSTT---CEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCCCEEEEEEEEEECcEEEEEECCCCC---eEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            35689999999     9999999963235   999999999999999999999999999999999999999999999999


Q ss_pred             ccCCchhHHHhhhcCCCCceeEeeEeeec-CCeeEEecCCChhhhchhhhhc
Q 030172          130 LEEDPLLETLEKVIPQDGSVISDSSSMSS-SNSNTIEPLPGLGAIFEELLQE  180 (182)
Q Consensus       130 ~~~~p~~~~~~~~~~~~g~~v~G~V~~v~-~~G~fV~l~~gv~gl~~~~~~~  180 (182)
                      +.++||....++|..  |+.+.|.|+++. ++|++++  +++.++...|..+
T Consensus        85 ~~~~~~~~~~~~~~~--g~~v~g~v~~v~~~~G~~~e--e~~~~~~w~l~~~  132 (275)
T 3aev_A           85 VTQQQRKAKLQEFKR--AQKAENLLRLAAEKLGKDFE--AAWREVWVPLEEE  132 (275)
T ss_dssp             CCHHHHHHHHHHHHH--HHHHHHHHHHHHHHHTCCHH--HHHHHTHHHHHHH
T ss_pred             cCcchhHHHHHhccC--CCeEEEEEEEchhhcCCCHH--HHHHHHHHHHHHH
Confidence            999999999999988  999999999999 8998654  6777776666544

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

Probab=99.76  E-value=1.9e-18  Score=141.76  Aligned_cols=122  Identities=11%  Similarity=0.051  Sum_probs=104.2

Q ss_pred             CCCCCCCccHHHhhhhcCCCeEEEEEEEEeCCCCEEEEEech----hHHhhhhcCCCCCCEEEEE-----eEeEEE-EEe
Q 030172            5 HSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR-----DYGAFI-HLR   74 (182)
Q Consensus         5 ~~~p~~e~~~~~~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~----~~~~~~~~~~~~G~iv~g~-----~~G~fV-~l~   74 (182)
                      .|+|.+|+++.+...-.+|+++.+. +.+|+ ++|+.+|+|.    .+|.....++++|+++.|+     ++|+|| .++
T Consensus        97 ~lvp~sel~~~~~~~~~~Gd~v~v~-l~iD~-~~Ri~ls~k~~~~~~~~~~~~~~~~~G~~V~g~V~~i~~~G~fV~~i~  174 (285)
T 3go5_A           97 IVVSLDILPELKELWPKKGDQLYIR-LEVDK-KDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPE  174 (285)
T ss_dssp             EEEEGGGSCSSGGGSCCTTCEEEEE-EEECT-TSCEEEEECCHHHHHHHCCCCCSCCTTCEEEEEEEEEETTEEEEEETT
T ss_pred             EEEEHHHCCcccccccCCCCEEEEE-EEECC-CCcEEEEehhhhhcchhhhhhhhCCCCCEEEEEEEEEeCCcEEEEEeC
Confidence            4799999998765555799999755 69998 6899999963    4677777899999999999     999999 985


Q ss_pred             cCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhh
Q 030172           75 FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK  141 (182)
Q Consensus        75 ~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~  141 (182)
                        +|   ++||||.||++.        .+++||.|+|+|+++|++++||.||+|+....++...++.
T Consensus       175 --~g---~~Glih~SEl~~--------~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~~~~~~~a~~  228 (285)
T 3go5_A          175 --NN---MLGFIHPSERYA--------EPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQM  228 (285)
T ss_dssp             --TT---EEEEECGGGCSS--------CCCTTCEEEEEEEEEETTTTEEEEECSCCCCCCCCHHHHH
T ss_pred             --CC---eEEEEEHHHccc--------cCCCCCEEEEEEEEEECCCCeEEEEeChhhhhccchHHHH
Confidence              55   999999999984        4899999999999999989999999999887777665543

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

Probab=99.76  E-value=9.2e-19  Score=125.58  Aligned_cols=90  Identities=37%  Similarity=0.667  Sum_probs=80.2

Q ss_pred             hHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCc-cccCccccccCCCEEEEEEEEEeCCC
Q 030172           47 AVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREK  120 (182)
Q Consensus        47 ~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~-~~~~~~~~~~~Gd~v~vkV~~id~~~  120 (182)
                      .+|+....++++|+++.|+     ++|+||+|+  +|   ++||||++++++. +..++.+.|++||.|+|+|+++|.++
T Consensus        19 ~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~--~~---~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~   93 (115)
T 2khi_A           19 SHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIE--EG---VEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEER   93 (115)
T ss_dssp             --CCCSSCSSCSSCEEEEEEEEEETTEEEEECS--TT---CEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTT
T ss_pred             CCHHHHhhcCCCCCEEEEEEEEEECCEEEEEEC--CC---CEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCC
Confidence            4787777889999999999     999999996  45   9999999999984 78889999999999999999999989


Q ss_pred             CeEEEEEeeccCCchhHHHhh
Q 030172          121 SRITLSIKQLEEDPLLETLEK  141 (182)
Q Consensus       121 ~ki~lS~k~~~~~p~~~~~~~  141 (182)
                      ++|.||+|++.++||+.+.++
T Consensus        94 ~rI~lslk~~~~~p~~~~~~~  114 (115)
T 2khi_A           94 RRISLGLKQCKANPWQQFAET  114 (115)
T ss_dssp             TEEEECCCCCCSSCCCCCCCC
T ss_pred             CEEEEEEEecCcCHHHHHHhh
Confidence            999999999999999876544

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

Probab=99.67  E-value=8.3e-17  Score=110.11  Aligned_cols=77  Identities=31%  Similarity=0.418  Sum_probs=69.2

Q ss_pred             hcCCCCCCEEEEE----eEeEEEEEecCCCceeEEEEEEcc-CcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        53 ~~~~~~G~iv~g~----~~G~fV~l~~~~g~~~~~glv~~s-els~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      +...++|+++.|+    +||+||+|...+|   ++||||+| ++++.++.++++.+ +||.|+|+|+++|+++++|.||+
T Consensus         6 y~~~~vG~~~~G~V~v~~fG~FVel~~~~~---~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lsl   81 (88)
T 1luz_A            6 YSLPNAGDVIKGRVYEKDYALYIYLFDYPH---FEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNY   81 (88)
T ss_dssp             SCCCCTTCEEEEEEEEETTEEEEEETTCTT---SEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEE
T ss_pred             ecCCCCCCEEEEEEEEEccEEEEEECCCCC---eEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEE
Confidence            4567899999998    9999999963225   99999999 99999999999999 99999999999999999999999


Q ss_pred             eeccCC
Q 030172          128 KQLEED  133 (182)
Q Consensus       128 k~~~~~  133 (182)
                      |++.++
T Consensus        82 k~~~~~   87 (88)
T 1luz_A           82 KRMCRH   87 (88)
T ss_dssp             EEECSC
T ss_pred             eecCCC
Confidence            998664

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

Probab=99.66  E-value=2e-16  Score=115.75  Aligned_cols=117  Identities=32%  Similarity=0.499  Sum_probs=90.1

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      ..+++|++|.|+     ++|+||+|.  +|   ++||||++++++.++.++.+.|++||.|+|+|+++|.++++|.||+|
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--EE---TQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIR   77 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEE--TT---EEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESH
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEEC--CC---cEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence            468999999999     999999997  55   99999999999999999999999999999999999998999999999


Q ss_pred             eccCCchhHHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          129 QLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       129 ~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .+.++|+......-.+   ..+..........| |-.|++.+..++.+.+.
T Consensus        78 ~~~~~p~~~~~~~~~~---~~~~~~~~~~~~~g-~~~~~~~l~~~~k~s~~  124 (130)
T 2k4k_A           78 ATQAAPEKKESKPRKP---KAAQVSEEASTPQG-FNTLKDKLEEWIEMSNR  124 (130)
T ss_dssp             HHHHSCCCCSCCTTTT---CTTCCSCCCSCSSS-SSCCCSTTCCCSSCCCC
T ss_pred             ecccCccccccccccc---cccccccccccccC-CCCHHHHHHHHHHHhhh
Confidence            9998887531110000   00100111112334 88888999988876553

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

Probab=99.65  E-value=1.5e-16  Score=112.97  Aligned_cols=81  Identities=32%  Similarity=0.531  Sum_probs=74.9

Q ss_pred             hHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCC
Q 030172           47 AVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS  121 (182)
Q Consensus        47 ~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~  121 (182)
                      .+|+.+...+++|+++.|+     ++|+||+|+  +|   ++||||++++++.++.++.+.|++||.|+|+|+++|++++
T Consensus        20 ~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~--~~---~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~~~~   94 (109)
T 2khj_A           20 HMFNNWVALNKKGAIVTGKVTAVDAKGATVELA--DG---VEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDRKNR   94 (109)
T ss_dssp             -CHHHHTTTCCSSSEEEEEEEEECSSCEEEECS--TT---CBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEETTTT
T ss_pred             CHHHHHhhcCCCCCEEEEEEEEEECCeEEEEEC--CC---CEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEECCCC
Confidence            5899998999999999999     999999996  45   9999999999999999999999999999999999999888


Q ss_pred             eEEEEEeeccC
Q 030172          122 RITLSIKQLEE  132 (182)
Q Consensus       122 ki~lS~k~~~~  132 (182)
                      ++.||+|.+.+
T Consensus        95 ki~LS~k~~~~  105 (109)
T 2khj_A           95 AISLSVRAKDE  105 (109)
T ss_dssp             EEEEETTSSSS
T ss_pred             EEEEEEeecCh
Confidence            99999998754

>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=5.4e-17  Score=117.02  Aligned_cols=89  Identities=27%  Similarity=0.351  Sum_probs=77.9

Q ss_pred             hHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC-
Q 030172           47 AVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK-  120 (182)
Q Consensus        47 ~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~-  120 (182)
                      .+|+.+...+++|++|.|+     +||+||+|... +   .+||||++++++.++.++.+.|++||.|+|+|+++|+++ 
T Consensus        11 ~~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~-~---~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~   86 (119)
T 2cqo_A           11 GRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGC-R---KQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKND   86 (119)
T ss_dssp             CCCCCSCCSCCTTCEEEEEEEEEETTEEEEECTTC-S---SCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSS
T ss_pred             cchhhhhcccCCCCEEEEEEEEEeCceEEEEECCC-c---EEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEecccc
Confidence            3566677789999999999     99999999411 2   699999999999999999999999999999999999754 


Q ss_pred             -CeEEEEEeeccCCchhHHH
Q 030172          121 -SRITLSIKQLEEDPLLETL  139 (182)
Q Consensus       121 -~ki~lS~k~~~~~p~~~~~  139 (182)
                       ++|.||+|++.++||+...
T Consensus        87 ~~~i~LSlk~~~~~~~~~~~  106 (119)
T 2cqo_A           87 RIKVSLSMKVVNQGTGKDLD  106 (119)
T ss_dssp             CEEEEEESTTBCSSSCCBSC
T ss_pred             CceEEEEEeecccCCccccC
Confidence             6999999999999997643

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

Probab=99.64  E-value=3.9e-16  Score=109.72  Aligned_cols=81  Identities=26%  Similarity=0.553  Sum_probs=71.4

Q ss_pred             hcCCCCCCEEEEE-----eEeEEEEEecC-CCceeEEEEEEccCc-CCccccCccccccCCCEEEEEEEEEeCCCCeEEE
Q 030172           53 SSRVNVEDIFVGR-----DYGAFIHLRFP-DGLYHLTGLVHVSEV-SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (182)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~-~g~~~~~glv~~sel-s~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~l  125 (182)
                      ...+++|+++.|+     +||+||+|... ++   ++||||++++ ++.++.++.+.|++||.|+|+|+++|+  ++|.|
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~---~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~--~~i~L   81 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKR---WEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG--TKTSL   81 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEECSSSSC---CEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET--TEEEE
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEEcCCCCC---eEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC--CeeEE
Confidence            3578999999999     99999999631 15   9999999999 667788999999999999999999996  69999


Q ss_pred             EEeeccCCchhHH
Q 030172          126 SIKQLEEDPLLET  138 (182)
Q Consensus       126 S~k~~~~~p~~~~  138 (182)
                      |+|++.++||...
T Consensus        82 Slk~~~~~~~~~~   94 (103)
T 2eqs_A           82 SMKDVDQETGEDL   94 (103)
T ss_dssp             ESTTBCTTTCCBC
T ss_pred             EEeecccCCchhc
Confidence            9999999999654

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

Probab=99.61  E-value=4.1e-15  Score=99.80  Aligned_cols=69  Identities=32%  Similarity=0.511  Sum_probs=62.4

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      ++++|+++.|+     ++|+||+|+  ++   ++||||++++++.++    +.|++||.|+|+|+++|++++++.||+|.
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--EQ---VRGLLRPRDMISLRL----ENLNVGDEIIVQAIDVRPEKREIDFKYIP   72 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEE--TT---EEEEECGGGCSSCCG----GGCCTTCEEEEEEEEEETTTTEEEEEECS
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEEC--CC---CEEEEEHHHCCcccc----eeeCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            57899999999     999999997  45   999999999998775    67999999999999999988999999998


Q ss_pred             ccC
Q 030172          130 LEE  132 (182)
Q Consensus       130 ~~~  132 (182)
                      +.+
T Consensus        73 ~~~   75 (80)
T 2k52_A           73 LEH   75 (80)
T ss_dssp             CC-
T ss_pred             ccc
Confidence            765

>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=99.58  E-value=8.5e-17  Score=130.72  Aligned_cols=104  Identities=27%  Similarity=0.386  Sum_probs=92.2

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      ..+++|+++.|+     +||+||+|+.++|   ++||||+|++++.++.++++.|++||.|.|+|+++|++++++.||+|
T Consensus         7 ~~~~vG~iv~G~V~~I~~~GaFV~l~e~~~---~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk   83 (266)
T 3cw2_C            7 KLPSEGEILIATVKQVFDYGSYVSLDEYGG---LQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLK   83 (266)
T ss_dssp             SSCCTTCEEEEEEEECCSSSBEEEETTTTS---EECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEEST
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCCCC---eEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEE
Confidence            357899999999     9999999953234   99999999999999999999999999999999999998999999999


Q ss_pred             eccCCchhHHHhhhcCCCCceeEeeEeeec-CCee
Q 030172          129 QLEEDPLLETLEKVIPQDGSVISDSSSMSS-SNSN  162 (182)
Q Consensus       129 ~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~-~~G~  162 (182)
                      .+..+||....+++..  |+.+.|.|+.+. ..|.
T Consensus        84 ~~~~~~~~~~~~~~~~--~~~~~~iv~~lae~~~~  116 (266)
T 3cw2_C           84 KVTDDERRKKNLQWKK--IQRLDKILELVSQKLKL  116 (266)
T ss_dssp             TSCTTHHHHHHHHHHH--HHHHHHHHHHHHHHTTC
T ss_pred             ecchhhHHHHHHhccc--cCccceeeeehhhhCCC
Confidence            9999999999999987  777888888776 3443

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

Probab=99.41  E-value=1.5e-14  Score=131.06  Aligned_cols=103  Identities=28%  Similarity=0.478  Sum_probs=2.1

Q ss_pred             EEeCCCCEEEEEech--------hHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccC
Q 030172           32 QANEEMKKLVFSEKD--------AVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD   98 (182)
Q Consensus        32 ~~d~~~~~i~lS~k~--------~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~   98 (182)
                      ++++ .+.+.++...        +.++.+...+++|++|.|+     +||+||+|.  +|   ++||||+|++++.++.+
T Consensus       604 di~d-dG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~--~g---~eGLvHiSels~~rv~~  677 (726)
T 4aid_A          604 DIND-DGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFF--GA---KDGLVHVSQISNERVAK  677 (726)
T ss_dssp             -----------CCSCHHHHHHHHHC-------------------------------------------------------
T ss_pred             eEEC-CceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEeccEEEEEEC--CC---cEEEEEHHHcCcccccC
Confidence            4553 4665555432        1355566789999999999     999999996  45   99999999999999999


Q ss_pred             ccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhh
Q 030172           99 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK  141 (182)
Q Consensus        99 ~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~  141 (182)
                      +.+.|++||.|+|+|+++|+ ++||.||+|.+.++|+.....+
T Consensus       678 ~~d~~kvGD~V~VkVi~iD~-~grI~LS~K~~~~~~G~~~~~k  719 (726)
T 4aid_A          678 PSDVLKEGQMVKVKLLGFDD-RGKTKLSMKVVDQETGEDLSKK  719 (726)
T ss_dssp             -------------------------------------------
T ss_pred             ccccCCCCCEEEEEEEEECC-CCcEEEEEeecccCcchhhhhh
Confidence            99999999999999999998 8999999999999998776433

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

Probab=99.36  E-value=5.7e-14  Score=127.52  Aligned_cols=101  Identities=30%  Similarity=0.560  Sum_probs=0.0

Q ss_pred             EEeCCCCEEEEEech--------hHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccC
Q 030172           32 QANEEMKKLVFSEKD--------AVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD   98 (182)
Q Consensus        32 ~~d~~~~~i~lS~k~--------~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~   98 (182)
                      +++. .+.+.++...        +.++.+..++++|++|.|+     +||+||+|.  +|   ++||||+|++++.++.+
T Consensus       594 dI~~-dg~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~--~g---~eGLvHiSel~~~~v~~  667 (723)
T 3cdi_A          594 EIED-DGTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIG--GG---KEGLVHISQIADKRVEK  667 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EecC-CccEEEecCCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEecceEEEEeC--CC---ceEEEEHHHcCCccccC
Confidence            4444 4566555442        1344556789999999999     999999996  45   99999999999999999


