Citrus Sinensis ID: 032149

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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------
Protein Sequence
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFML
Secondary Structure (PSIPRED)
ccccccccEEEEcccEEcccccEEEcccEEEEccccEEEEEEEEEEEEccccccccccccEEEEEcccccccccccccEEEEEEEEEcccEEEEEEEEEccEEccccEEEEEEEcccccccccHHHHHcccccccEEEEEEEEEEc
Secondary Structure Prediction (SSPRO)
cccccccccEEEccccccccccccccccEEEEEcccEEEEEEEEEEEEEcccccccccccEEEEEcccccccccccccEEEEEEEEEcccEEEEEEEEEcccccccccEEEEEcccccccccccEEEEcccccccHEHHEEEEEcc
Coil and Loop (DISEMBL)
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGllrtlspppdspdqrptvevtghkahgpvpepgSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIirqqdvrateidkvdmhlsfrpgdIVRASVVSFML
Flexible Loop (DISEMBL)
mvvkeeemvlvtpgevlgkateVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGhkahgpvpepgsvVIARVTKVMTRMASADIMCVGAKSVrekfsgiirqqdvrateidkvdmhlsfrpgdivrASVVSFML
Low Complexity Region (SEG)
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFML
Disordered region (IsUnstruct)
********VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLR******************************SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVV****
Disordered Region (DISOPRED)
******E***VTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLS************************EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV**TEIDKVDMHLSFRPGDIVRASVVSFML
Disordered Region (DISEMBL)
********VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSP*************TGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFML
Disordered Region (DISPRO)
*******MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFML
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFML
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	146	2.2.26 [Sep-21-2011]
Q9DAA6	195	Exosome complex component	yes	no	0.863	0.646	0.378	5e-17
Q9Y3B2	195	Exosome complex component	yes	no	0.863	0.646	0.378	5e-17
O59821	181	Exosome complex component	yes	no	0.856	0.690	0.364	2e-14
P53859	292	Exosome complex component	yes	no	0.630	0.315	0.285	2e-07
Q32CG3	599	Sulfite reductase [NADPH]	yes	no	0.493	0.120	0.369	0.0006
Q31XM4	599	Sulfite reductase [NADPH]	yes	no	0.493	0.120	0.369	0.0007
B1IU77	599	Sulfite reductase [NADPH]	yes	no	0.493	0.120	0.369	0.0007
A7ZQK7	599	Sulfite reductase [NADPH]	yes	no	0.493	0.120	0.369	0.0007
Q3YY94	599	Sulfite reductase [NADPH]	yes	no	0.493	0.120	0.369	0.0007
Q83QD9	599	Sulfite reductase [NADPH]	yes	no	0.493	0.120	0.369	0.0008

>sp|Q9DAA6|EXOS1_MOUSE Exosome complex component CSL4 OS=Mus musculus GN=Exosc1 PE=2 SV=1

 Score = 86.7 bits (213), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 50/132 (37%), Positives = 72/132 (54%), Gaps = 6/132 (4%)

Query: 13  PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
           PGE L    E   G G Y    +G +++SL G L   S         P V V        
Sbjct: 10  PGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMKTS----ENGAVPVVSVMRETESQL 63

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
           +P+ G+VV  +V+ + +R A   I+ VG+  ++  F G IR++D+RATE DKV+++ SFR
Sbjct: 64  LPDVGAVVTCKVSSINSRFAKVHILYVGSTPLKNAFRGTIRKEDIRATEKDKVEIYKSFR 123

Query: 133 PGDIVRASVVSF 144
           PGDIV A V+S 
Sbjct: 124 PGDIVLAKVISL 135

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC1 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC6 and EXOSC8.
Mus musculus (taxid: 10090)

>sp|Q9Y3B2|EXOS1_HUMAN Exosome complex component CSL4 OS=Homo sapiens GN=EXOSC1 PE=1 SV=1

 Score = 86.7 bits (213), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 50/132 (37%), Positives = 72/132 (54%), Gaps = 6/132 (4%)

Query: 13  PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
           PGE L    E   G G Y    +G +++SL G L   S         P V V        
Sbjct: 10  PGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 63

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
           +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ SFR
Sbjct: 64  LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFR 123

Query: 133 PGDIVRASVVSF 144
           PGDIV A V+S 
Sbjct: 124 PGDIVLAKVISL 135

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC1 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC6 and EXOSC8.