Q ss_pred             ccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHH
Q 030172           99 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETL  139 (182)
Q Consensus        99 ~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~  139 (182)
                      +.+.|++||.|+|+|+++|+ +++|.||+|.+.++||....
T Consensus       668 ~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~~~~~~g~~~~  707 (723)
T 3cdi_A          668 VTDYLQMGQEVPVKVLEVDR-QGRIRLSIKEATEQSQPAAA  707 (723)
T ss_dssp             -----------------------------------------
T ss_pred             cccccCCCCEEEEEEEEECC-CCcEEEEEEeccCCCCcccC
Confidence            99999999999999999998 99999999999888886643

>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=99.34  E-value=1.2e-14  Score=132.47  Aligned_cols=104  Identities=21%  Similarity=0.416  Sum_probs=37.3

Q ss_pred             EEeCCCCEEEEEechh--------HHhhhh--cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCc----C
Q 030172           32 QANEEMKKLVFSEKDA--------VWNKYS--SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV----S   92 (182)
Q Consensus        32 ~~d~~~~~i~lS~k~~--------~~~~~~--~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sel----s   92 (182)
                      +++. .+.+.+|....        .++.+.  ..+++|++|.|+     +||+||+|.  +|   ++||||+|++    +
T Consensus       632 dI~~-dG~v~Is~~~~~~~~~a~~~i~~i~~p~~~~vG~i~~G~V~~i~~fGaFV~l~--~g---~eGLvHiSel~~~~s  705 (757)
T 1e3p_A          632 TIED-DGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGAFVSLL--PG---KDGLLHISQIRKLAG  705 (757)
T ss_dssp             ---------CCCBSSHHHHCC---------------------CBEEECC-CSCEECCC--------CCCCC---------
T ss_pred             EecC-CceEEEecCCHHHHHHHHHHHHHhcchhhcccccEEEEEEEEccccEEEEEEc--CC---cEEEEEhHHhccccC
Confidence            5554 57787776541        223334  678899999999     999999996  45   9999999999    9


Q ss_pred             CccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhh
Q 030172           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKV  142 (182)
Q Consensus        93 ~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~  142 (182)
                      |.++.++.+.|++||.|+|+|+++|+ ++||.||+|.+.++||.....++
T Consensus       706 ~~rv~~~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~~~~~pw~~~~~~~  754 (757)
T 1e3p_A          706 GKRVENVEDVLGVGQKVQVEIAEIDS-RGKLSLIPVIEGEEAASDEKKDD  754 (757)
T ss_dssp             ----------CCSSCBCCCCCCCCCS-SCC--------------------
T ss_pred             CCcccCcccccCCCCEEEEEEEEECC-CCCEEEEEecCCCCchhhhhhcc
Confidence            99999999999999999999999998 99999999999999998766554

>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=99.32  E-value=2.2e-12  Score=99.49  Aligned_cols=79  Identities=27%  Similarity=0.505  Sum_probs=67.5

Q ss_pred             hhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcccc-----------CccccccCCCEEEEEEE
Q 030172           51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVI  114 (182)
Q Consensus        51 ~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~-----------~~~~~~~~Gd~v~vkV~  114 (182)
                      .....+.+|+++.|+     ++|+||+|+   +   .+||+|++++++.++.           ++.+.|++||.|+|+|+
T Consensus        74 ~i~~~~~~Gev~~G~V~~v~~~G~fV~l~---~---~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~  147 (187)
T 1go3_E           74 TLVYIPEMYELIEGEVVDVVEFGSFVRLG---P---LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIV  147 (187)
T ss_dssp             EEEECCCTTCEEEEEEEEEETTEEEEECS---S---SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEE
T ss_pred             EEEEccCCCCEEEEEEEEEeCcEEEEEEc---C---ccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEE
Confidence            345678999999999     999999995   2   8999999999988765           78899999999999999


Q ss_pred             EEeCCCC-----eEEEEEeeccCCch
Q 030172          115 KIDREKS-----RITLSIKQLEEDPL  135 (182)
Q Consensus       115 ~id~~~~-----ki~lS~k~~~~~p~  135 (182)
                      ++|.+++     ++.||+|+....|+
T Consensus       148 ~vd~~~~~p~~~~I~lS~k~~~LG~~  173 (187)
T 1go3_E          148 AISLKAERKRGSKIALTMRQPYLGKL  173 (187)
T ss_dssp             EEECCC-----CEEEEECCSTTCEEH
T ss_pred             EEEcccCCCCccEEEEEEcCCCCCcH
Confidence            9998654     99999998665443

>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=99.29  E-value=3.1e-12  Score=98.05  Aligned_cols=80  Identities=28%  Similarity=0.566  Sum_probs=65.7

Q ss_pred             HhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc-----------cCccccccCCCEEEEE
Q 030172           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVK  112 (182)
Q Consensus        49 ~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~-----------~~~~~~~~~Gd~v~vk  112 (182)
                      +.....++.+|+++.|+     ++|+||+++   .   .+||+|++++.+.+.           ++..+.|++||.|+||
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---P---MDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRAR  145 (180)
T ss_dssp             EEEEEECCCTTCEEEEEEEEEETTEEEEECS---S---SEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEE
T ss_pred             hheeeeeccCCCEEEEEEeeeccceEEEEEC---C---ccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEE
Confidence            34455689999999999     999999995   2   899999999999876           4777889999999999


Q ss_pred             EEEEeCC----CCeEEEEEeeccCCc
Q 030172          113 VIKIDRE----KSRITLSIKQLEEDP  134 (182)
Q Consensus       113 V~~id~~----~~ki~lS~k~~~~~p  134 (182)
                      |+++|.+    ..+|.||+|+.-.-+
T Consensus       146 V~~v~~~~~~~~~rI~ls~k~~gLG~  171 (180)
T 4ayb_E          146 VISVASTVTGRLPRIALTMRQPYLGK  171 (180)
T ss_dssp             EEEECC-------CEEEECCSTTCEE
T ss_pred             EEEEeCCCCcccCcEEEEcCCCCCCC
Confidence            9999863    458999999854333

>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=99.26  E-value=4.7e-12  Score=90.88  Aligned_cols=76  Identities=16%  Similarity=0.247  Sum_probs=62.7

Q ss_pred             hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCc-CCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV-SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sel-s~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      ..++++|+++.|+     +||+||+|+ .++   ..+++|.++. +|.+..++.+.|++||.|+|+|+++|.+++++.||
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-VDG---TRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS   91 (119)
T ss_dssp             TTTCCTTCEEEEEEEEECSSEEEEECC-CSS---CEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEE
T ss_pred             HhcCCCCCEEEEEEEEEeCceEEEEEC-CCC---eEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEEE
Confidence            3679999999999     999999996 234   7777776664 34445688899999999999999999988999999


Q ss_pred             EeeccC
Q 030172          127 IKQLEE  132 (182)
Q Consensus       127 ~k~~~~  132 (182)
                      +|+...
T Consensus        92 lk~~~l   97 (119)
T 1wi5_A           92 VGHSEV   97 (119)
T ss_dssp             CCCCCS
T ss_pred             Echhhc
Confidence            997643

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

Probab=99.23  E-value=1.1e-11  Score=117.49  Aligned_cols=74  Identities=15%  Similarity=0.110  Sum_probs=68.6

Q ss_pred             hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcc-ccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~-~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      ..++++|+++.|+     +||+||+|+  .|   ++||||+|++++.+ +.++.+.|++||.|+|+|+++|.++++|.||
T Consensus       897 ~~~l~~G~iv~G~V~~V~~fGaFV~L~--~g---veGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LS  971 (1219)
T 3psi_A          897 EKTFFKGSIIPVRVERFWHNDIICTTN--SE---VECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVS  971 (1219)
T ss_dssp             TTTSCTTCEEEEEEEEECSSCEEEECT--TS---CEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEE
T ss_pred             HhhCCCCCEEEEEEEEEecceEEEEeC--CC---ceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence            3689999999999     999999996  56   99999999999998 8999999999999999999999999999999


Q ss_pred             Eeecc
Q 030172          127 IKQLE  131 (182)
Q Consensus       127 ~k~~~  131 (182)
                      +|...
T Consensus       972 lk~~d  976 (1219)
T 3psi_A          972 LLDHD  976 (1219)
T ss_dssp             CCHHH
T ss_pred             ecHHH
Confidence            99553

>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=99.15  E-value=7.1e-12  Score=114.55  Aligned_cols=74  Identities=28%  Similarity=0.544  Sum_probs=67.8

Q ss_pred             hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      ..++++|+++.|+     +||+||+|+  .+   ++||||+|++++.++.++.+.|++||.|+|+|+++|.++++|.||+
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--VH---QDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSM  723 (785)
T ss_dssp             STTCCTTCBCCCEEEEEETTEEEEECS--SS---SEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECC
T ss_pred             hhhcCCCCEEEEEEEEEecCCeEEEeC--CC---cEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEE
Confidence            3568899999888     999999996  45   8999999999999999999999999999999999999999999999


Q ss_pred             eecc
Q 030172          128 KQLE  131 (182)
Q Consensus       128 k~~~  131 (182)
                      |...
T Consensus       724 k~~~  727 (785)
T 3bzc_A          724 RMSD  727 (785)
T ss_dssp             SSCC
T ss_pred             ecCC
Confidence            9654

>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=99.15  E-value=6.3e-11  Score=92.93  Aligned_cols=77  Identities=19%  Similarity=0.205  Sum_probs=65.4

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCC---ceeEEEEEEccCcCCcccc--CccccccCCCEEEEEEEEEeCCCCeE
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRI  123 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g---~~~~~glv~~sels~~~~~--~~~~~~~~Gd~v~vkV~~id~~~~ki  123 (182)
                      ..+++|++|.|+     ++|+||+|...++   ..+.+|+||++|+++.+..  ++++.|++||.|+|+|++++..++++
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            468999999999     9999999952210   0027899999999999888  99999999999999999999866789


Q ss_pred             EEEEeec
Q 030172          124 TLSIKQL  130 (182)
Q Consensus       124 ~lS~k~~  130 (182)
                      .||+|+.
T Consensus       157 ~LS~k~~  163 (209)
T 2nn6_I          157 LLTTAEN  163 (209)
T ss_dssp             EEECCSS
T ss_pred             EEEEecC
Confidence            9999975

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

Probab=99.12  E-value=6.2e-12  Score=117.63  Aligned_cols=73  Identities=15%  Similarity=0.110  Sum_probs=0.0

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcc-ccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~-~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      .++++|+++.|+     +||+||+|+  .|   ++||||+|++++.+ +.++.+.|++||.|+|+|+++|.++++|.||+
T Consensus       901 ~~l~~G~iv~G~V~~V~~fGaFV~L~--~g---veGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSl  975 (1030)
T 3psf_A          901 KTFFKGSIIPVRVERFWHNDIICTTN--SE---VECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSL  975 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhcCCCEEEEEEEEEccCeEEEEeC--CC---cEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEe
Confidence            678999999999     999999996  46   99999999999998 89999999999999999999999999999999


Q ss_pred             eecc
Q 030172          128 KQLE  131 (182)
Q Consensus       128 k~~~  131 (182)
                      |...
T Consensus       976 k~~d  979 (1030)
T 3psf_A          976 LDHD  979 (1030)
T ss_dssp             ----
T ss_pred             chHH
Confidence            9664

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

Probab=99.09  E-value=2e-10  Score=87.98  Aligned_cols=68  Identities=26%  Similarity=0.390  Sum_probs=60.3

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecC--------CCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFP--------DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK  120 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~--------~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~  120 (182)
                      ..++ |++|.|+     ++|+||+|...        ++   .+|+||++++++.+..++++.|++||.|+|+|++     
T Consensus        54 y~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~---~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~-----  124 (179)
T 3m7n_A           54 EIVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNR---GIGILHVSNVDEGYVKEISEAVGYLDILKARVIG-----  124 (179)
T ss_dssp             CCCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTC---EEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE-----
T ss_pred             ccCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccC---eeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC-----
Confidence            3567 9999999     99999999731        03   8999999999999999999999999999999998     


Q ss_pred             CeEEEEEeec
Q 030172          121 SRITLSIKQL  130 (182)
Q Consensus       121 ~ki~lS~k~~  130 (182)
                      +++.||+|+.
T Consensus       125 ~~i~LS~k~~  134 (179)
T 3m7n_A          125 DNLRLSTKEE  134 (179)
T ss_dssp             TTTEEECCST
T ss_pred             CeEEEEEecC
Confidence            7899999864

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=99.04  E-value=4.8e-11  Score=99.73  Aligned_cols=109  Identities=18%  Similarity=0.142  Sum_probs=78.6

Q ss_pred             CCCCccHHH----hhhhcCCCeEEEEEEEEeCCCCEEEEEechhH--------HhhhhcCCC--CCCEEEEE-----eEe
Q 030172            8 KEPQKSIHE----IAKGLTGSIISVKVIQANEEMKKLVFSEKDAV--------WNKYSSRVN--VEDIFVGR-----DYG   68 (182)
Q Consensus         8 p~~e~~~~~----~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~~--------~~~~~~~~~--~G~iv~g~-----~~G   68 (182)
                      |..++++.+    .....+|+++.+.|...|.. +....+.|+..        .+..+..++  .|+++.|+     ++|
T Consensus        71 ~~~~Isl~ea~~~d~~~~vGd~ie~~I~~~dfg-R~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~  149 (344)
T 1hh2_P           71 PATQISLEEAKKIDPLAEVGSIVKKELNVKNFG-RIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEW  149 (344)
T ss_dssp             TTSCEEHHHHHHHCTTCCTTCEEEEECCCCCSS-SCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSE
T ss_pred             cccEEeHHHHhhhCccccCCCEEEEEEccccCc-cHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCc
Confidence            444566654    24456999999999777653 33444434321        222345555  89999999     889


Q ss_pred             EEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCC--eEEEEEee
Q 030172           69 AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ  129 (182)
Q Consensus        69 ~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~--ki~lS~k~  129 (182)
                      +||+++   +   .+|++|.+|++      |.+.|++||.|+|.|++++.+++  ++.||.+.
T Consensus       150 v~VDlG---k---~EgiLp~sE~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~  200 (344)
T 1hh2_P          150 ADIRIG---K---LETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRV  200 (344)
T ss_dssp             EEEEET---T---EEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESSS
T ss_pred             EEEEeC---C---eEEEEeHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEeec
Confidence            999995   4   99999999987      56789999999999999997655  56666653

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...

Probab=99.01  E-value=3e-10  Score=86.34  Aligned_cols=65  Identities=15%  Similarity=0.144  Sum_probs=53.1

Q ss_pred             hhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCc----------cccccCCCEEEEEEEE
Q 030172           51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----------RDILNEGDEVRVKVIK  115 (182)
Q Consensus        51 ~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~----------~~~~~~Gd~v~vkV~~  115 (182)
                      ....+..+|+++.|+     +||+||+++   .   .+||||+|++++.+.-++          ++.+++||.|+|+|++
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            345678899999999     999999995   2   899999999986543222          2679999999999999


Q ss_pred             EeCCCC
Q 030172          116 IDREKS  121 (182)
Q Consensus       116 id~~~~  121 (182)
                      +|.+++
T Consensus       150 vd~~~~  155 (171)
T 1y14_B          150 CISQVS  155 (171)
T ss_dssp             EEEETT
T ss_pred             EEcCCC
Confidence            998664

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

Probab=98.96  E-value=3.7e-10  Score=79.71  Aligned_cols=54  Identities=7%  Similarity=0.087  Sum_probs=40.6

Q ss_pred             EEEEeeccCCchhHHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          124 TLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       124 ~lS~k~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .-|+|++.++||+.+...+.+  |+++.|+|+++.+||+||++.+|++||||....
T Consensus        11 ~~~iKq~~~~p~~~~~~~~~~--G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel   64 (109)
T 2khj_A           11 SSGLVPRGSHMFNNWVALNKK--GAIVTGKVTAVDAKGATVELADGVEGYLRASEA   64 (109)
T ss_dssp             ----------CHHHHTTTCCS--SSEEEEEEEEECSSCEEEECSTTCBCCBCTTCC
T ss_pred             ccchhhcccCHHHHHhhcCCC--CCEEEEEEEEEECCeEEEEECCCCEEEEEHHHc
Confidence            458999999999998888877  999999999999999999999999999997643

>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=98.93  E-value=1.7e-10  Score=103.97  Aligned_cols=116  Identities=13%  Similarity=0.089  Sum_probs=80.0