Homo sapiens (taxid: 9606)

>sp|O59821|CSL4_SCHPO Exosome complex component csl4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=csl4 PE=3 SV=2

 Score = 77.8 bits (190), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 50/137 (36%), Positives = 74/137 (54%), Gaps = 12/137 (8%)

Query: 8   MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH 67
           M LV PG+V+ +     A  G    K    + ++ TG+     P  +S      VE T  
Sbjct: 1   MNLVLPGQVVARG----APNGEGTVKRGDYIISTRTGIF---DPEKNSVTYPRKVEETA- 52

Query: 68  KAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDM 127
                +P  GS+V+ARV+++  R A+ +I  V     +++F G+I  QD+RATE +KV +
Sbjct: 53  ----VLPNVGSIVLARVSRINARQATVNISVVDDVCTKDEFQGVIHVQDIRATEKNKVKV 108

Query: 128 HLSFRPGDIVRASVVSF 144
             SFRPGDIVRA V+S 
Sbjct: 109 QNSFRPGDIVRALVISL 125

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P53859|CSL4_YEAST Exosome complex component CSL4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CSL4 PE=1 SV=1

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 36/126 (28%), Positives = 56/126 (44%), Gaps = 34/126 (26%)

Query: 53  PDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAK---------- 102
           P +   R T +   +     +P+ G +V+ RVT++  + A+ +I+ V  K          
Sbjct: 112 PGTEKGRKTNKYANNDFANNLPKEGDIVLTRVTRLSLQRANVEILAVEDKPSPIDSGIGS 171

Query: 103 ------------------------SVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVR 138
                                    + E F GIIR QDVR+T+ D+V +   F+PGDIVR
Sbjct: 172 NGSGIVAAGGGSGAATFSVSQASSDLGETFRGIIRSQDVRSTDRDRVKVIECFKPGDIVR 231

Query: 139 ASVVSF 144
           A V+S 
Sbjct: 232 AQVLSL 237

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q32CG3|CYSJ_SHIDS Sulfite reductase [NADPH] flavoprotein alpha-component OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=cysJ PE=3 SV=1

 Score = 43.1 bits (100), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 64  VTGHKAHGPVPEPG-SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI 122
           V   K+  PV  P  SV    V ++ T   S D   V + SV +K +G   ++DVR  EI
Sbjct: 202 VDALKSRAPVAAPSQSVATGAVNEIHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEI 261

Query: 123 DKVDMHLSFRPGD 135
           D  D  L ++PGD
Sbjct: 262 DLGDSDLRYQPGD 274

Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L-cysteine from sulfate. The flavoprotein component catalyzes the electron flow from NADPH -> FAD -> FMN to the hemoprotein component.

Shigella dysenteriae serotype 1 (strain Sd197) (taxid: 300267)

EC: 1

EC: .

EC: 8

EC: .

EC: 1

EC: .

EC: 2

>sp|Q31XM4|CYSJ_SHIBS Sulfite reductase [NADPH] flavoprotein alpha-component OS=Shigella boydii serotype 4 (strain Sb227) GN=cysJ PE=3 SV=1

 Score = 42.7 bits (99), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 64  VTGHKAHGPVPEPG-SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI 122
           V   K+  PV  P  SV    V ++ T   S D   V + SV +K +G   ++DVR  EI
Sbjct: 202 VDALKSRAPVAAPSQSVATGAVNEIHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEI 261

Query: 123 DKVDMHLSFRPGD 135
           D  D  L ++PGD
Sbjct: 262 DLGDSGLRYQPGD 274

Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L-cysteine from sulfate. The flavoprotein component catalyzes the electron flow from NADPH -> FAD -> FMN to the hemoprotein component.

Shigella boydii serotype 4 (strain Sb227) (taxid: 300268)

EC: 1

EC: .

EC: 8

EC: .

EC: 1

EC: .

EC: 2

>sp|B1IU77|CYSJ_ECOLC Sulfite reductase [NADPH] flavoprotein alpha-component OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=cysJ PE=3 SV=1

 Score = 42.7 bits (99), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 64  VTGHKAHGPVPEPG-SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI 122
           V   K+  PV  P  SV    V ++ T   S D   V + SV +K +G   ++DVR  EI
Sbjct: 202 VDALKSRAPVAAPSQSVATGAVNEIHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEI 261

Query: 123 DKVDMHLSFRPGD 135
           D  D  L ++PGD
Sbjct: 262 DLGDSGLRYQPGD 274

Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L-cysteine from sulfate. The flavoprotein component catalyzes the electron flow from NADPH -> FAD -> FMN to the hemoprotein component.

Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) (taxid: 481805)

EC: 1

EC: .

EC: 8

EC: .

EC: 1

EC: .

EC: 2

>sp|A7ZQK7|CYSJ_ECO24 Sulfite reductase [NADPH] flavoprotein alpha-component OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=cysJ PE=3 SV=1

 Score = 42.7 bits (99), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 64  VTGHKAHGPVPEPG-SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI 122
           V   K+  PV  P  SV    V ++ T   S D   V + SV +K +G   ++DVR  EI
Sbjct: 202 VDALKSRAPVAAPSQSVATGAVNEIHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEI 261

Query: 123 DKVDMHLSFRPGD 135
           D  D  L ++PGD
Sbjct: 262 DLGDSGLRYQPGD 274

Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L-cysteine from sulfate. The flavoprotein component catalyzes the electron flow from NADPH -> FAD -> FMN to the hemoprotein component.

Escherichia coli O139:H28 (strain E24377A / ETEC) (taxid: 331111)

EC: 1

EC: .

EC: 8

EC: .

EC: 1

EC: .

EC: 2

>sp|Q3YY94|CYSJ_SHISS Sulfite reductase [NADPH] flavoprotein alpha-component OS=Shigella sonnei (strain Ss046) GN=cysJ PE=3 SV=1

 Score = 42.7 bits (99), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 64  VTGHKAHGPVPEPG-SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI 122
           V   K+  PV  P  SV    V ++ T   S D   V + SV +K +G   ++DVR  EI
Sbjct: 202 VDALKSRAPVAAPSQSVATGAVNEIHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEI 261

Query: 123 DKVDMHLSFRPGD 135
           D  D  L ++PGD
Sbjct: 262 DLGDSGLRYQPGD 274

Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L-cysteine from sulfate. The flavoprotein component catalyzes the electron flow from NADPH -> FAD -> FMN to the hemoprotein component.

Shigella sonnei (strain Ss046) (taxid: 300269)

EC: 1

EC: .

EC: 8

EC: .

EC: 1

EC: .

EC: 2

>sp|Q83QD9|CYSJ_SHIFL Sulfite reductase [NADPH] flavoprotein alpha-component OS=Shigella flexneri GN=cysJ PE=3 SV=3

 Score = 42.7 bits (99), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 64  VTGHKAHGPVPEPG-SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI 122
           V   K+  PV  P  SV    V ++ T   S D   V + SV +K +G   ++DVR  EI
Sbjct: 202 VDALKSRAPVAAPSQSVATGAVNEIHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEI 261

Query: 123 DKVDMHLSFRPGD 135
           D  D  L ++PGD
Sbjct: 262 DLGDSGLRYQPGD 274

Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L-cysteine from sulfate. The flavoprotein component catalyzes the electron flow from NADPH -> FAD -> FMN to the hemoprotein component.