Q ss_pred             CCCCCCCCCCccHHHhhhhcCCCeEEEEEEEEeCCCCE-EEEEec--hh---------HHhhhhcCCCCCC--EEEEE--
Q 030172            2 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKK-LVFSEK--DA---------VWNKYSSRVNVED--IFVGR--   65 (182)
Q Consensus         2 ~p~~~~p~~e~~~~~~~~~~vG~~v~~~v~~~d~~~~~-i~lS~k--~~---------~~~~~~~~~~~G~--iv~g~--   65 (182)
                      ||+|  +|+|+-.|+.++.++...-..   ...  ... -.+|.+  .+         .|...+.+-++|+  ++.|+  
T Consensus       497 SPIR--RY~DLivHR~l~a~l~~~~~~---~~~--~~~~~~~s~~er~a~~aer~~~~~~~~~~l~~~vGe~~~f~g~V~  569 (644)
T 2id0_A          497 SPIR--KYGDMINHRLLKAVIKGETAT---RPQ--DEITVQMAERRRLNRMAERDVGDWLYARFLKDKAGTDTRFAAEIV  569 (644)
T ss_dssp             CTTT--BHHHHHHHHHHHHHTTC-------CCC--TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSCCCEEEEEE
T ss_pred             Chhh--cchHHHHHHHHHHHHcCCCCC---ccH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCceEEEEEE
Confidence            8999  999999999888876443111   000  010 011111  11         2223344567888  88887  


Q ss_pred             ---eEeEEEEEecCCCceeEEEEEEccCcCC--ccc----------cCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           66 ---DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI----------QDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        66 ---~~G~fV~l~~~~g~~~~~glv~~sels~--~~~----------~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                         ++|+||+|.. .|   ++||||++++++  .+.          .+..+.|++||.|+|+|.++|.++++|.+++.
T Consensus       570 ~V~~~G~fV~L~~-~g---ieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~vd~~~~~I~~~l~  643 (644)
T 2id0_A          570 DISRGGMRVRLVD-NG---AIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARPV  643 (644)
T ss_dssp             EEETTEEEEEETT-TC---CEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTTEEEEEEC
T ss_pred             EEeCCceEEEEcC-Cc---EEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEEEeCCCCEEEEEEc
Confidence               9999999952 35   999999999973  221          14456799999999999999999999999874

>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=98.93  E-value=1.3e-09  Score=85.77  Aligned_cols=78  Identities=19%  Similarity=0.184  Sum_probs=61.9

Q ss_pred             hhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCcc----------ccccCCCEEEEEEEE
Q 030172           51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR----------DILNEGDEVRVKVIK  115 (182)
Q Consensus        51 ~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~----------~~~~~Gd~v~vkV~~  115 (182)
                      ......++|+++.|+     +||+||+|+ +     .+||||+++|++.+..++.          +.+++||.|+|+|++
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            345678999999999     999999995 1     8999999999865443332          679999999999999


Q ss_pred             EeCCCC---eEEEEEeeccCCch
Q 030172          116 IDREKS---RITLSIKQLEEDPL  135 (182)
Q Consensus       116 id~~~~---ki~lS~k~~~~~p~  135 (182)
                      +|.+++   ++. |+|+....||
T Consensus       150 vd~~~~~i~~Ig-Smk~~~LG~~  171 (215)
T 2b8k_G          150 CISQVSSIHAIG-SIKEDYLGAI  171 (215)
T ss_dssp             EEEETTEEEEEE-ECCSTTCEEC
T ss_pred             EEcCCCccEEEE-EcCCCCCCCc
Confidence            998764   666 8887655444

>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=98.92  E-value=1.9e-09  Score=81.89  Aligned_cols=71  Identities=15%  Similarity=0.260  Sum_probs=56.1

Q ss_pred             hhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCc------------cccccCCCEEEEEEE
Q 030172           52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI------------RDILNEGDEVRVKVI  114 (182)
Q Consensus        52 ~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~------------~~~~~~Gd~v~vkV~  114 (182)
                      ...+..+|+++.|+     +||+||+++   .   .+||||+++|++.+.-++            .+.|++||.|+|||+
T Consensus        75 ~~~~~~~Gev~~G~V~~v~~fG~fV~l~---~---~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~  148 (172)
T 2c35_B           75 IVFRPFKGEVVDAVVTQVNKVGLFTEIG---P---MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIV  148 (172)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEEET---T---EEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEE
T ss_pred             EEeeCCCCCEEEEEEEEEeCCEEEEEEC---C---EEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEE
Confidence            34578899999999     999999995   2   789999999986533222            557999999999999


Q ss_pred             EEeCCCC---eEEEEEee
Q 030172          115 KIDREKS---RITLSIKQ  129 (182)
Q Consensus       115 ~id~~~~---ki~lS~k~  129 (182)
                      ++|.+++   ++. |+|+
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            9998655   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=98.88  E-value=1.6e-09  Score=87.12  Aligned_cols=70  Identities=26%  Similarity=0.381  Sum_probs=62.6

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc---cCccccccCCCEEEEEEEEEeCCCCeEEE
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI---QDIRDILNEGDEVRVKVIKIDREKSRITL  125 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~---~~~~~~~~~Gd~v~vkV~~id~~~~ki~l  125 (182)
                      ..+++|++|.|+     ++|+||+|+  .+   .+|+||++++++.+.   .++++.|++||.|.|+|++++. .+++.|
T Consensus        70 y~p~~GDiV~G~V~~v~~~ga~VdI~--~~---~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~-~~~i~L  143 (251)
T 2je6_I           70 YYPKINDIVIGLVEDVEIYGWVVDIK--AP---YKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVL  143 (251)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECS--SS---SCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEE
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEcC--CC---eEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECC-CCcEEE
Confidence            367999999999     899999997  23   899999999998877   8889999999999999999996 579999


Q ss_pred             EEee
Q 030172          126 SIKQ  129 (182)
Q Consensus       126 S~k~  129 (182)
                      |+|+
T Consensus       144 S~r~  147 (251)
T 2je6_I          144 SVKG  147 (251)
T ss_dssp             ECCS
T ss_pred             EEcc
Confidence            9875

>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=98.83  E-value=6.9e-09  Score=82.35  Aligned_cols=70  Identities=26%  Similarity=0.351  Sum_probs=62.1

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCc-cccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~-~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      ..+++||+|.|+     ++|+||+|+.  .   .+|++|+++++.. +..++++.|++||.|.|+|++++. .+++.||+
T Consensus        53 y~p~~GDiV~G~V~~v~~~~a~V~I~~--~---~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~-~~~i~LS~  126 (229)
T 2ba0_A           53 YTPSVGDVVIGIIREVAANGWAVDIYS--P---YQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTM  126 (229)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSS--S---SCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEEC
T ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCC--C---eEEEEEHHHccccccccchhcccCCCCEEEEEEEEECC-CCcEEEEE
Confidence            357999999999     8999999962  3   8999999999974 678899999999999999999996 68999998


Q ss_pred             ee
Q 030172          128 KQ  129 (182)
Q Consensus       128 k~  129 (182)
                      |+
T Consensus       127 r~  128 (229)
T 2ba0_A          127 KD  128 (229)
T ss_dssp             CS
T ss_pred             cc
Confidence            75

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

Probab=98.80  E-value=1.3e-09  Score=77.69  Aligned_cols=53  Identities=8%  Similarity=-0.019  Sum_probs=38.0

Q ss_pred             EEEEeeccCCchhHHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          124 TLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       124 ~lS~k~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      .-|+|++..+||+.....+..  |+++.|+|+++.+||+||++.+|++||||...
T Consensus        10 ~~~~k~~~~~p~~~~~~~~~~--G~~~~G~V~~v~~~G~FV~l~~~~~Glvhise   62 (115)
T 2khi_A           10 HSSGLVPRGSHWVAIAKRYPE--GTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSE   62 (115)
T ss_dssp             -----------CCCSSCSSCS--SCEEEEEEEEEETTEEEEECSTTCEEEEETTS
T ss_pred             ccchhhcccCCHHHHhhcCCC--CCEEEEEEEEEECCEEEEEECCCCEEEEEHHH
Confidence            348899999999987767776  99999999999999999999999999999654

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=98.79  E-value=1.4e-09  Score=82.81  Aligned_cols=73  Identities=19%  Similarity=0.287  Sum_probs=58.3

Q ss_pred             HhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccC----------ccccccCCCEEEEEE
Q 030172           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD----------IRDILNEGDEVRVKV  113 (182)
Q Consensus        49 ~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~----------~~~~~~~Gd~v~vkV  113 (182)
                      ......+...|+++.|+     ++|+||+++   .   .+||||+++|++.+.-+          ..+.+++||.|+|||
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---P---LNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKI  148 (172)
T ss_dssp             EEEEEECCCTTCEEECCCCEEETTEEECCBT---T---BCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEE
T ss_pred             EEEeeeccCCCCEEEEEEEEEEcceEEEEeC---C---eEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEE
Confidence            44456789999999999     999999995   2   78999999997654433          356899999999999


Q ss_pred             EEEeCCCC---eEEEEEe
Q 030172          114 IKIDREKS---RITLSIK  128 (182)
Q Consensus       114 ~~id~~~~---ki~lS~k  128 (182)
                      +++|.+.+   +|. |+|
T Consensus       149 ~~vd~~~~~~~~Ig-tm~  165 (172)
T 3h0g_G          149 VGTRTDATEIFAIA-TMK  165 (172)
T ss_dssp             EEEEESSSCEEEEE-ECC
T ss_pred             EEEECCCCCceEEE-EcC
Confidence            99998764   444 555

>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1

Probab=98.77  E-value=5.2e-09  Score=83.39  Aligned_cols=70  Identities=17%  Similarity=0.352  Sum_probs=60.9

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCc----cccCccccccCCCEEEEEEEEEeCCCCeEE
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQDIRDILNEGDEVRVKVIKIDREKSRIT  124 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~----~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~  124 (182)
                      ..+++|++|.|+     ++|+||+|+  .+   .+|++|+++++..    +..++++.|++||.|.|+|++++. .+++.
T Consensus        62 y~p~~GDiV~G~V~~v~~~~~~V~I~--~~---~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~-~~~i~  135 (235)
T 2z0s_A           62 YVPQAGDVVIGLIQSVGIMNWFVDIN--SP---YVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPL  135 (235)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECS--SS---SCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEE
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeC--CC---eEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECC-CCcEE
Confidence            467999999999     899999997  23   8999999999863    457888999999999999999996 56899


Q ss_pred             EEEee
Q 030172          125 LSIKQ  129 (182)
Q Consensus       125 lS~k~  129 (182)
                      ||+|+
T Consensus       136 LS~k~  140 (235)
T 2z0s_A          136 LTVQG  140 (235)
T ss_dssp             EECCS
T ss_pred             EEEec
Confidence            99874

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

Probab=98.63  E-value=3.7e-08  Score=68.52  Aligned_cols=75  Identities=15%  Similarity=0.034  Sum_probs=54.5

Q ss_pred             CCCCCEEEEE--------eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           56 VNVEDIFVGR--------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        56 ~~~G~iv~g~--------~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      ...++.++|+        .|| |+.-.. +|   .++|+|++++.+...                               
T Consensus        11 ~~~~~~~~G~Vk~fn~~kGfG-FI~~~~-gg---~dvfvH~s~l~~~~~-------------------------------   54 (101)
T 2bh8_A           11 RLQSGKMTGIVKWFNADKGFG-FITPDD-GS---KDVFVHFSAGSSGAA-------------------------------   54 (101)
T ss_dssp             -----CEEEEEEEEEGGGTEE-EEEESS-SS---CEEEEECCCSCSSSC-------------------------------
T ss_pred             ccccccceeEEEEEECCCCCE-EEEeCC-CC---cEEEEEEEEEecCCc-------------------------------
Confidence            3455667777        578 887641 24   899999999987632                               


Q ss_pred             eeccCCchhHHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          128 KQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       128 k~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                                .......  |+.+++.|+++.+||+||+|.++++||||-..
T Consensus        55 ----------~~~~l~~--Ge~V~g~V~~i~~fG~fv~l~~~~eGlvhis~   93 (101)
T 2bh8_A           55 ----------VRGNPQQ--GDRVEGKIKSITDFGIFIGLDGGIDGLVHLSD   93 (101)
T ss_dssp             ----------CCCCCCT--TCEEEEEEEECCSEEEEECTTSCEEEEEEEEE
T ss_pred             ----------cccCCCC--CCEEEEEEEEeCCcEEEEEcCCCceEEEEHHH
Confidence                      0122334  99999999999999999999999999998653

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=98.54  E-value=1.2e-09  Score=100.13  Aligned_cols=116  Identities=19%  Similarity=0.177  Sum_probs=69.3

Q ss_pred             CCCCCCCCCCccHHHhhhhcCCCeEE-EEEEEEeCCCCEE-----EEEec--hh---------HHhhhhcCCCCCCEEEE
Q 030172            2 SPSHSCKEPQKSIHEIAKGLTGSIIS-VKVIQANEEMKKL-----VFSEK--DA---------VWNKYSSRVNVEDIFVG   64 (182)
Q Consensus         2 ~p~~~~p~~e~~~~~~~~~~vG~~v~-~~v~~~d~~~~~i-----~lS~k--~~---------~~~~~~~~~~~G~iv~g   64 (182)
                      ||+|  +|+|+-.|+.++.+++..-. -..    .....+     .+|.+  .+         .|...+.+-+. +++.|
T Consensus       603 SPIR--RY~DLivHR~L~~~l~~~~~~~~~----~~~~~l~~~~~~~s~~er~A~~aer~~~~~~~~~~l~~~~-~~~~g  675 (760)
T 2vnu_D          603 SPIR--RYCDVVAHRQLAGAIGYEPLSLTH----RDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVMRNNE-STETG  675 (760)
T ss_dssp             CTTT--BHHHHHHHHHHHHHTTSSCCCGGG----GCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCC-SEEEE
T ss_pred             chHh--hhHHHHHHHHHHHHHccCCCcccc----cCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHhhcCc-eEEEE
Confidence            8999  99999999988887754310 000    000000     00101  01         12222223344 68888


Q ss_pred             E-----eEeEEEEEecCCCceeEEEEEEccCcC--Cccc-----------cC----ccccccCCCEEEEEEEEEeCC---
Q 030172           65 R-----DYGAFIHLRFPDGLYHLTGLVHVSEVS--WDLI-----------QD----IRDILNEGDEVRVKVIKIDRE---  119 (182)
Q Consensus        65 ~-----~~G~fV~l~~~~g~~~~~glv~~sels--~~~~-----------~~----~~~~~~~Gd~v~vkV~~id~~---  119 (182)
                      +     ++|+||.|.. .|   ++|+||+++++  ..+.           .+    ..+.|++||.|+|+|+.+|.+   
T Consensus       676 ~V~~V~~~G~fV~l~~-~g---iEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd~~~~~  751 (760)
T 2vnu_D          676 YVIKVFNNGIVVLVPK-FG---VEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITS  751 (760)
T ss_dssp             EEEEEETTEEEEEETT-TT---EEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC--------
T ss_pred             EEEEEECCeEEEEEeC-CC---cEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCCEEEEEEEEEECcccc
Confidence            7     9999999962 26   99999999996  3331           22    257899999999999999987   


Q ss_pred             CCeEEEEEe
Q 030172          120 KSRITLSIK  128 (182)
Q Consensus       120 ~~ki~lS~k  128 (182)
                      ++||.||+|
T Consensus       752 ~~kI~lslk  760 (760)
T 2vnu_D          752 KRKAELLLK  760 (760)
T ss_dssp             CCEEEC---
T ss_pred             CCcEEEEeC
Confidence            699999986

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=98.49  E-value=1.7e-09  Score=101.15  Aligned_cols=117  Identities=20%  Similarity=0.183  Sum_probs=76.6

Q ss_pred             CCCCCCCCCCccHHHhhhhcCCCeEEEEEEEEeCCCCEE-----EEEech--h---------HHhhhhcCCCCCCEEEEE
Q 030172            2 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKL-----VFSEKD--A---------VWNKYSSRVNVEDIFVGR   65 (182)
Q Consensus         2 ~p~~~~p~~e~~~~~~~~~~vG~~v~~~v~~~d~~~~~i-----~lS~k~--~---------~~~~~~~~~~~G~iv~g~   65 (182)
                      ||+|  +|+|+-.|+.++.+++..-.-.   .......+     .+|.++  +         .|...+.+-+ |+++.|+
T Consensus       820 SPIR--RY~DLivHR~L~a~L~~~~~~~---~~~~~~~l~~i~~~~s~~er~A~~aeR~~~~~~~~~~l~~~-ge~~~g~  893 (977)
T 2wp8_J          820 SPIR--RYCDVVAHRQLAGAIGYEPLSL---THRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVMRNN-ESTETGY  893 (977)
T ss_dssp             CTTT--BHHHHHHHHHHHHHTTSSCCCG---GGGCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCEEEEE
T ss_pred             chHh--hHHHHHHHHHHHHHhcCCCCcc---cccCHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhhccc-ceEEEEE
Confidence            8999  9999999998888775431000   00000000     001110  1         1222222334 8898888


Q ss_pred             -----eEeEEEEEecCCCceeEEEEEEccCcC--Cccc-----------cC----ccccccCCCEEEEEEEEEeCC---C
Q 030172           66 -----DYGAFIHLRFPDGLYHLTGLVHVSEVS--WDLI-----------QD----IRDILNEGDEVRVKVIKIDRE---K  120 (182)
Q Consensus        66 -----~~G~fV~l~~~~g~~~~~glv~~sels--~~~~-----------~~----~~~~~~~Gd~v~vkV~~id~~---~  120 (182)
                           ++|+||.|.. .|   ++|+||+++++  ..+.           .+    ..+.|++||.|+|+|..+|.+   +
T Consensus       894 V~~V~~~G~fV~L~~-~g---iEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~vd~~~~~~  969 (977)
T 2wp8_J          894 VIKVFNNGIVVLVPK-FG---VEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSK  969 (977)
T ss_dssp             EEEECSSEEEEECTT-TC---CEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCCCCSSSCC
T ss_pred             EEEEcCCeEEEEEcC-CC---eEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEEcCcccCC
Confidence                 9999999962 26   99999999997  4331           12    357899999999999999863   3