Shigella flexneri (taxid: 623)

EC: 1

EC: .

EC: 8

EC: .

EC: 1

EC: .

EC: 2

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	146
255634132	189	unknown [Glycine max]	0.965	0.746	0.787	7e-58
224125764	199	predicted protein [Populus trichocarpa]	0.958	0.703	0.784	9e-58
255562013	593	conserved hypothetical protein [Ricinus	0.952	0.234	0.779	1e-57
357441291	1109	Ammonium transporter [Medicago truncatul	0.958	0.126	0.757	2e-57
363814479	197	uncharacterized protein LOC100796154 [Gl	0.965	0.715	0.780	5e-57
225430615	200	PREDICTED: exosome complex component CSL	0.986	0.72	0.75	6e-55
297805862	191	hypothetical protein ARALYDRAFT_494089 [	0.910	0.696	0.748	7e-52
9758066	145	unnamed protein product [Arabidopsis tha	0.924	0.931	0.737	3e-51
42568189	191	exosome complex component CSL4 [Arabidop	0.910	0.696	0.733	6e-51
449453260	196	PREDICTED: exosome complex component CSL	0.945	0.704	0.714	5e-50

>gi|255634132|gb|ACU17429.1| unknown [Glycine max]

 Score =  228 bits (580), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 111/141 (78%), Positives = 122/141 (86%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
           +E+E V+VTPGEVLG+ ++VKAG+GAY A HN  VYASLTG   T+ P PDS D RPTVE
Sbjct: 3   EEKEAVMVTPGEVLGRTSDVKAGRGAYAALHNNTVYASLTGFRHTVPPAPDSSDLRPTVE 62

Query: 64  VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID 123
           VTGHKAHGPVP+PGSVVIARVTKVM R ASADIMCVG KSVREKF+GIIRQQDVRATEID
Sbjct: 63  VTGHKAHGPVPQPGSVVIARVTKVMARSASADIMCVGPKSVREKFTGIIRQQDVRATEID 122

Query: 124 KVDMHLSFRPGDIVRASVVSF 144
           KVDMHLSF PGDIVRA V+S 
Sbjct: 123 KVDMHLSFHPGDIVRALVLSL 143

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224125764|ref|XP_002319669.1| predicted protein [Populus trichocarpa] gi|118483759|gb|ABK93772.1| unknown [Populus trichocarpa] gi|222858045|gb|EEE95592.1| predicted protein [Populus trichocarpa]

 Score =  228 bits (580), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 113/144 (78%), Positives = 124/144 (86%), Gaps = 4/144 (2%)

Query: 5   EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNG----LVYASLTGLLRTLSPPPDSPDQRP 60
           +EE  + TPGEVLGKATE+KAGKGAY+  +       V++SLTGL RTLSP PDSPDQRP
Sbjct: 2   QEEGEMATPGEVLGKATELKAGKGAYIGSYRDTDIQYVFSSLTGLRRTLSPSPDSPDQRP 61

Query: 61  TVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT 120
           TVEVTGHKAHG VPEPGSVVIARVTKVM + ASADIMCVG KSV+EKF+GIIRQQDVRAT
Sbjct: 62  TVEVTGHKAHGAVPEPGSVVIARVTKVMAKTASADIMCVGPKSVQEKFTGIIRQQDVRAT 121

Query: 121 EIDKVDMHLSFRPGDIVRASVVSF 144
           EIDKVDMHLSFRPGDIVRA V+S 
Sbjct: 122 EIDKVDMHLSFRPGDIVRALVLSL 145

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562013|ref|XP_002522015.1| conserved hypothetical protein [Ricinus communis] gi|223538819|gb|EEF40419.1| conserved hypothetical protein [Ricinus communis]

 Score =  227 bits (579), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 113/145 (77%), Positives = 125/145 (86%), Gaps = 6/145 (4%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNG----LVYASLTGLLRTLSPPPDSPDQR 59
           ++EEMV  TPGEVLGKA+E+KAGKGAYVA +       VY+SL+G LRTL+P PDSPDQR
Sbjct: 397 EKEEMV--TPGEVLGKASELKAGKGAYVAPYRNTDIFYVYSSLSGFLRTLAPTPDSPDQR 454

Query: 60  PTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRA 119
           PTVEVTG KA G VPE GSVVIARVTKVM +MASADIMCVG KSVREKF+G+IRQQDVRA
Sbjct: 455 PTVEVTGLKARGAVPEAGSVVIARVTKVMAKMASADIMCVGPKSVREKFTGLIRQQDVRA 514

Query: 120 TEIDKVDMHLSFRPGDIVRASVVSF 144
           TEIDKVDMHLSFRPGDIVRA V+S 
Sbjct: 515 TEIDKVDMHLSFRPGDIVRAVVLSL 539

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441291|ref|XP_003590923.1| Ammonium transporter [Medicago truncatula] gi|355479971|gb|AES61174.1| Ammonium transporter [Medicago truncatula]

 Score =  226 bits (576), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 106/140 (75%), Positives = 118/140 (84%)

Query: 5   EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEV 64
           E E  +VTPGEV+GK  +VKAG+G Y + HN  VYASLTG   T+ P  DSPDQRP VEV
Sbjct: 2   EAERDMVTPGEVIGKTHDVKAGRGTYTSTHNNTVYASLTGFRHTIPPASDSPDQRPIVEV 61

Query: 65  TGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDK 124
           TGHKAHGPVPEPGSVVI RVTKVMT++A ADIMCVG KSVREKF+G+IRQQDVRATEIDK
Sbjct: 62  TGHKAHGPVPEPGSVVIVRVTKVMTKIAEADIMCVGQKSVREKFTGVIRQQDVRATEIDK 121

Query: 125 VDMHLSFRPGDIVRASVVSF 144
           VDMHLSFRPGDIV+A V+S 
Sbjct: 122 VDMHLSFRPGDIVKALVLSL 141

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363814479|ref|NP_001242874.1| uncharacterized protein LOC100796154 [Glycine max] gi|255640712|gb|ACU20640.1| unknown [Glycine max]

 Score =  225 bits (573), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 110/141 (78%), Positives = 121/141 (85%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
           +E+E V+VTPGEVLG+ ++VKAG+GAY A HN  VYASLTG   T+ P PDS D RPTVE
Sbjct: 3   EEKEAVMVTPGEVLGRTSDVKAGRGAYAALHNNTVYASLTGFRHTVPPAPDSSDLRPTVE 62

Query: 64  VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID 123
           VTGHKAHGPVP+PGSVVIARVTKVM R ASADIMCVG KSVR KF+GIIRQQDVRATEID
Sbjct: 63  VTGHKAHGPVPQPGSVVIARVTKVMARSASADIMCVGPKSVRGKFTGIIRQQDVRATEID 122

Query: 124 KVDMHLSFRPGDIVRASVVSF 144
           KVDMHLSF PGDIVRA V+S 
Sbjct: 123 KVDMHLSFHPGDIVRALVLSL 143

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225430615|ref|XP_002266663.1| PREDICTED: exosome complex component CSL4 [Vitis vinifera] gi|296085148|emb|CBI28643.3| unnamed protein product [Vitis vinifera]

 Score =  218 bits (555), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 108/144 (75%), Positives = 118/144 (81%)

Query: 1   MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRP 60
           M  +EE   LVTPGEVLGK +++KAG+GAY    NG VYASLTG    + P P S DQRP
Sbjct: 1   MQEREEAEELVTPGEVLGKGSQLKAGRGAYFLPQNGTVYASLTGRRSLIPPSPLSSDQRP 60