Q ss_pred             CeEEEEEe
Q 030172          121 SRITLSIK  128 (182)
Q Consensus       121 ~ki~lS~k  128 (182)
                      +||.||+|
T Consensus       970 ~kI~Lslk  977 (977)
T 2wp8_J          970 RKAELLLK  977 (977)
T ss_dssp             CCCCEEEC
T ss_pred             CceEEEeC
Confidence            89999987

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=98.39  E-value=3.1e-07  Score=71.52  Aligned_cols=63  Identities=11%  Similarity=0.178  Sum_probs=52.6

Q ss_pred             hhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc-------------------cCccccccCCC
Q 030172           52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGD  107 (182)
Q Consensus        52 ~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~-------------------~~~~~~~~~Gd  107 (182)
                      ...+..+|+++.|+     ++|+||+++   .   ++|++|.+++.+.+.                   .+....|++||
T Consensus        75 ~~f~p~~GEv~~G~Vs~vt~~GifV~lg---~---~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd  148 (203)
T 3ayh_B           75 IIFRPFRGEVMLGKIKSCSEEGIRVTIS---F---FDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDE  148 (203)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEECS---S---CCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTC
T ss_pred             EEEccCCCCEEEEEEEEEeccEEEEEEe---C---ceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCC
Confidence            35678999999999     999999995   2   899999999977653                   44566799999


Q ss_pred             EEEEEEEEEeCCC
Q 030172          108 EVRVKVIKIDREK  120 (182)
Q Consensus       108 ~v~vkV~~id~~~  120 (182)
                      .|++||++++...
T Consensus       149 ~VrvrV~~v~~~~  161 (203)
T 3ayh_B          149 EIRFQIESEDFVD  161 (203)
T ss_dssp             EEEEEEEEEEECC
T ss_pred             EEEEEEEEEEccc
Confidence            9999999998643

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=98.31  E-value=3.8e-07  Score=71.77  Aligned_cols=66  Identities=8%  Similarity=0.095  Sum_probs=52.7

Q ss_pred             hhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc--------------cCccccccCCCEEEE
Q 030172           51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI--------------QDIRDILNEGDEVRV  111 (182)
Q Consensus        51 ~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~--------------~~~~~~~~~Gd~v~v  111 (182)
                      ....+..+|+++.|+     ++|+||+|.  +-   ++|++|++++...+.              .+....|++||.|++
T Consensus        74 ~~~f~p~vGEv~~G~Is~Vt~fGifVeL~--g~---~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~Vrv  148 (218)
T 2ckz_B           74 AVVFKPFLGEIVTGWISKCTAEGIKVSLL--GI---FDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRF  148 (218)
T ss_dssp             EEEECCCTTCEEEEEEEEEETTEEEEECT--TS---CCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEE
T ss_pred             EEEecCCCCCEEEEEEEEEccCcEEEEcc--Cc---cceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEE
Confidence            345688999999999     999999994  22   899999999966543              334567999999999


Q ss_pred             EEEEEeCCCC
Q 030172          112 KVIKIDREKS  121 (182)
Q Consensus       112 kV~~id~~~~  121 (182)
                      ||.++|..++
T Consensus       149 rV~~v~~~~~  158 (218)
T 2ckz_B          149 RIEREVFVDV  158 (218)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEcccC
Confidence            9999997554

>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=98.18  E-value=9e-07  Score=72.97  Aligned_cols=70  Identities=21%  Similarity=0.258  Sum_probs=56.1

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCc----cc------cCccccccCCCEEEEEEEEEeC
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LI------QDIRDILNEGDEVRVKVIKIDR  118 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~----~~------~~~~~~~~~Gd~v~vkV~~id~  118 (182)
                      ..+++|++|.|+     ++++||+|+.+     ..+++|++++++.    +.      .++++.|++||.|.|+|++++.
T Consensus        91 Y~P~vGDvViG~Vt~V~~~~a~VdI~s~-----~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~  165 (308)
T 2nn6_H           91 YIGEVGDIVVGRITEVQQKRWKVETNSR-----LDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS  165 (308)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSS-----SCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEECCC-----cCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCC
Confidence            368899999999     89999999733     6789999998753    12      2455789999999999999995


Q ss_pred             CCCeEEEEEee
Q 030172          119 EKSRITLSIKQ  129 (182)
Q Consensus       119 ~~~ki~lS~k~  129 (182)
                       .+++.||+|+
T Consensus       166 -~~~i~LStr~  175 (308)
T 2nn6_H          166 -DGAVSLHTRS  175 (308)
T ss_dssp             -TTEEEEECCS
T ss_pred             -CCCEEEEecC
Confidence             7899999885

>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=98.17  E-value=2.7e-06  Score=74.56  Aligned_cols=70  Identities=24%  Similarity=0.444  Sum_probs=57.1

Q ss_pred             cCCCCCCEEEEE-----eE--eEEEEEecCCCceeEEEEEEccCcCCccc---------cCccccccCCCEEEEEEEEEe
Q 030172           54 SRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWDLI---------QDIRDILNEGDEVRVKVIKID  117 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~--G~fV~l~~~~g~~~~~glv~~sels~~~~---------~~~~~~~~~Gd~v~vkV~~id  117 (182)
                      ....+|.+|.|+     ++  ||||+++  .|   ..||+|++++++.++         .++.+.+++||.|.|+|++..
T Consensus        41 ~~~~vGnIY~GkV~rv~p~~~aAFVdiG--~g---k~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~  115 (517)
T 2bx2_L           41 HEQKKANIYKGKITRIEPSLEAAFVDYG--AE---RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE  115 (517)
T ss_dssp             SCCCTTCEEEEEEEEEETTTTEEEEESS--SS---SCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECC
T ss_pred             CcCCCCCEEEEEEEEeccCCceEEEEeC--CC---cEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeec
Confidence            456799999999     66  9999997  45   899999999988763         345678999999999999988


Q ss_pred             CCCCeEEEEEe
Q 030172          118 REKSRITLSIK  128 (182)
Q Consensus       118 ~~~~ki~lS~k  128 (182)
                      ..++...||..
T Consensus       116 ~g~KGa~lTt~  126 (517)
T 2bx2_L          116 RGNKGAALTTF  126 (517)
T ss_dssp             CTTCCCEEESS
T ss_pred             cccCCceEEee
Confidence            76666666554

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

Probab=98.17  E-value=2.8e-06  Score=71.33  Aligned_cols=79  Identities=10%  Similarity=0.192  Sum_probs=56.7

Q ss_pred             hcCCC--CCCEEEEE-e--------EeEEEEEecC-CCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC
Q 030172           53 SSRVN--VEDIFVGR-D--------YGAFIHLRFP-DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK  120 (182)
Q Consensus        53 ~~~~~--~G~iv~g~-~--------~G~fV~l~~~-~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~  120 (182)
                      +..++  .|+++.|+ .        .++||+|+.. .+   .+|++|.+|+.      |.+.|++||.|+|.|++++.+.
T Consensus       123 ~~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k---~EgiLP~~Eqi------P~E~~~~GDrVkvyV~~V~~~~  193 (366)
T 1k0r_A          123 YGEFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKA---SEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGA  193 (366)
T ss_dssp             ----CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSC---EEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCS
T ss_pred             HHHHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccc---eEEEEcHHHcC------CCccCCCCCEEEEEEEEEecCC
Confidence            44555  99999999 2        5899999720 13   89999999987      4688999999999999999876


Q ss_pred             CeEEEEEeeccCCchhHHHh
Q 030172          121 SRITLSIKQLEEDPLLETLE  140 (182)
Q Consensus       121 ~ki~lS~k~~~~~p~~~~~~  140 (182)
                      +...+.+..+.++.....++
T Consensus       194 kgpqI~LSRT~p~lv~~Lfe  213 (366)
T 1k0r_A          194 REPLITLSRTHPNLVRKLFS  213 (366)
T ss_dssp             SSCEEEEESSCHHHHHHHHH
T ss_pred             CccEEEEEeCChHHHHHHHH
Confidence            55555555554555444443

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

Probab=98.13  E-value=9.5e-07  Score=63.10  Aligned_cols=48  Identities=4%  Similarity=-0.087  Sum_probs=38.7

Q ss_pred             ccCCchhHHHhhhcCCCCceeEeeEeeecCCeeEEecCC-Chhhhchhhhh
Q 030172          130 LEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLP-GLGAIFEELLQ  179 (182)
Q Consensus       130 ~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~-gv~gl~~~~~~  179 (182)
                      +.+++|......+..  |+++.|+|+++.+||+||+|.+ +++||||-...
T Consensus         8 ~~~~~~~~~~~~~~v--G~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel   56 (119)
T 2cqo_A            8 MNSGRPETMENLPAL--YTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHM   56 (119)
T ss_dssp             SCCCCCCCSCCSCCT--TCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHH
T ss_pred             ccccchhhhhcccCC--CCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHC
Confidence            356778776655555  9999999999999999999954 46999997653

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

Probab=98.04  E-value=2.8e-06  Score=56.24  Aligned_cols=34  Identities=6%  Similarity=-0.043  Sum_probs=31.3

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .|+++.|+|+++.+||+||++.+|++||||....
T Consensus         5 ~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel   38 (80)
T 2k52_A            5 PGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDM   38 (80)
T ss_dssp             TTCEEEEEEEEEETTEEEEEEETTEEEEECGGGC
T ss_pred             CCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHC
Confidence            3999999999999999999999999999997654

>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=98.00  E-value=1.1e-05  Score=61.27  Aligned_cols=67  Identities=15%  Similarity=0.142  Sum_probs=56.3

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEec-CCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRF-PDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~-~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      .+++||+|.|+     ..+++|+|+. +     ..|++|++++. ....+.+..|++||.|.|+|.+++. .+.+.||..
T Consensus         4 ~P~~gDvViG~V~~v~~~~~~VdI~~~~-----~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV~~~~~-~~~~~Ltc~   76 (175)
T 2ja9_A            4 IPSVNDFVIGVIIGTFSDSYKVSLQNFS-----SSVSLSYMAFP-NASKKNRPTLQVGDLVYARVCTAEK-ELEAEIECF   76 (175)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESSTTS-----CCEEEETTSST-TCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEESS
T ss_pred             cCCCcCEEEEEEEEEECcEEEEEECCCC-----ccEEEEHHHCC-chhhhhhccCCCCCEEEEEEEEecC-CCceEEEec
Confidence            57899999999     7889999973 2     78999999886 3356788889999999999999986 567888843

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

Probab=97.97  E-value=8.5e-06  Score=56.44  Aligned_cols=71  Identities=28%  Similarity=0.399  Sum_probs=48.7

Q ss_pred             cCCCeEEEEEEEEeCCCCEEEEEech----------hHHhhhh--cCCCCCCEEEEE-----eEeEEEEEecCCCceeEE
Q 030172           21 LTGSIISVKVIQANEEMKKLVFSEKD----------AVWNKYS--SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLT   83 (182)
Q Consensus        21 ~vG~~v~~~v~~~d~~~~~i~lS~k~----------~~~~~~~--~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~   83 (182)
                      ..++..+-+|..+|..++.=.++...          +....-.  ..+++|++|.+.     +||+||+|.  ++   ++
T Consensus        12 ~~~~~~~G~Vk~fn~~kGfGFI~~~~gg~dvfvH~s~l~~~~~~~~~l~~Ge~V~g~V~~i~~fG~fv~l~--~~---~e   86 (101)
T 2bh8_A           12 LQSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFGIFIGLD--GG---ID   86 (101)
T ss_dssp             ----CEEEEEEEEEGGGTEEEEEESSSSCEEEEECCCSCSSSCCCCCCCTTCEEEEEEEECCSEEEEECTT--SC---EE
T ss_pred             cccccceeEEEEEECCCCCEEEEeCCCCcEEEEEEEEEecCCccccCCCCCCEEEEEEEEeCCcEEEEEcC--CC---ce
Confidence            35677888999888766543333221          1111112  579999999999     899999995  45   99


Q ss_pred             EEEEccCcCCccc
Q 030172           84 GLVHVSEVSWDLI   96 (182)
Q Consensus        84 glv~~sels~~~~   96 (182)
                      ||||+|+++|.++
T Consensus        87 Glvhis~i~~~~~   99 (101)
T 2bh8_A           87 GLVHLSDISWAQA   99 (101)
T ss_dssp             EEEEEEEEEECCC
T ss_pred             EEEEHHHCccCcC
Confidence            9999999998764

>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=97.94  E-value=7.7e-09  Score=79.35  Aligned_cols=87  Identities=13%  Similarity=0.069  Sum_probs=65.4

Q ss_pred             CCCCCCCccHHH--hhhh-c-CCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----e-EeEEE
Q 030172            5 HSCKEPQKSIHE--IAKG-L-TGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----D-YGAFI   71 (182)
Q Consensus         5 ~~~p~~e~~~~~--~~~~-~-vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~-~G~fV   71 (182)
                      .|++.+++++..  .... + +|++|.++|+.+|++++++.+|.++   .+|.....+++.|+.+.|.     + +|  +
T Consensus        43 GLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~~~~p~~~~~~~~~~g~~v~g~v~~i~~~~g--v  120 (182)
T 1kl9_A           43 GMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLE--Y  120 (182)
T ss_dssp             EEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--C
T ss_pred             EEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeecCcChHHHHHHhccCCCEEEEEEEEchhhcC--C
Confidence            357778887653  2222 2 8999999999999999999999986   5788888889999998888     5 99  7


Q ss_pred             EEecCCCceeEEEEEEccCcCCcc-ccC
Q 030172           72 HLRFPDGLYHLTGLVHVSEVSWDL-IQD   98 (182)
Q Consensus        72 ~l~~~~g~~~~~glv~~sels~~~-~~~   98 (182)
                      +|.  +|   ++||+|+++++|.+ +.+
T Consensus       121 ~l~--~g---iegl~h~s~~~~~~~~~~  143 (182)
T 1kl9_A          121 TKD--EQ---LESLFQRTAWVFDDKYKR  143 (182)
T ss_dssp             CSH--HH---HHHHHHHTHHHHHHHHTC
T ss_pred             ccc--CC---hhheEEeeecchhhhcCC
Confidence            775  45   99999999887753 444

>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=97.93  E-value=4.9e-07  Score=82.56  Aligned_cols=75  Identities=17%  Similarity=0.212  Sum_probs=34.0

Q ss_pred             eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCC
Q 030172           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ  145 (182)
Q Consensus        66 ~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~  145 (182)
                      ++|+||+|+       -+|.+|++..++.......+.+                        +.. .+|     ..+.+ 
T Consensus       626 ~~G~~IdI~-------~dG~v~Is~~~~~~~~~a~~~i------------------------~~i-~~p-----~~~~v-  667 (757)
T 1e3p_A          626 DTGAEITIE-------DDGTIYIGAADGPAAEAARATI------------------------NGI-ANP-----TSPEV-  667 (757)
T ss_dssp             CCCSCC---------------CCCBSSHHHHCC-----------------------------------------------
T ss_pred             hhCCEEEec-------CCceEEEecCCHHHHHHHHHHH------------------------HHh-cch-----hhccc-
Confidence            899999996       4789999998876543321111                        000 123     23444 


Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                       |+++.|+|+++.+||+||+|.+|++||||-...
T Consensus       668 -G~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel  700 (757)
T 1e3p_A          668 -GERILGSVVKTTTFGAFVSLLPGKDGLLHISQI  700 (757)
T ss_dssp             ------CBEEECC-CSCEECCC---CCCCC----
T ss_pred             -ccEEEEEEEEccccEEEEEEcCCcEEEEEhHHh
Confidence             999999999999999999999999999997653

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

Probab=97.87  E-value=7.9e-06  Score=55.18  Aligned_cols=32  Identities=25%  Similarity=0.271  Sum_probs=29.1

Q ss_pred             CCCceeEeeEeeecCCeeEEecC--CChhhhchhh
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPL--PGLGAIFEEL  177 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~--~gv~gl~~~~  177 (182)
                      ..|+++.|+|+ +++||+||+|.  +|++||+|-.
T Consensus        10 ~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis   43 (88)
T 1luz_A           10 NAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAES   43 (88)
T ss_dssp             CTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGG
T ss_pred             CCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEee
Confidence            45999999999 99999999997  4899999976

>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=97.85  E-value=8.2e-06  Score=56.63  Aligned_cols=34  Identities=3%  Similarity=-0.130  Sum_probs=31.2

Q ss_pred             CCceeEeeEeeecCCeeEEecCC---Chhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLP---GLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~---gv~gl~~~~~~  179 (182)
                      .|+++.|+|+++.+||+||++.+   +++||||-...
T Consensus        12 vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel   48 (103)
T 2eqs_A           12 IGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISEL   48 (103)
T ss_dssp             TTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGT
T ss_pred             CCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHC
Confidence            49999999999999999999986   99999997764

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

Probab=97.82  E-value=2.5e-06  Score=77.59  Aligned_cols=37  Identities=8%  Similarity=-0.037  Sum_probs=0.0

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .+.+  |+++.|+|+++.+||+||++.+|++||+|-...
T Consensus       624 ~~~v--G~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel  660 (723)
T 3cdi_A          624 EIEV--GRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQI  660 (723)
T ss_dssp             ---------------------------------------
T ss_pred             hhhc--CcEEEEEEEEEecceEEEEeCCCceEEEEHHHc
Confidence            4444  999999999999999999999999999996643

>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=97.66  E-value=0.00019  Score=57.22  Aligned_cols=67  Identities=18%  Similarity=0.242  Sum_probs=54.1

Q ss_pred             CCCCCCEEEEE-e--------EeEEEEEec-CCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC--Ce
Q 030172           55 RVNVEDIFVGR-D--------YGAFIHLRF-PDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SR  122 (182)
Q Consensus        55 ~~~~G~iv~g~-~--------~G~fV~l~~-~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~--~k  122 (182)
                      .-+.|+++.|+ .        ..+||+|+. .++   .+|++|.+|+.      |.+.|++||.|+|.|++++...  .+
T Consensus         4 ~~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k---~EgiLP~~Eqi------p~E~~~~GDrIkayV~~V~~~~~gpq   74 (251)
T 2asb_A            4 STREGEIVAGVIQRDSRANARGLVVVRIGTETKA---SEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPL   74 (251)
T ss_dssp             CCCTTCEEEEEEECCHHHHHTTCEEEEECSSSSC---EEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCE
T ss_pred             hhcCCCEEEEEEEEccccccCCeEEEEeCCCCcc---eEEEEcHHHcC------CCccCCCCCEEEEEEEEEEcCCCCCE
Confidence            45689999998 2        269999972 013   89999999976      5688999999999999998754  68


Q ss_pred             EEEEEeec
Q 030172          123 ITLSIKQL  130 (182)
Q Consensus       123 i~lS~k~~  130 (182)
                      |.||....
T Consensus        75 IiLSRt~p   82 (251)
T 2asb_A           75 ITLSRTHP   82 (251)
T ss_dssp             EEEESSCH
T ss_pred             EEEEeccH
Confidence            99998753

>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=97.65  E-value=1.5e-05  Score=56.61  Aligned_cols=50  Identities=16%  Similarity=0.187  Sum_probs=36.5

Q ss_pred             EEeeccCCchhHHHhhhcCCCCceeEeeEeeecCCeeEEecC-CChhhhchhhh
Q 030172          126 SIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL-PGLGAIFEELL  178 (182)
Q Consensus       126 S~k~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~-~gv~gl~~~~~  178 (182)
                      |++....+.+.. .+.+..  |+++.|+|+++++||+||+|. +++.||++.-+
T Consensus         4 sl~P~~vn~~~~-~~~l~~--G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~   54 (119)
T 1wi5_A            4 GSSGKNVNRVLS-AEALKP--GMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLK   54 (119)
T ss_dssp             CCCCSCSSCCCC-TTTCCT--TCEEEEEEEEECSSEEEEECCCSSCEEEEEHHH
T ss_pred             ccCHHHhhcccc-HhcCCC--CCEEEEEEEEEeCceEEEEECCCCeEEEEEEec
Confidence            344333444332 235555  999999999999999999998 68888887655

>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=97.56  E-value=7.7e-05  Score=64.81  Aligned_cols=108  Identities=11%  Similarity=0.183  Sum_probs=70.6

Q ss_pred             CCCCCCCCCCccHHHhhhhcCCCeEEEEEEEEeCCC-----CEEEEEechh---------HHhhhhcCCCCCCEEEEEeE
Q 030172            2 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM-----KKLVFSEKDA---------VWNKYSSRVNVEDIFVGRDY   67 (182)
Q Consensus         2 ~p~~~~p~~e~~~~~~~~~~vG~~v~~~v~~~d~~~-----~~i~lS~k~~---------~~~~~~~~~~~G~iv~g~~~   67 (182)
                      ||+|  +|+|+-.|+.++.++...-     .++.+.     ..+....+.+         .|...+-.-+.|+.+.    
T Consensus       340 SPIR--RY~DLivHr~L~a~l~~~~-----~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~~l~~~~g~~f~----  408 (469)
T 2r7d_A          340 SPMR--RYLDLVVHQQLRAFLAGRD-----PLSSKVMAAHIAESQMNADATRQAERLSRRHHTLRFIAAQPERVWD----  408 (469)
T ss_dssp             CTTT--BHHHHHHHHHHHHHHTTCC-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCEE----
T ss_pred             Cccc--ccHHHHHHHHHHHHHcCCC-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCEEE----
Confidence            8999  9999999998887764430     000000     0000000000         1222233446888887    


Q ss_pred             eEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           68 GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        68 G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      |+++++.   +   .+|+||++++...  ......|++||.|+|+|.++|..+++|.+...
T Consensus       409 g~vv~l~---~---~~glV~v~~l~~d--~~~~~~~~lGd~V~V~v~~vd~~~~~i~f~~~  461 (469)
T 2r7d_A          409 AVVVDRR---G---AQATLLIPDLAFD--VQVNTPAAPGTALQVQFADIDLPQMRVRARSV  461 (469)
T ss_dssp             EEEEEEE---T---TEEEEEEGGGTEE--EEEECCCCTTCEEEEEEEEEETTTTEEEEEEC
T ss_pred             EEEEEEe---C---cEEEEEECCCCeE--EecCCcCCCCCEEEEEEEEEccCCCEEEEEEE
Confidence            4678875   2   6899999999865  22335699999999999999999999987653

>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=97.45  E-value=8.2e-05  Score=56.06  Aligned_cols=33  Identities=15%  Similarity=0.251  Sum_probs=30.6

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .|+++.|+|+++++||+||++.+ .+||+|-...
T Consensus        83 ~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l  115 (171)
T 1y14_B           83 KGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLM  115 (171)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGS
T ss_pred             CCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHC
Confidence            49999999999999999999988 9999998754

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=97.37  E-value=8.3e-06  Score=68.08  Aligned_cols=76  Identities=14%  Similarity=0.031  Sum_probs=53.8

Q ss_pred             cccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhH-----HHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchh
Q 030172          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE-----TLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEE  176 (182)
Q Consensus       102 ~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~-----~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~  176 (182)
                      .+.+||.+.+.|...|. .+....+.|+.....+.+     ..+.|....|++++|+|.++.++|+||++. +++|++|.
T Consensus        86 ~~~vGd~ie~~I~~~df-gR~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlG-k~EgiLp~  163 (344)
T 1hh2_P           86 LAEVGSIVKKELNVKNF-GRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIG-KLETRLPK  163 (344)
T ss_dssp             TCCTTCEEEEECCCCCS-SSCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEET-TEEEEEEG
T ss_pred             cccCCCEEEEEEccccC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeC-CeEEEEeH
Confidence            37899999999987775 333333334432222222     234554345999999999999999999996 99999998


Q ss_pred             hhh
Q 030172          177 LLQ  179 (182)
Q Consensus       177 ~~~  179 (182)
                      ..+
T Consensus       164 sE~  166 (344)
T 1hh2_P          164 KEW  166 (344)
T ss_dssp             GGS
T ss_pred             HHc
Confidence            764

>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=97.30  E-value=0.00015  Score=56.76  Aligned_cols=34  Identities=15%  Similarity=0.219  Sum_probs=31.0

Q ss_pred             CCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      ..|+++.|+|+++++||+||++.+ ++||+|-...
T Consensus        82 ~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l  115 (215)
T 2b8k_G           82 FKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLM  115 (215)
T ss_dssp             CTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGS
T ss_pred             CCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHC
Confidence            359999999999999999999988 9999998754

>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=97.09  E-value=0.00031  Score=55.58  Aligned_cols=68  Identities=13%  Similarity=0.057  Sum_probs=34.6

Q ss_pred             cCCCEEEEEEEE-EeCCCCeEEEEEeeccCCchhHHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          104 NEGDEVRVKVIK-IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       104 ~~Gd~v~vkV~~-id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      ..++.+.+.+.+ ++..+.+..+|++...        .+|.+..|++|.|+|+++.++|+||++..+++|++|....
T Consensus        31 ~~~~~I~Asv~G~v~~~~~~~~vsV~p~~--------~~y~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei   99 (235)
T 2z0s_A           31 DYKGVKRATVVGLLREKGDGGGRAFVKLK--------EIYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDF   99 (235)
T ss_dssp             -------------------------------------CCCCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHH
T ss_pred             EECCEEEEEEeEEEEEeCCccEEEEEeCC--------CccCCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHh
Confidence            344556666655 2322232334444221        2355667999999999999999999999999999987654

>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=96.98  E-value=0.0004  Score=52.85  Aligned_cols=32  Identities=9%  Similarity=-0.002  Sum_probs=28.8

Q ss_pred             CCCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL  177 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~  177 (182)
                      ..|+++.|+|+++.+||+||++.+ ++||+|-.
T Consensus        80 ~~Gev~~G~V~~v~~~G~fV~l~~-~eglvhis  111 (187)
T 1go3_E           80 EMYELIEGEVVDVVEFGSFVRLGP-LDGLIHVS  111 (187)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSS-SEEEEEGG
T ss_pred             CCCCEEEEEEEEEeCcEEEEEEcC-ccEEEEhH
Confidence            359999999999999999999965 99999864

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1

Probab=96.97  E-value=0.00053  Score=51.53  Aligned_cols=33  Identities=9%  Similarity=0.006  Sum_probs=29.3

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .|+++.|+|+++++||+||++. .++||+|-...
T Consensus        81 ~Gev~~G~V~~v~~fG~fV~l~-~~~glvhis~l  113 (172)
T 2c35_B           81 KGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSI  113 (172)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGS
T ss_pred             CCCEEEEEEEEEeCCEEEEEEC-CEEEEEEHHHC
Confidence            4999999999999999999995 57799998754

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

Probab=96.94  E-value=0.00013  Score=66.40  Aligned_cols=33  Identities=3%  Similarity=-0.057  Sum_probs=0.0

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      .|+++.|+|+++.+||+||+|.+|++||||-..
T Consensus       637 vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSe  669 (726)
T 4aid_A          637 VGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQ  669 (726)
T ss_dssp             ---------------------------------
T ss_pred             CCcEEEEEEEEEeccEEEEEECCCcEEEEEHHH
Confidence            499999999999999999999999999999653

>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=96.89  E-value=0.00089  Score=54.57  Aligned_cols=69  Identities=7%  Similarity=-0.069  Sum_probs=55.7

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      ..+++||+|.|+     ...+.|+|..+     ..|++|.+++.. ...+.+..|++||.|.|+|++++. .+...||..
T Consensus       123 YiP~vGDiVIG~Vt~v~~~~~~VdI~s~-----~~a~L~~~~f~G-atk~~r~~f~~GDlV~ArV~s~~~-~~~~eLsc~  195 (289)
T 2nn6_G          123 YVPVKGDHVIGIVTAKSGDIFKVDVGGS-----EPASLSYLSFEG-ATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCI  195 (289)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSS-----SCCCEESCSSSC-CSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECS
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEECCC-----ceeEEehhhcCc-chhhhhhhcCCCCEEEEEEEEcCC-CCceEEEec
Confidence            357899999999     55689999732     789999998762 356788889999999999999985 567888874


Q ss_pred             e
Q 030172          129 Q  129 (182)
Q Consensus       129 ~  129 (182)
                      .
T Consensus       196 ~  196 (289)
T 2nn6_G          196 D  196 (289)
T ss_dssp             B
T ss_pred             c
Confidence            3

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

Probab=96.81  E-value=0.00057  Score=65.34  Aligned_cols=38  Identities=11%  Similarity=0.051  Sum_probs=33.2

Q ss_pred             hhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          140 EKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       140 ~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      +.+.+  |+++.|+|++|++||+||+|++|++||||-...
T Consensus       898 ~~l~~--G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSel  935 (1219)
T 3psi_A          898 KTFFK--GSIIPVRVERFWHNDIICTTNSEVECVVNAQRH  935 (1219)
T ss_dssp             TTSCT--TCEEEEEEEEECSSCEEEECTTSCEEEECTTSS
T ss_pred             hhCCC--CCEEEEEEEEEecceEEEEeCCCceEEEEHHHc
Confidence            34455  999999999999999999999999999996543

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=96.78  E-value=0.0005  Score=51.81  Aligned_cols=35  Identities=14%  Similarity=0.072  Sum_probs=30.2

Q ss_pred             CCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          144 PQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       144 ~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      +..|++++|+|+++++||+||++. .++||+|....
T Consensus        82 p~~Gev~~G~V~~v~~fG~FV~l~-~~~glVh~s~l  116 (172)
T 3h0g_G           82 PFRGEVVDAIVTTVNKMGFFANIG-PLNVFVSSHLV  116 (172)
T ss_dssp             CCTTCEEECCCCEEETTEEECCBT-TBCCEEEGGGS
T ss_pred             cCCCCEEEEEEEEEEcceEEEEeC-CeEEEEEHHHC
Confidence            335999999999999999999996 57899997654

>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=96.73  E-value=0.00086  Score=50.70  Aligned_cols=34  Identities=6%  Similarity=-0.034  Sum_probs=29.4

Q ss_pred             CCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          144 PQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       144 ~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      +..|+++.|+|+++++||+||++. .++||+|-..
T Consensus        79 p~~Gev~~G~V~~v~~~G~fv~l~-~~~glvh~s~  112 (180)
T 4ayb_E           79 PVVQEVVEGEVLQVDNYGVFVNLG-PMDGLVHISQ  112 (180)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGG
T ss_pred             ccCCCEEEEEEeeeccceEEEEEC-CccceEEeee
Confidence            345999999999999999999995 5999998654

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

Probab=96.71  E-value=0.00085  Score=50.91  Aligned_cols=38  Identities=16%  Similarity=-0.030  Sum_probs=33.8

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEecCC----------Chhhhchhhhh
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEPLP----------GLGAIFEELLQ  179 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~----------gv~gl~~~~~~  179 (182)
                      .|.+. |++|.|+|+++.++|+||++.+          +++||+|....
T Consensus        53 ~y~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei  100 (179)
T 3m7n_A           53 PEIVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNV  100 (179)
T ss_dssp             CCCCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGT
T ss_pred             cccCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHc
Confidence            46677 9999999999999999999987          99999997653

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

Probab=96.68  E-value=0.00022  Score=67.06  Aligned_cols=38  Identities=11%  Similarity=0.051  Sum_probs=0.0

Q ss_pred             hhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          140 EKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       140 ~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      +.+.+  |+++.|+|++|++||+||+|++|++||||-...
T Consensus       901 ~~l~~--G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSel  938 (1030)
T 3psf_A          901 KTFFK--GSIIPVRVERFWHNDIICTTNSEVECVVNAQRH  938 (1030)
T ss_dssp             ----------------------------------------
T ss_pred             HHhcC--CCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHc
Confidence            34455  999999999999999999999999999996543

>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=96.65  E-value=0.00062  Score=62.48  Aligned_cols=34  Identities=6%  Similarity=-0.048  Sum_probs=31.0

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .|+++.|+|++|++||+||++..+++||||-...
T Consensus       654 vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~L  687 (785)
T 3bzc_A          654 PGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISAL  687 (785)
T ss_dssp             TTCBCCCEEEEEETTEEEEECSSSSEEEEETTTS
T ss_pred             CCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHc
Confidence            4999999999999999999999999999986543

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A

Probab=96.50  E-value=0.00018  Score=54.53  Aligned_cols=61  Identities=11%  Similarity=0.036  Sum_probs=44.2

Q ss_pred             CCCCCCCccHHHh--hhh-c-CCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE
Q 030172            5 HSCKEPQKSIHEI--AKG-L-TGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR   65 (182)
Q Consensus         5 ~~~p~~e~~~~~~--~~~-~-vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~   65 (182)
                      .|+|.+++++...  ... + +|+++.++|+.+|++++++.+|++.   .+|.....+++.|+.+.|+
T Consensus        43 GLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~~~~~~~~~~~~~~g~~v~g~  110 (175)
T 2a19_A           43 GMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSI  110 (175)
T ss_dssp             EEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEecCcChHHHHHHhccCCCcceEE
Confidence            4678888887532  222 2 8999999999999999999999986   4788777788888877775

>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=96.37  E-value=4.6e-05  Score=62.78  Aligned_cols=68  Identities=13%  Similarity=0.028  Sum_probs=54.5

Q ss_pred             CCCCCCCccHHH--hhhh--cCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----e-EeEEE
Q 030172            5 HSCKEPQKSIHE--IAKG--LTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----D-YGAFI   71 (182)
Q Consensus         5 ~~~p~~e~~~~~--~~~~--~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~-~G~fV   71 (182)
                      .|++.+++++..  ....  -+|+.|.++|+.+|++++++.+|++.   .+|......++.|+++.|+     + ||+|+
T Consensus        41 GLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~~G~fi  120 (308)
T 1q8k_A           41 GMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTK  120 (308)
T ss_dssp             EEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCS
T ss_pred             EEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEecccChHHHHHHHccCCCeeEEEEEEcccccCCcc
Confidence            457777877642  1222  28999999999999999999999986   5888888889999998888     5 69987


Q ss_pred             E
Q 030172           72 H   72 (182)
Q Consensus        72 ~   72 (182)
                      +
T Consensus       121 ~  121 (308)
T 1q8k_A          121 D  121 (308)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=96.36  E-value=0.0024  Score=51.04  Aligned_cols=39  Identities=5%  Similarity=-0.102  Sum_probs=34.2