Query: 61  TVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT 120
           TVEVTGH AHG +PEPGS+VIARVTKVM RMASADIMCVG KSVREKF+GIIRQQDVRAT
Sbjct: 61  TVEVTGHSAHGAIPEPGSIVIARVTKVMARMASADIMCVGPKSVREKFTGIIRQQDVRAT 120

Query: 121 EIDKVDMHLSFRPGDIVRASVVSF 144
           EIDKVDMH SFRPGDIVRA V+S 
Sbjct: 121 EIDKVDMHSSFRPGDIVRALVLSL 144

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297805862|ref|XP_002870815.1| hypothetical protein ARALYDRAFT_494089 [Arabidopsis lyrata subsp. lyrata] gi|297316651|gb|EFH47074.1| hypothetical protein ARALYDRAFT_494089 [Arabidopsis lyrata subsp. lyrata]

 Score =  208 bits (529), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 101/135 (74%), Positives = 116/135 (85%), Gaps = 2/135 (1%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
           LVTPG+V+GKATE KAGKGAYV  ++  +YASLTG  R +SP P+S DQR  VEVTGHKA
Sbjct: 5   LVTPGDVIGKATEFKAGKGAYV--NDTTIYASLTGTRRIVSPLPESLDQRAVVEVTGHKA 62

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHL 129
           HGP+PEPGSVVIARVTKVM RMA+ DI+CVG+K+VRE F+G+IRQQDVRATEIDKVDMH 
Sbjct: 63  HGPIPEPGSVVIARVTKVMARMAAVDILCVGSKAVRENFAGVIRQQDVRATEIDKVDMHQ 122

Query: 130 SFRPGDIVRASVVSF 144
           SFR GDIVRA V+S 
Sbjct: 123 SFRAGDIVRAMVLSL 137

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|9758066|dbj|BAB08645.1| unnamed protein product [Arabidopsis thaliana]

 Score =  206 bits (524), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 101/137 (73%), Positives = 116/137 (84%), Gaps = 2/137 (1%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
           LVTPG+V+GKATE KAGKGAYV  ++  +YASLTG  R +SP P+S DQR  VEVTGHKA
Sbjct: 5   LVTPGDVIGKATEFKAGKGAYV--NDATIYASLTGTCRIVSPLPESIDQRAIVEVTGHKA 62

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHL 129
           HGP+PE GSVVIARVTKVMT+MA+ DI+CVG+K+VRE F+G+IRQQDVRATEIDKVDMH 
Sbjct: 63  HGPIPETGSVVIARVTKVMTKMAAVDILCVGSKAVRENFAGVIRQQDVRATEIDKVDMHQ 122

Query: 130 SFRPGDIVRASVVSFML 146
           SF  GDIVRA VVS  L
Sbjct: 123 SFHAGDIVRAMVVSLRL 139

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42568189|ref|NP_568559.2| exosome complex component CSL4 [Arabidopsis thaliana] gi|124301132|gb|ABN04818.1| At5g38890 [Arabidopsis thaliana] gi|222423301|dbj|BAH19626.1| AT5G38890 [Arabidopsis thaliana] gi|332006986|gb|AED94369.1| exosome complex component CSL4 [Arabidopsis thaliana]

 Score =  205 bits (521), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 99/135 (73%), Positives = 115/135 (85%), Gaps = 2/135 (1%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
           LVTPG+V+GKATE KAGKGAYV  ++  +YASLTG  R +SP P+S DQR  VEVTGHKA
Sbjct: 5   LVTPGDVIGKATEFKAGKGAYV--NDATIYASLTGTCRIVSPLPESIDQRAIVEVTGHKA 62

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHL 129
           HGP+PE GSVVIARVTKVMT+MA+ DI+CVG+K+VRE F+G+IRQQDVRATEIDKVDMH 
Sbjct: 63  HGPIPETGSVVIARVTKVMTKMAAVDILCVGSKAVRENFAGVIRQQDVRATEIDKVDMHQ 122