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .|.+..|++|.|+|+++.++|+||++..+.+|++|-...
T Consensus        69 ~y~p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei  107 (251)
T 2je6_I           69 FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNL  107 (251)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHH
T ss_pred             ccCCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHh
Confidence            355667999999999999999999999999999987654

>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=95.88  E-value=0.0051  Score=47.73  Aligned_cols=36  Identities=14%  Similarity=0.242  Sum_probs=30.1

Q ss_pred             hcCCCCceeEeeEeeecCCeeEEecC--------CChhhhchhh
Q 030172          142 VIPQDGSVISDSSSMSSSNSNTIEPL--------PGLGAIFEEL  177 (182)
Q Consensus       142 ~~~~~g~~v~G~V~~v~~~G~fV~l~--------~gv~gl~~~~  177 (182)
                      |.+..|++|.|+|+++.++|+||++.        .+++|++|..
T Consensus        77 y~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhis  120 (209)
T 2nn6_I           77 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKE  120 (209)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEE
T ss_pred             CCCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHH
Confidence            44556999999999999999999973        6889998743

>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=95.85  E-value=0.0062  Score=47.90  Aligned_cols=39  Identities=13%  Similarity=0.124  Sum_probs=34.2

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      +|.+..|++|.|+|+++.++|+||++....+|++|-+..
T Consensus        52 ~y~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev   90 (229)
T 2ba0_A           52 RYTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSEN   90 (229)
T ss_dssp             SCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGC
T ss_pred             cccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHc
Confidence            355667999999999999999999999889999987654

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=95.82  E-value=0.0058  Score=47.77  Aligned_cols=32  Identities=16%  Similarity=0.143  Sum_probs=27.5

Q ss_pred             CCCceeEeeEeeecCCeeEEecCCChhhhchh
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPLPGLGAIFEE  176 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~  176 (182)
                      ..|+++.|+|++++++|+||+|.+-++||++-
T Consensus        80 ~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~  111 (218)
T 2ckz_B           80 FLGEIVTGWISKCTAEGIKVSLLGIFDDIFIP  111 (218)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECTTSCCCEEEE
T ss_pred             CCCCEEEEEEEEEccCcEEEEccCccceEEEc
Confidence            35999999999999999999996667887653

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=95.56  E-value=0.0079  Score=46.39  Aligned_cols=30  Identities=17%  Similarity=0.151  Sum_probs=26.4

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEE  176 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~  176 (182)
                      .|+++.|+|++++++|+||+| +.++||++-
T Consensus        81 ~GEv~~G~Vs~vt~~GifV~l-g~~eglv~~  110 (203)
T 3ayh_B           81 RGEVMLGKIKSCSEEGIRVTI-SFFDDIFIP  110 (203)
T ss_dssp             TTCEEEEEEEEEETTEEEEEC-SSCCCEEEE
T ss_pred             CCCEEEEEEEEEeccEEEEEE-eCceEEEEc
Confidence            499999999999999999999 578887653

>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=94.85  E-value=0.015  Score=50.93  Aligned_cols=33  Identities=0%  Similarity=-0.094  Sum_probs=30.3

Q ss_pred             CCceeEeeEeeecCC--eeEEecCCChhhhchhhh
Q 030172          146 DGSVISDSSSMSSSN--SNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~--G~fV~l~~gv~gl~~~~~  178 (182)
                      +|.++.|+|+++.++  ||||++.+|-+||+|-..
T Consensus        45 vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhise   79 (517)
T 2bx2_L           45 KANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKE   79 (517)
T ss_dssp             TTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGG
T ss_pred             CCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHH
Confidence            499999999999998  999999999999998543

>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=94.33  E-value=0.028  Score=50.51  Aligned_cols=34  Identities=12%  Similarity=0.031  Sum_probs=30.0

Q ss_pred             CCCc--eeEeeEeeecCCeeEEec-CCChhhhchhhh
Q 030172          145 QDGS--VISDSSSMSSSNSNTIEP-LPGLGAIFEELL  178 (182)
Q Consensus       145 ~~g~--~v~G~V~~v~~~G~fV~l-~~gv~gl~~~~~  178 (182)
                      ..|+  +++|+|+++.+||+||+| +.|++||+|-..
T Consensus       557 ~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~  593 (644)
T 2id0_A          557 KAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPF  593 (644)
T ss_dssp             GTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGG
T ss_pred             ccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchh
Confidence            3588  999999999999999999 589999998744

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

Probab=94.16  E-value=0.0029  Score=51.16  Aligned_cols=61  Identities=8%  Similarity=-0.054  Sum_probs=44.7

Q ss_pred             CCCCCCCccHHH--hhh-h-cCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE
Q 030172            5 HSCKEPQKSIHE--IAK-G-LTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR   65 (182)
Q Consensus         5 ~~~p~~e~~~~~--~~~-~-~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~   65 (182)
                      .|+|.++++...  ... . -+|+.+.++|+.+|++++++.+|++.   .+|.....+++.|+.+.|.
T Consensus        39 GlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~~~~~~~~~~~~~~~g~~v~g~  106 (275)
T 3aev_A           39 AFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENL  106 (275)
T ss_dssp             EEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEeecCcchhHHHHHhccCCCeEEEE
Confidence            356777776532  111 2 38999999999999999999999986   4676666667777776666

>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=93.52  E-value=0.25  Score=33.04  Aligned_cols=63  Identities=14%  Similarity=0.161  Sum_probs=44.7

Q ss_pred             hcCCCCCCEEEEE----eEeEEEEEecCCCceeEEEEEEcc-CcCCccccCccccccCCCEEEEEEEEEeCC
Q 030172           53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDRE  119 (182)
Q Consensus        53 ~~~~~~G~iv~g~----~~G~fV~l~~~~g~~~~~glv~~s-els~~~~~~~~~~~~~Gd~v~vkV~~id~~  119 (182)
                      ..++.+|++.+|.    +.-.+|.|.+.+|   .+|++--. .+-.++..+.++.+ +|..|+++|+.+|..
T Consensus        27 ~~~~~~g~VtkGiVy~kd~~fyV~L~dY~g---lEaii~dYvnv~~dr~~klkkkL-VGKtIkVqVIRvD~l   94 (102)
T 1jjg_A           27 AMDLSPGSVHEGIVYFKDGIFKVRLLGYEG---HECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADGL   94 (102)
T ss_dssp             CCCCCSSCEEEEEEEEETTEEEEECTTTSS---CEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECSS
T ss_pred             ccccCCCceEeeEEEEeCCEEEEEecCCCC---ceeeeehhhhhhHHHHHHHHHHh-cCceEEEEEEEeccE
Confidence            3578999999999    5556888865545   88887311 12233445555555 899999999999863

>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=92.00  E-value=0.077  Score=44.42  Aligned_cols=42  Identities=7%  Similarity=0.084  Sum_probs=32.3

Q ss_pred             HHhhhcCCCCceeEeeEee----ecCCeeEEecCC---Chhhhchhhhh
Q 030172          138 TLEKVIPQDGSVISDSSSM----SSSNSNTIEPLP---GLGAIFEELLQ  179 (182)
Q Consensus       138 ~~~~~~~~~g~~v~G~V~~----v~~~G~fV~l~~---gv~gl~~~~~~  179 (182)
                      ....|....|++++|+|.+    +.+.++||++..   +++|++|.-.+
T Consensus       122 i~~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eq  170 (366)
T 1k0r_A          122 TYGEFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQ  170 (366)
T ss_dssp             -----CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGS
T ss_pred             HHHHHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHc
Confidence            3456654569999999999    999999999976   59999998765

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=91.14  E-value=0.11  Score=48.91  Aligned_cols=31  Identities=10%  Similarity=-0.064  Sum_probs=26.1

Q ss_pred             CceeEeeEeeecCCeeEEecCC-Chhhhchhh
Q 030172          147 GSVISDSSSMSSSNSNTIEPLP-GLGAIFEEL  177 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~-gv~gl~~~~  177 (182)
                      |+.+.|+|+++.+||+||.|.+ |++||+|-.
T Consensus       887 ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis  918 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLD  918 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEECTTTCCEEEEEGG
T ss_pred             ceEEEEEEEEEcCCeEEEEEcCCCeEEEEEec
Confidence            7788899999988999999877 888888754

>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=90.58  E-value=0.12  Score=42.34  Aligned_cols=35  Identities=11%  Similarity=0.191  Sum_probs=29.7

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEecCCChhhhch
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE  175 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~  175 (182)
                      +|.|..|++|.|+|+++.++|+||++....+|+++
T Consensus        90 rY~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~  124 (308)
T 2nn6_H           90 RYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLL  124 (308)
T ss_dssp             CCCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEE
T ss_pred             ccCCCCCCEEEEEEEEEeCceEEEEECCCcCCcee
Confidence            36666799999999999999999999766777664

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

Probab=89.98  E-value=0.35  Score=34.29  Aligned_cols=26  Identities=31%  Similarity=0.473  Sum_probs=24.5

Q ss_pred             CCCeEEEEEEEEeCCCCEEEEEechh
Q 030172           22 TGSIISVKVIQANEEMKKLVFSEKDA   47 (182)
Q Consensus        22 vG~~v~~~v~~~d~~~~~i~lS~k~~   47 (182)
                      +|++|.++|+.+|.+++++.+|.+..
T Consensus        54 vGd~V~vkV~~vd~~~~kI~LSlk~~   79 (130)
T 2k4k_A           54 VGDEVQVKVLAVDEEKGKISLSIRAT   79 (130)
T ss_dssp             TTCEEEEEEEEEETTTTEEEEESHHH
T ss_pred             CCCEEEEEEEEEeCCCCEEEEEEeec
Confidence            89999999999999899999999874

>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=89.00  E-value=0.19  Score=45.93  Aligned_cols=31  Identities=10%  Similarity=-0.087  Sum_probs=25.6

Q ss_pred             ceeEeeEeeecCCeeEEecCC-Chhhhchhhh
Q 030172          148 SVISDSSSMSSSNSNTIEPLP-GLGAIFEELL  178 (182)
Q Consensus       148 ~~v~G~V~~v~~~G~fV~l~~-gv~gl~~~~~  178 (182)
                      +.+.|+|+++.++|+||.|.+ |++||+|-..
T Consensus       671 ~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~  702 (760)
T 2vnu_D          671 STETGYVIKVFNNGIVVLVPKFGVEGLIRLDN  702 (760)
T ss_dssp             SEEEEEEEEEETTEEEEEETTTTEEEEEEHHH
T ss_pred             eEEEEEEEEEECCeEEEEEeCCCcEEEEEecc
Confidence            688889999999999999877 8888887543

>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=87.95  E-value=0.059  Score=43.23  Aligned_cols=42  Identities=17%  Similarity=-0.027  Sum_probs=32.1

Q ss_pred             CCCCCCCccHHH--hh-hh-cCCCeEEEEEEEEeCCCCEEEEEech
Q 030172            5 HSCKEPQKSIHE--IA-KG-LTGSIISVKVIQANEEMKKLVFSEKD   46 (182)
Q Consensus         5 ~~~p~~e~~~~~--~~-~~-~vG~~v~~~v~~~d~~~~~i~lS~k~   46 (182)
                      .|++.++++...  .. +. .+|+.+.++|+.+|+.++++.+|++.
T Consensus        39 GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~   84 (266)
T 3cw2_C           39 AFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (266)
T ss_dssp             CBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEESTT
T ss_pred             EEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            467777776432  11 11 38999999999999989999999985

>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae}

Probab=86.17  E-value=4.6  Score=30.96  Aligned_cols=64  Identities=11%  Similarity=0.078  Sum_probs=41.9

Q ss_pred             hhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCcc------------ccccCCCEEEEEEE
Q 030172           52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR------------DILNEGDEVRVKVI  114 (182)
Q Consensus        52 ~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~------------~~~~~Gd~v~vkV~  114 (182)
                      ....+..|+++.|+     +.|+.+-+.++     ..++|+...+...+.-++.            +.-++|+.|+.||.
T Consensus       123 iVFrPf~GevL~G~V~~~s~~~Ig~~~~G~-----Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~  197 (214)
T 2rf4_A          123 YVWQPQVGDVLEGYIFIQSASHIGLLIHDA-----FNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVR  197 (214)
T ss_dssp             EEECCCTTCEEEEEECCCCSSCEEEEETTT-----EEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEE
T ss_pred             EEEecCCCCEEEEEEEEECCCcEEEEEeCC-----EEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEE
Confidence            34578999999999     54555433212     7789999888543321111            11236999999999


Q ss_pred             EEeCCC
Q 030172          115 KIDREK  120 (182)
Q Consensus       115 ~id~~~  120 (182)
                      +++...
T Consensus       198 ~~~~~~  203 (214)
T 2rf4_A          198 NVHTTG  203 (214)
T ss_dssp             EEECCS
T ss_pred             EEEecC
Confidence            998643

---

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	182
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	6e-13
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	9e-12
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	3e-11
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	6e-11
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	2e-10
d1wi5a_	119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	1e-08
d1y14b1	91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	3e-08
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	5e-08
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	7e-08
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	1e-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	2e-07
d2c35b1	94	b.40.4.5 (B:78-171) C-terminal domain of RNA polym	1e-05
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	0.001
d2nn6i1	125	b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H	0.002
d2ix0a3	87	b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Esche	0.002
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	0.003

>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 = 59.0 bits (143), 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

>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 = 56.2 bits (135), Expect = 9e-12
 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

>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 = 54.9 bits (132), Expect = 3e-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

>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 = 53.2 bits (128), Expect = 6e-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

>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 = 52.7 bits (126), Expect = 2e-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 = 48.6 bits (115), Expect = 1e-08
 Identities = 11/82 (13%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           D+G  + +    G+      + + +    +  ++    L  G  +   V K+      ++
Sbjct: 34  DHGYLVDI----GVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVS 89

Query: 125 LSIKQLEEDPLLETLEKVIPQD 146
           LS+   E    + T ++    +
Sbjct: 90  LSVGHSEVSTAIATEQQSWNLN 111

>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 = 47.2 bits (112), Expect = 3e-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

>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 = 46.2 bits (109), Expect = 5e-08
 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 = 46.6 bits (110), Expect = 7e-08
 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

>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 = 45.3 bits (107), Expect = 1e-07
 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

>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 = 45.0 bits (106), 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 = 44.5 bits (105), Expect = 2e-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 = 39.9 bits (93), Expect = 1e-05
 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 = 34.4 bits (79), Expect = 0.001
 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

>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 = 34.5 bits (79), 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

>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 = 33.6 bits (77), 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

>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 = 33.3 bits (76), Expect = 0.003
 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

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	182
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.73
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.72
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.69
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.68
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.6
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.59
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.49
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.48
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.46
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.22
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.21
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	99.11
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.94
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.84
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.81
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.62
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	98.37
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	98.27
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	98.19
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.15
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	98.13
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	98.11
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.1
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.09
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	98.08
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	98.04
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	98.0
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.73
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	97.69
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	97.62
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	97.44
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	97.2
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	96.85
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	96.76
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	96.69
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	96.53
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	96.13
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	95.69
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	95.15
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	91.93
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	89.8
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	87.8
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	85.58

>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=99.73  E-value=9.4e-19  Score=115.09  Aligned_cols=70  Identities=40%  Similarity=0.772  Sum_probs=65.5

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      ++++|+++.|+     +||+||+|+  +|   ++||||+++++|.++.+|++.|++||.|+|+|+++|+ ++|+.||+|+
T Consensus         2 d~kvG~iv~G~V~~v~~~G~fV~l~--~~---~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~-~~ri~LS~k~   75 (76)
T d1sroa_           2 EIEVGRVYTGKVTRIVDFGAFVAIG--GG---KEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKE   75 (76)
T ss_dssp             CCCTTSEEEEEEEEEETTEEEEECS--SS---CCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCT-TCCCEEEECC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEeC--CC---CEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECC-CCCEEEEEEc
Confidence            68999999999     999999996  45   9999999999999999999999999999999999996 6899999997


Q ss_pred             c
Q 030172          130 L  130 (182)
Q Consensus       130 ~  130 (182)
                      +
T Consensus        76 a   76 (76)
T d1sroa_          76 A   76 (76)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.72  E-value=8.3e-18  Score=112.97  Aligned_cols=71  Identities=31%  Similarity=0.505  Sum_probs=54.0

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      +++|+++.|+     ++|+||+|...+|   ++||||+++++|.+..++.+.|++||.|+|+|+++|++++++.||+|+
T Consensus        11 p~~G~iv~G~V~~i~~~G~fV~l~~~~~---i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~ki~LS~Kq   86 (86)
T d1kl9a2          11 PEVEDVVMVNVRSIAEMGAYVSLLEYNN---IEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTT---EEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEEecCCC---EEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEEEEEeeC
Confidence            3689999999     9999999964345   999999999999999999999999999999999999999999999984

>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=99.69  E-value=9.4e-18  Score=112.17  Aligned_cols=72  Identities=36%  Similarity=0.612  Sum_probs=61.5

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      .+++|+++.|+     ++|+||+|...+|   ++||||.++++|.+..++.+.|++||.|+|+|+++|++++++.||+|+
T Consensus         8 ~p~~G~iv~G~V~~v~~~G~fV~l~~~~g---i~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2           8 LPSEGEILIATVKQVFDYGSYVSLDEYGG---LQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             SCCTTCCCEEEEEEEETTEEEEEETTTTT---EEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCcCC---EEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence            45789999999     9999999964345   999999999999999999999999999999999999999999999985