Query: 130 SFRPGDIVRASVVSF 144
           SF  GDIVRA V+S 
Sbjct: 123 SFHAGDIVRAMVLSL 137

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449453260|ref|XP_004144376.1| PREDICTED: exosome complex component CSL4-like [Cucumis sativus] gi|449515303|ref|XP_004164689.1| PREDICTED: exosome complex component CSL4-like [Cucumis sativus]

 Score =  202 bits (513), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 100/140 (71%), Positives = 114/140 (81%), Gaps = 2/140 (1%)

Query: 5   EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEV 64
           E++   VTPGEVLG  ++ K G+GAYV   +  VYASL+G  R + PP DS D R TVEV
Sbjct: 5   EKDTEFVTPGEVLGNFSDFKPGRGAYVT--DNTVYASLSGFRRIIHPPSDSSDLRSTVEV 62

Query: 65  TGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDK 124
           TGHKAHG VP PGS+VI RVTKVMT+MASADIMCVG KSV+EKF+GIIRQQDVRATEIDK
Sbjct: 63  TGHKAHGAVPAPGSIVIVRVTKVMTKMASADIMCVGPKSVKEKFTGIIRQQDVRATEIDK 122

Query: 125 VDMHLSFRPGDIVRASVVSF 144
           VDMHLSFRPGDIV+A V+S 
Sbjct: 123 VDMHLSFRPGDIVKALVLSL 142

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	146
TAIR|locus:2152297	191	AT5G38890 [Arabidopsis thalian	0.904	0.691	0.738	4.7e-48
UNIPROTKB|G4ML19	213	MGG_08628 "3'-5' exoribonuclea	0.575	0.394	0.470	4.1e-21
DICTYBASE|DDB_G0285377	156	DDB_G0285377 "3'-5' exoribonuc	0.897	0.839	0.385	4.9e-21
ZFIN|ZDB-GENE-080926-3	194	exosc1 "exosome component 1" [	0.883	0.664	0.386	1.4e-18
UNIPROTKB|Q9Y3B2	195	EXOSC1 "Exosome complex compon	0.856	0.641	0.389	1.6e-17
FB|FBgn0032346	204	Csl4 "Csl4" [Drosophila melano	0.938	0.671	0.354	2e-17
UNIPROTKB|Q5E9E9	195	EXOSC1 "Uncharacterized protei	0.856	0.641	0.381	2e-17
UNIPROTKB|E2RT56	207	EXOSC1 "Uncharacterized protei	0.856	0.603	0.381	2.5e-17
MGI|MGI:1913833	195	Exosc1 "exosome component 1" [	0.856	0.641	0.389	2.5e-17
UNIPROTKB|F1S8Y4	196	EXOSC1 "Uncharacterized protei	0.856	0.637	0.378	2.9e-16

TAIR|locus:2152297 AT5G38890 [Arabidopsis thaliana (taxid:3702)]

 Score = 502 (181.8 bits), Expect = 4.7e-48, P = 4.7e-48
 Identities = 99/134 (73%), Positives = 115/134 (85%)

Query:    10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
             LVTPG+V+GKATE KAGKGAYV  ++  +YASLTG  R +SP P+S DQR  VEVTGHKA
Sbjct:     5 LVTPGDVIGKATEFKAGKGAYV--NDATIYASLTGTCRIVSPLPESIDQRAIVEVTGHKA 62

Query:    70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHL 129
             HGP+PE GSVVIARVTKVMT+MA+ DI+CVG+K+VRE F+G+IRQQDVRATEIDKVDMH 
Sbjct:    63 HGPIPETGSVVIARVTKVMTKMAAVDILCVGSKAVRENFAGVIRQQDVRATEIDKVDMHQ 122

Query:   130 SFRPGDIVRASVVS 143
             SF  GDIVRA V+S
Sbjct:   123 SFHAGDIVRAMVLS 136

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0006626 "protein targeting to mitochondrion" evidence=RCA