>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=99.68  E-value=2.5e-17  Score=112.40  Aligned_cols=76  Identities=29%  Similarity=0.563  Sum_probs=70.8

Q ss_pred             hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (182)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~  127 (182)
                      ..++++|+++.|+     ++|+||+|+  +|   ++||||.+++++.+..++++.|++||.|+|+|+++|+++++|.||+
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--VH---QDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSM   87 (94)
T ss_dssp             GGGCCTTCEEEEEEEEEETTEEEEECS--SS---SCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEES
T ss_pred             HhcCCCCCEEEEEEEEEECcEEEEEeC--CC---ceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEE
Confidence            4689999999999     999999996  45   9999999999999999999999999999999999999999999999


Q ss_pred             eeccCCc
Q 030172          128 KQLEEDP  134 (182)
Q Consensus       128 k~~~~~p  134 (182)
                      |.. ++|
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            975 555

>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=99.60  E-value=1.2e-15  Score=106.15  Aligned_cols=81  Identities=28%  Similarity=0.497  Sum_probs=69.8

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc-----------cCccccccCCCEEEEEEEEEeCC
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDRE  119 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~-----------~~~~~~~~~Gd~v~vkV~~id~~  119 (182)
                      +++|+++.|+     +||+||+|+   +   ++||||+++|++.++           .++.+.|++||.|+|+|+++|.+
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~---~---ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~   74 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLG---P---LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLK   74 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS---S---SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECC
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEee---C---eEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchh
Confidence            4689999999     999999994   4   999999999999876           47788999999999999999987


Q ss_pred             CCe-----EEEEEeeccCCchhHHHhhh
Q 030172          120 KSR-----ITLSIKQLEEDPLLETLEKV  142 (182)
Q Consensus       120 ~~k-----i~lS~k~~~~~p~~~~~~~~  142 (182)
                      +++     +.||+|+...+||+...+++
T Consensus        75 ~~~~~~~~i~ls~K~~~~~~~e~~~~~~  102 (106)
T d1go3e1          75 AERKRGSKIALTMRQPYLGKLEWIEEEK  102 (106)
T ss_dssp             C-----CEEEEECCSTTCEEHHHHHHHH
T ss_pred             hccccCceeecccccCCCCcchhhhhHh
Confidence            765     78999999999998766544

>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=99.59  E-value=1.4e-15  Score=101.08  Aligned_cols=74  Identities=26%  Similarity=0.354  Sum_probs=65.5

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcc-ccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~-~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k  128 (182)
                      .+++|+++.|+     ++|+||+|+  ++   ++||||++|+++.+ ..++++.|++||.|.|+|+++|+ ++++.||+|
T Consensus         2 ~Pk~Gd~V~G~V~~v~~~g~~V~i~--~~---~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~LS~k   75 (83)
T d2ba0a1           2 TPSVGDVVIGIIREVAANGWAVDIY--SP---YQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMK   75 (83)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS--SS---SCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECC
T ss_pred             cCCCCCEEEEEEEEEECCEEEEecC--CC---eeEEEecccccccccccChhhhcccccEEEEEEEEECC-CCCEEEEec
Confidence            36889999999     999999997  44   99999999999875 78999999999999999999996 689999999


Q ss_pred             eccCCc
Q 030172          129 QLEEDP  134 (182)
Q Consensus       129 ~~~~~p  134 (182)
                      +....+
T Consensus        76 ~~~~~k   81 (83)
T d2ba0a1          76 DRICRP   81 (83)
T ss_dssp             SSSCEE
T ss_pred             CCCCCC
Confidence            865544

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.49  E-value=1.4e-14  Score=97.14  Aligned_cols=70  Identities=26%  Similarity=0.380  Sum_probs=62.3

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc---cCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI---QDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~---~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      .+++|+++.|+     ++|+||+|+  ++   ++||||++++++.+.   .++++.|++||.|.|+|+++|+ .+++.||
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--AP---YKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLS   77 (87)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS--SS---SCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEE
T ss_pred             cCCCCCEEEEEEEEEECCEEEEEeC--CC---EEEEEehHHhCCceeccccccchhhcccceEEEEEEEECC-CCCEEEE
Confidence            47889999999     999999996  34   999999999999865   4678899999999999999996 6899999


Q ss_pred             Eeec
Q 030172          127 IKQL  130 (182)
Q Consensus       127 ~k~~  130 (182)
                      +|+.
T Consensus        78 ~k~~   81 (87)
T d2je6i1          78 VKGK   81 (87)
T ss_dssp             CCST
T ss_pred             EecC
Confidence            9964

>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=99.48  E-value=1.8e-14  Score=102.04  Aligned_cols=78  Identities=15%  Similarity=0.233  Sum_probs=69.3

Q ss_pred             hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcc-ccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (182)
Q Consensus        53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~-~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS  126 (182)
                      ...+++|+++.|+     ++|+||+|+ .++   ++||||++++++.+ ..+|.+.|++||.|+|+|+++|+.++++.||
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 AEALKPGMLLTGTVSSLEDHGYLVDIG-VDG---TRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS   91 (119)
T ss_dssp             TTTCCTTCEEEEEEEEECSSEEEEECC-CSS---CEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEE
T ss_pred             HhhcCCCCEEEEEEEEEeccEEEEEEe-ccc---cceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEE
Confidence            3679999999999     999999995 234   99999999999875 7889999999999999999999999999999


Q ss_pred             EeeccCCc
Q 030172          127 IKQLEEDP  134 (182)
Q Consensus       127 ~k~~~~~p  134 (182)
                      +|......
T Consensus        92 ~k~~~~~~   99 (119)
T d1wi5a_          92 VGHSEVST   99 (119)
T ss_dssp             CCCCCSCC
T ss_pred             ecHHHhhh
Confidence            99876433

>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=99.46  E-value=2.1e-14  Score=96.40  Aligned_cols=70  Identities=17%  Similarity=0.332  Sum_probs=62.2

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcccc----CccccccCCCEEEEEEEEEeCCCCeEEE
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----DIRDILNEGDEVRVKVIKIDREKSRITL  125 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~----~~~~~~~~Gd~v~vkV~~id~~~~ki~l  125 (182)
                      .+++|+++.|+     ++|+||+|+  ++   .+||||.+++++.+..    ++++.|++||.|.|+|+++|+ ++++.|
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--SP---YVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPLL   77 (88)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECS--SS---SCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEEE
T ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC--CC---eEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECC-CCCEEE
Confidence            57899999999     999999996  34   8999999999998754    778899999999999999996 679999


Q ss_pred             EEeec
Q 030172          126 SIKQL  130 (182)
Q Consensus       126 S~k~~  130 (182)
                      |+|+.
T Consensus        78 s~k~~   82 (88)
T d2z0sa1          78 TVQGE   82 (88)
T ss_dssp             ECCSS
T ss_pred             EEecC
Confidence            99964

>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=99.22  E-value=1.7e-12  Score=88.05  Aligned_cols=70  Identities=23%  Similarity=0.291  Sum_probs=58.4

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCc----------cccCccccccCCCEEEEEEEEEeCC
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----------LIQDIRDILNEGDEVRVKVIKIDRE  119 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~----------~~~~~~~~~~~Gd~v~vkV~~id~~  119 (182)
                      .+++|++|.|+     ++|+||+|+  .+   .+|+||+++++|.          ...++++.|++||.|.|+|+++|. 
T Consensus         5 ~P~vGdiV~G~V~~v~~~g~~V~I~--~~---~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~-   78 (95)
T d2nn6h1           5 IGEVGDIVVGRITEVQQKRWKVETN--SR---LDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-   78 (95)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECS--SS---SCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-
T ss_pred             cCCCCCEEEEEEEEEecCcEEEEeC--CC---ceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECC-
Confidence            46789999999     999999996  33   8999999999763          234567889999999999999997 


Q ss_pred             CCeEEEEEeec
Q 030172          120 KSRITLSIKQL  130 (182)
Q Consensus       120 ~~ki~lS~k~~  130 (182)
                      ++++.||+|+.
T Consensus        79 dg~i~Ls~r~~   89 (95)
T d2nn6h1          79 DGAVSLHTRSL   89 (95)
T ss_dssp             TTEEEEECCSS
T ss_pred             CCCEEEEeccc
Confidence            69999999864

>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=99.21  E-value=1.1e-13  Score=86.99  Aligned_cols=50  Identities=32%  Similarity=0.657  Sum_probs=29.0

Q ss_pred             eEeEEEEEecCCCceeEEEEEEccCcCCc----cccCccccccCCCEEEEEEEEEeCCC
Q 030172           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQDIRDILNEGDEVRVKVIKIDREK  120 (182)
Q Consensus        66 ~~G~fV~l~~~~g~~~~~glv~~sels~~----~~~~~~~~~~~Gd~v~vkV~~id~~~  120 (182)
                      +|||||+|.  +|   ++||||+|+|++.    ++.+|++.|++||.|+|+|+++|+++
T Consensus         8 ~fG~FV~l~--~g---~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           8 TFGAFVSLL--PG---KDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             -CSCEECCC--------CCCCC-------------------CCSSCBCCCCCCCCCSSC
T ss_pred             eceEEEEec--CC---ceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCCC
Confidence            999999996  45   9999999999864    67899999999999999999999743

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=99.11  E-value=1.3e-10  Score=77.33  Aligned_cols=64  Identities=13%  Similarity=0.122  Sum_probs=51.6

Q ss_pred             CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcccc------------CccccccCCCEEEEEEEEEeCCCC
Q 030172           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ------------DIRDILNEGDEVRVKVIKIDREKS  121 (182)
Q Consensus        59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~------------~~~~~~~~Gd~v~vkV~~id~~~~  121 (182)
                      ++.+.|.     ++|+||+|.. .+   ++||||+++|++.+..            +..+.|++||.|+|+|+++|++++
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-NG---AIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETR   79 (87)
T ss_dssp             CCCEEEEEEEEETTEEEEEETT-TC---CEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTT
T ss_pred             CCEEEEEEEEEEcCeEEEEEec-CC---cEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccC
Confidence            4455555     9999999952 35   9999999999987532            234679999999999999999999


Q ss_pred             eEEEE
Q 030172          122 RITLS  126 (182)
Q Consensus       122 ki~lS  126 (182)
                      +|.+.
T Consensus        80 ~I~~~   84 (87)
T d2ix0a3          80 SIIAR   84 (87)
T ss_dssp             EEEEE
T ss_pred             eEEEE
Confidence            98753

>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=98.94  E-value=2.2e-09  Score=71.62  Aligned_cols=63  Identities=19%  Similarity=0.197  Sum_probs=53.9

Q ss_pred             CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc----------cCccccccCCCEEEEEEEEEeCCCC
Q 030172           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----------QDIRDILNEGDEVRVKVIKIDREKS  121 (182)
Q Consensus        57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~----------~~~~~~~~~Gd~v~vkV~~id~~~~  121 (182)
                      -.|+++.|+     ++|+||+++   .   ++||+|.++|.+.+.          .+..+.|+.||.|+|||+++|.+++
T Consensus         2 f~Gev~~g~I~~v~~~G~fv~lg---~---~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~   75 (91)
T d1y14b1           2 FKGEVVDGTVVSCSQHGFEVQVG---P---MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVS   75 (91)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEET---T---EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETT
T ss_pred             CCCCEEEEEEEEEEeeEEEEEEc---C---eEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccC
Confidence            368999998     999999995   2   899999999987754          3456679999999999999999999


Q ss_pred             eEEE
Q 030172          122 RITL  125 (182)
Q Consensus       122 ki~l  125 (182)
                      ++..
T Consensus        76 ~i~~   79 (91)
T d1y14b1          76 SIHA   79 (91)
T ss_dssp             EEEE
T ss_pred             ccEE
Confidence            8854

>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=98.84  E-value=5e-09  Score=70.33  Aligned_cols=64  Identities=14%  Similarity=0.261  Sum_probs=53.8

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc------------cCccccccCCCEEEEEEEEEeC
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVKVIKIDR  118 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~------------~~~~~~~~~Gd~v~vkV~~id~  118 (182)
                      +-.|+++.|+     ++|+||+++   .   ++||+|.++|.+.+.            .+....|+.||.|++||++++.
T Consensus         2 Pf~Gev~~g~V~~v~~~G~fv~lg---~---~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~   75 (94)
T d2c35b1           2 PFKGEVVDAVVTQVNKVGLFTEIG---P---MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV   75 (94)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEET---T---EEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEec---C---ceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEec
Confidence            3468999998     999999995   2   999999999998752            3445679999999999999999


Q ss_pred             CCCeEEE
Q 030172          119 EKSRITL  125 (182)
Q Consensus       119 ~~~ki~l  125 (182)
                      +.+++..
T Consensus        76 ~~~~I~~   82 (94)
T d2c35b1          76 DKNDIFA   82 (94)
T ss_dssp             ETTEEEE
T ss_pred             CcCcceE
Confidence            8888863

>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=98.81  E-value=2.4e-09  Score=71.17  Aligned_cols=69  Identities=7%  Similarity=-0.050  Sum_probs=60.3

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      .+++||+|.|+     .+++||+|+.  +   ..|++|++++. ...++.+..+++||.|.|+|.++|. .+++.||..+
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 VPVKGDHVIGIVTAKSGDIFKVDVGG--S---EPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCID   75 (88)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECSS--S---SCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECSB
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEcCC--C---eeEEEeHHHcC-ccccccCcccCCCCEEEEEEEEeCC-CCCEEEEEEc
Confidence            46899999999     8899999973  2   88999999996 4678889999999999999999996 7899999876


Q ss_pred             c
Q 030172          130 L  130 (182)
Q Consensus       130 ~  130 (182)
                      .
T Consensus        76 ~   76 (88)
T d2nn6g1          76 S   76 (88)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=98.62  E-value=2.5e-08  Score=66.38  Aligned_cols=69  Identities=14%  Similarity=0.086  Sum_probs=60.2

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      .+++||+|.|+     ..++||+|+.+     ..|++|.++.......+.+..+++||.|.|+|.++|+ .+.+.||.++
T Consensus         4 ~P~~gD~ViG~V~~~~~~~~~vdI~~~-----~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~-~~~~~Lsc~~   77 (90)
T d2ja9a1           4 IPSVNDFVIGVIIGTFSDSYKVSLQNF-----SSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEK-ELEAEIECFD   77 (90)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESSTT-----SCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEESSC
T ss_pred             cCCCCCEEEEEEEEEeCCcEEEEcCCc-----chhhhhhhhccCccccccCCccCCCCEEEEEEEEECC-CCCEEEEEec
Confidence            46899999999     78999999732     7888898887777888999999999999999999996 7889999865

>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=98.37  E-value=9.8e-08  Score=61.32  Aligned_cols=34  Identities=9%  Similarity=-0.067  Sum_probs=31.6

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .|+++.|+|+++.+||+||++.+|++||||....
T Consensus         5 vG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sel   38 (76)
T d1sroa_           5 VGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQI   38 (76)
T ss_dssp             TTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSS
T ss_pred             CCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHh
Confidence            4999999999999999999999999999997654

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.27  E-value=9.8e-07  Score=61.86  Aligned_cols=74  Identities=20%  Similarity=0.229  Sum_probs=58.5

Q ss_pred             CCCCCEEEEE-----eEeEEEEEecCCC---ceeEEEEEEccCcC--CccccCccccccCCCEEEEEEEEEeCCCCeEEE
Q 030172           56 VNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVS--WDLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (182)
Q Consensus        56 ~~~G~iv~g~-----~~G~fV~l~~~~g---~~~~~glv~~sels--~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~l  125 (182)
                      +++|++|.|+     ...++++|...+|   ...+.|++|.+++.  .....++.+.|++||.|+|+|+++...+..+.|
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            6789999999     7779999964332   01367999999984  334567889999999999999999875667889


Q ss_pred             EEee
Q 030172          126 SIKQ  129 (182)
Q Consensus       126 S~k~  129 (182)
                      |.++
T Consensus        85 st~~   88 (125)
T d2nn6i1          85 TTAE   88 (125)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            9875

>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=98.19  E-value=5.5e-07  Score=58.50  Aligned_cols=38  Identities=13%  Similarity=0.103  Sum_probs=33.5

Q ss_pred             hcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          142 VIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       142 ~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |.|+.|+++.|+|+++.++|+||++.++++||||....
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~   38 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSEN   38 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGC
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEecCCCeeEEEecccc
Confidence            34567999999999999999999999999999996543

>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Thermotoga maritima [TaxId: 2336]

Probab=98.15  E-value=7.1e-06  Score=51.84  Aligned_cols=60  Identities=18%  Similarity=0.144  Sum_probs=48.5

Q ss_pred             CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCC--eEEEE
Q 030172           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLS  126 (182)
Q Consensus        55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~--ki~lS  126 (182)
                      +-+.|+++.|+     +..++|+|+   +   .+|++|.+|..      |.+.|++||.|+|-|.+++...+  +|.||
T Consensus         5 ~~~~geiv~G~V~r~~~~~~~Vdlg---~---~eaiLp~~eqi------p~E~~~~Gdrik~~i~~V~~~~kgpqI~lS   71 (72)
T d1hh2p1           5 SELKGTVTTAEVIRVMGEWADIRIG---K---LETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVS   71 (72)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEEET---T---EEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             hhccCcEEEEEEEEEcCCCEEEEEC---C---cEEECCHHHcC------CCCCCCCCCEEEEEEEEEEEcCCCCeEEEe
Confidence            45789999999     566899995   4   99999999865      67889999999999999976443  45554

>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=98.13  E-value=7.1e-07  Score=58.53  Aligned_cols=39  Identities=5%  Similarity=-0.102  Sum_probs=35.0

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      .|.|+.|+++.|+|+++.++|+||++.++++||||....
T Consensus         2 ~Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~   40 (87)
T d2je6i1           2 FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNL   40 (87)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHH
T ss_pred             cccCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHh
Confidence            356678999999999999999999999999999997654

>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=98.11  E-value=3.6e-07  Score=60.91  Aligned_cols=41  Identities=10%  Similarity=0.095  Sum_probs=35.9

Q ss_pred             HhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhhcc
Q 030172          139 LEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQED  181 (182)
Q Consensus       139 ~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~~  181 (182)
                      .+++.+  |++++|+|+++.++|+||++.+|++||||....-+
T Consensus        13 ~~~~k~--G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~   53 (94)
T d3bzka4          13 LKDLKP--GMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSE   53 (94)
T ss_dssp             GGGCCT--TCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCS
T ss_pred             HhcCCC--CCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhc
Confidence            456666  99999999999999999999999999999876543

>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=98.10  E-value=9.4e-07  Score=57.79  Aligned_cols=34  Identities=6%  Similarity=-0.083  Sum_probs=31.1

Q ss_pred             CCceeEeeEeeecCCeeEEecC--CChhhhchhhhh
Q 030172          146 DGSVISDSSSMSSSNSNTIEPL--PGLGAIFEELLQ  179 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~--~gv~gl~~~~~~  179 (182)
                      .|+++.|+|+++.++|+||+|.  +|++||||....
T Consensus        13 ~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sel   48 (86)
T d1kl9a2          13 VEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSEL   48 (86)
T ss_dssp             TTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC
T ss_pred             CCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeec
Confidence            5999999999999999999996  689999998764

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.09  E-value=8.5e-07  Score=57.70  Aligned_cols=35  Identities=11%  Similarity=0.069  Sum_probs=31.3

Q ss_pred             CCCceeEeeEeeecCCeeEEecC--CChhhhchhhhh
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPL--PGLGAIFEELLQ  179 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~--~gv~gl~~~~~~  179 (182)
                      +.|++++|+|+++.+||+||+|.  +|++||||....
T Consensus        10 ~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sel   46 (84)
T d2ahob2          10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEV   46 (84)
T ss_dssp             CTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGC
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEcccc
Confidence            45999999999999999999997  589999997653

>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=98.08  E-value=3.1e-07  Score=56.66  Aligned_cols=28  Identities=14%  Similarity=0.154  Sum_probs=19.4

Q ss_pred             eeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       152 G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |+|+++.+|||||+|.+|++||||-...
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihisei   28 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQI   28 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC----
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHc
Confidence            7899999999999999999999997655

>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=98.04  E-value=1.4e-06  Score=57.13  Aligned_cols=38  Identities=13%  Similarity=0.025  Sum_probs=34.6

Q ss_pred             hcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          142 VIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       142 ~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |.|+.|+.+.|+|+++.++|+||++.++++||+|....
T Consensus         3 Y~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~   40 (88)
T d2z0sa1           3 YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDF   40 (88)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHH
T ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHh
Confidence            55667999999999999999999999999999997765

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=98.00  E-value=2e-06  Score=58.50  Aligned_cols=35  Identities=6%  Similarity=-0.114  Sum_probs=30.8

Q ss_pred             CCCceeEeeEeeecCCeeEEecCCChhhhchhhhhc
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE  180 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~  180 (182)
                      ..|+++.|+|+++.+||+||+| ++++||||...-.
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel-~~ieGlv~~s~l~   36 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRL-GPLDGLIHVSQIM   36 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEC-SSSEEEEEGGGSC
T ss_pred             CCCCEEEEEEEEEeeeEEEEEe-eCeEEEEEeeccc
Confidence            3599999999999999999999 5799999976543

>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=97.73  E-value=7.4e-05  Score=47.43  Aligned_cols=61  Identities=20%  Similarity=0.294  Sum_probs=46.7

Q ss_pred             CCCCEEEEE----eE-----eEEEEEec-CCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC--CeEE
Q 030172           57 NVEDIFVGR----DY-----GAFIHLRF-PDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRIT  124 (182)
Q Consensus        57 ~~G~iv~g~----~~-----G~fV~l~~-~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~--~ki~  124 (182)
                      +.|+++.|+    +.     -++|+|+. .++   ++|++|.+|.-      |.+.|++||.|+|.|.+++...  -+|.
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~---~EaiLp~~eqi------p~E~y~~Gdrik~~i~~V~~~~kGp~Ii   73 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKA---SEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLIT   73 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSC---EEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEE
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCC---EEEECCHHHcC------CCcccCCCCEEEEEEEEEEecCCCCEEE
Confidence            679999999    22     27999963 134   99999988855      6788999999999999998643  2444


Q ss_pred             EE
Q 030172          125 LS  126 (182)
Q Consensus       125 lS  126 (182)
                      ||
T Consensus        74 lS   75 (76)
T d2asba1          74 LS   75 (76)
T ss_dssp             EE
T ss_pred             Ee
Confidence            44

>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=97.69  E-value=9.4e-06  Score=56.11  Aligned_cols=37  Identities=19%  Similarity=0.302  Sum_probs=32.6

Q ss_pred             hhhcCCCCceeEeeEeeecCCeeEEec-CCChhhhchhhh
Q 030172          140 EKVIPQDGSVISDSSSMSSSNSNTIEP-LPGLGAIFEELL  178 (182)
Q Consensus       140 ~~~~~~~g~~v~G~V~~v~~~G~fV~l-~~gv~gl~~~~~  178 (182)
                      +.+.+  |++++|+|+++.++|+||++ .++++||||...
T Consensus        17 ~~l~~--G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~e   54 (119)
T d1wi5a_          17 EALKP--GMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLK   54 (119)
T ss_dssp             TTCCT--TCEEEEEEEEECSSEEEEECCCSSCEEEEEHHH
T ss_pred             hhcCC--CCEEEEEEEEEeccEEEEEEeccccceEEeHHH
Confidence            34555  99999999999999999999 589999999864

>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=97.62  E-value=1.1e-05  Score=53.60  Aligned_cols=38  Identities=11%  Similarity=0.115  Sum_probs=34.4

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      +|.|.+|+++.|+|+++.++|+||++.++.+|++|-..
T Consensus         3 ~Y~P~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~   40 (95)
T d2nn6h1           3 RYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSS   40 (95)
T ss_dssp             CCCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSC
T ss_pred             cccCCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHH
Confidence            57777899999999999999999999999999998653

>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=97.44  E-value=3.4e-05  Score=50.32  Aligned_cols=34  Identities=9%  Similarity=0.003  Sum_probs=29.7

Q ss_pred             CCCceeEeeEeeecCCeeEEecC-CChhhhchhhh
Q 030172          145 QDGSVISDSSSMSSSNSNTIEPL-PGLGAIFEELL  178 (182)
Q Consensus       145 ~~g~~v~G~V~~v~~~G~fV~l~-~gv~gl~~~~~  178 (182)
                      +.++.++|.|+++.++|+||+|. .+++||+|-..
T Consensus         2 ~~~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~   36 (87)
T d2ix0a3           2 GTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPF   36 (87)
T ss_dssp             TSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGG
T ss_pred             CCCCEEEEEEEEEEcCeEEEEEecCCcEEEEEehh
Confidence            35889999999999999999995 58999999654

>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=97.20  E-value=0.00012  Score=47.80  Aligned_cols=34  Identities=12%  Similarity=0.149  Sum_probs=30.3

Q ss_pred             CCceeEeeEeeecCCeeEEecCCChhhhchhhhhc
Q 030172          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE  180 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~  180 (182)
                      .|+++.|+|+++.++|+||++. .++||+|.....
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg-~~eg~i~~~~l~   36 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVG-PMKVFVTKHLMP   36 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSC
T ss_pred             CCCEEEEEEEEEEeeEEEEEEc-CeEEEEEhhhcC
Confidence            3899999999999999999995 689999987654

>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=96.85  E-value=0.0018  Score=40.84  Aligned_cols=73  Identities=30%  Similarity=0.421  Sum_probs=54.5

Q ss_pred             CCCCCCEEEEE----eEeEEEEEecCCCceeEEEEEEc-cCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172           55 RVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHV-SEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (182)
Q Consensus        55 ~~~~G~iv~g~----~~G~fV~l~~~~g~~~~~glv~~-sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~  129 (182)
                      -+.+|++.+|+    +.-.+|.|....|   .++++-- -++..++..+.++.+ +|..|+++|+.+|..++.|.++.|.
T Consensus         5 lPnigdVtkGiVy~kd~~fyV~L~dY~g---~ea~l~dy~~~~~d~~~klk~kL-VGKtIkvqVIR~d~lKGYIDVr~~~   80 (85)
T d1luza_           5 LPNAGDVIKGRVYEKDYALYIYLFDYPH---FEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKR   80 (85)
T ss_dssp             CCCTTCEEEEEEEEETTEEEEEETTCTT---SEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEE
T ss_pred             cCCCCceeeeEEEEeCCEEEEEecCCCC---ceEEeeehhhhhhHHHHHHHHHh-cCceEEEEEEEEcceeeEEEehhhh
Confidence            46789999999    6667888875545   8888731 122223445556655 8999999999999999999999986


Q ss_pred             cc
Q 030172          130 LE  131 (182)
Q Consensus       130 ~~  131 (182)
                      ..
T Consensus        81 ~~   82 (85)
T d1luza_          81 MC   82 (85)
T ss_dssp             EC
T ss_pred             hh
Confidence            43

>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=96.76  E-value=0.00049  Score=44.70  Aligned_cols=38  Identities=13%  Similarity=0.107  Sum_probs=34.0

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      +|.|..|+.|-|+|+++..++.||++.....|++|-+.
T Consensus         1 rY~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~   38 (88)
T d2nn6g1           1 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLS   38 (88)
T ss_dssp             SCCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCS
T ss_pred             CCcCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHH
Confidence            35667799999999999999999999999999999654

>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=96.69  E-value=0.0014  Score=42.38  Aligned_cols=62  Identities=27%  Similarity=0.512  Sum_probs=42.9

Q ss_pred             CEEEEE-------eEeEEEEEecCCCceeEEEEEEccCcCCcccc---------CccccccCCCEEEEEEEEEeCCCCeE
Q 030172           60 DIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKIDREKSRI  123 (182)
Q Consensus        60 ~iv~g~-------~~G~fV~l~~~~g~~~~~glv~~sels~~~~~---------~~~~~~~~Gd~v~vkV~~id~~~~ki  123 (182)
                      .||.|+       =.+|||+++  .+   ..||+|++|+...+..         +..+.++.||.|-|.|.+=...++--
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG--~~---k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGp   76 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYG--AE---RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGA   76 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESS--SS---SCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCC
T ss_pred             CcEEEEEEEecCCceEEEEEeC--CC---ccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccCCCCc
Confidence            356666       236999997  33   8899999998766532         44567899999999997654333333


Q ss_pred             EEE
Q 030172          124 TLS  126 (182)
Q Consensus       124 ~lS  126 (182)
                      .||
T Consensus        77 rlT   79 (87)
T d1smxa_          77 ALT   79 (87)
T ss_dssp             EEE
T ss_pred             eEE
Confidence            333

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.53  E-value=0.00078  Score=44.00  Aligned_cols=33  Identities=9%  Similarity=-0.004  Sum_probs=29.3

Q ss_pred             CceeEeeEeeecCCeeEEecCCChhhhchhhhhc
Q 030172          147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE  180 (182)
Q Consensus       147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~  180 (182)
                      |+++.|+|+++.++|+||++. .++||+|.-...
T Consensus         5 Gev~~g~V~~v~~~G~fv~lg-~~~~~v~~~~l~   37 (94)
T d2c35b1           5 GEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIP   37 (94)
T ss_dssp             TCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSC
T ss_pred             CCEEEEEEEEEEeeEEEEEec-CceEEEEhhhcC
Confidence            899999999999999999995 689999876543

>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=96.13  E-value=0.002  Score=41.83  Aligned_cols=38  Identities=11%  Similarity=0.020  Sum_probs=33.1

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL  178 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~  178 (182)
                      +|.|..|+.|-|+|+++..++.||++.+...|++|-.+
T Consensus         2 rY~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~   39 (90)
T d2ja9a1           2 RYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYM   39 (90)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETT
T ss_pred             CccCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhh
Confidence            56677899999999999999999999988999876443

>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=95.69  E-value=0.012  Score=37.84  Aligned_cols=62  Identities=15%  Similarity=0.187  Sum_probs=45.6

Q ss_pred             hcCCCCCCEEEEE----eEeEEEEEecCCCceeEEEEEE-ccCcCCccccCccccccCCCEEEEEEEEEeC
Q 030172           53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDR  118 (182)
Q Consensus        53 ~~~~~~G~iv~g~----~~G~fV~l~~~~g~~~~~glv~-~sels~~~~~~~~~~~~~Gd~v~vkV~~id~  118 (182)
                      ..++.+|++.+|.    +.-++|.|.+..|   .+|++- --++-.++..+.++.+ +|..|+|+|+.+|.
T Consensus        27 ~~~~~~G~V~kGiVy~rd~~fyV~L~dY~g---~eail~dY~n~~~dr~~klkkkL-VGKTIkVqVIRvDk   93 (102)
T d1jjga_          27 AMDLSPGSVHEGIVYFKDGIFKVRLLGYEG---HECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG   93 (102)
T ss_dssp             CCCCCSSCEEEEEEEEETTEEEEECTTTSS---CEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS
T ss_pred             ecccCCCcEeeeEEEEeCCEEEEEecCCCC---ceeeeeehhhhhHHHHHHHHHHh-cCceEEEEEEEecc
Confidence            4578999999999    6667888875545   888852 2233444555666655 89999999999983

>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=95.15  E-value=0.0083  Score=37.10  Aligned_cols=37  Identities=11%  Similarity=-0.075  Sum_probs=31.8

Q ss_pred             hcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172          142 VIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (182)
Q Consensus       142 ~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~  179 (182)
                      |....|++++|+|.++....++|++. +++|++|+..+
T Consensus         4 f~~~~geiv~G~V~r~~~~~~~Vdlg-~~eaiLp~~eq   40 (72)
T d1hh2p1           4 YSELKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEW   40 (72)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGS
T ss_pred             HhhccCcEEEEEEEEEcCCCEEEEEC-CcEEECCHHHc
Confidence            43445999999999999999999994 89999998765

>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=91.93  E-value=0.041  Score=35.07  Aligned_cols=29  Identities=0%  Similarity=-0.063  Sum_probs=26.2

Q ss_pred             ceeEeeEeeecC--CeeEEecCCChhhhchh
Q 030172          148 SVISDSSSMSSS--NSNTIEPLPGLGAIFEE  176 (182)
Q Consensus       148 ~~v~G~V~~v~~--~G~fV~l~~gv~gl~~~  176 (182)
                      .++.|+|.++.+  .+|||++..+-+||+|-
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~   32 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPL   32 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEG
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEe
Confidence            478899999998  89999999999999974

>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=89.80  E-value=0.23  Score=29.96  Aligned_cols=45  Identities=13%  Similarity=0.226  Sum_probs=35.1

Q ss_pred             cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEE
Q 030172           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI  116 (182)
Q Consensus        54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~i  116 (182)
                      ..++.|++-+|.     ..|+||+++       ++-+..+.+           .|+.|+.+.+||.++
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            357899999998     778999996       444444332           378999999999998

>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=87.80  E-value=0.078  Score=32.83  Aligned_cols=35  Identities=9%  Similarity=0.049  Sum_probs=28.6

Q ss_pred             CCceeEeeEeeecCC----eeEEecC---CChhhhchhhhhc
Q 030172          146 DGSVISDSSSMSSSN----SNTIEPL---PGLGAIFEELLQE  180 (182)
Q Consensus       146 ~g~~v~G~V~~v~~~----G~fV~l~---~gv~gl~~~~~~~  180 (182)
                      .|++++|+|.++...    -++|+|.   ++++|++|+-.+-
T Consensus         4 ~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqi   45 (76)
T d2asba1           4 EGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV   45 (76)
T ss_dssp             TTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC
T ss_pred             cceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcC
Confidence            499999999999753    2799995   6899999987763

>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=85.58  E-value=0.33  Score=32.67  Aligned_cols=36  Identities=11%  Similarity=0.226  Sum_probs=28.3

Q ss_pred             hhcCCCCceeEeeEeeecCCeeEEec--------CCChhhhchh
Q 030172          141 KVIPQDGSVISDSSSMSSSNSNTIEP--------LPGLGAIFEE  176 (182)
Q Consensus       141 ~~~~~~g~~v~G~V~~v~~~G~fV~l--------~~gv~gl~~~  176 (182)
                      ++-|++|++|-|+|+++.+..++|++        ...+.|+++.
T Consensus         2 ~~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~   45 (125)
T d2nn6i1           2 QLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRK   45 (125)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEE
T ss_pred             CcCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccH
Confidence            34566799999999999999999998        3456666653