UNIPROTKB|G4ML19 MGG_08628 "3'-5' exoribonuclease CSL4" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 177 (67.4 bits), Expect = 4.1e-21, Sum P(2) = 4.1e-21
 Identities = 40/85 (47%), Positives = 55/85 (64%)

Query:    60 PTVEVTGHK-AHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVR 118
             PT+ V   + A   +PE G VV+ RVT+V  + A   I+ VG   +  ++ G+IR +DVR
Sbjct:    76 PTISVQRRRRAAAALPEVGDVVLCRVTRVSHQQAIVAILVVGDAVLDAEWQGVIRVRDVR 135

Query:   119 ATEIDKVDMHLSFRPGDIVRASVVS 143
             ATE D+V +  SFRPGDIVRA V+S
Sbjct:   136 ATEKDRVKIGESFRPGDIVRAQVIS 160

GO:0005575 "cellular_component" evidence=ND

GO:0009405 "pathogenesis" evidence=IMP

DICTYBASE|DDB_G0285377 DDB_G0285377 "3'-5' exoribonuclease CSL4 homolog" [Dictyostelium discoideum (taxid:44689)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 57/148 (38%), Positives = 88/148 (59%)

Query:    10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQ----------- 58
             ++TPG+ L K ++  + +G YV  H G +Y+S+ G    +    D+ ++           
Sbjct:     9 IITPGQRLCKESDFISSEGTYV--HKGYIYSSVLGFKHVIKRNIDTTNENNVNNSNNSNE 66

Query:    59 ----RPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQ 114
                 +  + V   K    VPE GS+V  +V ++  ++AS  I+CVG K+++E F+GIIR 
Sbjct:    67 IENNKDYIVVLKEKEPSVVPEIGSIVTVQVLRINPKLASVAILCVGTKALKETFNGIIRI 126

Query:   115 QDVRATEIDKVDMHLSFRPGDIVRASVV 142
             QDVRATEIDKV+++ SFRPGDIV A +V
Sbjct:   127 QDVRATEIDKVEIYKSFRPGDIVLAQIV 154

GO:0003723 "RNA binding" evidence=IEA

GO:0000178 "exosome (RNase complex)" evidence=IEA

ZFIN|ZDB-GENE-080926-3 exosc1 "exosome component 1" [Danio rerio (taxid:7955)]

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 53/137 (38%), Positives = 80/137 (58%)

Query:     8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTG-LLRTLSPPPDSPDQRPTVEVTG 66
             M L  PGE L    +   G G Y+ +H G ++ASL G +LR      +  ++ P + V  
Sbjct:     4 MKLCVPGERLCSTEDCIPGTGTYL-RH-GYIFASLAGYVLRK-----NEGEELPVISVVR 56

Query:    67 HKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVD 126
                   +P+ G++V  +VT +  R A   I+ VG+  ++++F G IR++DVRATE DKV+
Sbjct:    57 ETEAQLLPDVGAIVTCKVTSINPRFAKVHILYVGSTPLKDRFRGTIRREDVRATEKDKVE 116

Query:   127 MHLSFRPGDIVRASVVS 143
              + SFRPGDIV A V+S
Sbjct:   117 TYKSFRPGDIVLAKVIS 133

GO:0000178 "exosome (RNase complex)" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=ISS

UNIPROTKB|Q9Y3B2 EXOSC1 "Exosome complex component CSL4" [Homo sapiens (taxid:9606)]

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 51/131 (38%), Positives = 73/131 (55%)

Query:    13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
             PGE L    E   G G Y  +H G +++SL G L   S         P V V        
Sbjct:    10 PGERLCNLEEGSPGSGTYT-RH-GYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 63

Query:    73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
             +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ SFR
Sbjct:    64 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFR 123

Query:   133 PGDIVRASVVS 143
             PGDIV A V+S
Sbjct:   124 PGDIVLAKVIS 134

GO:0006364 "rRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0005730 "nucleolus" evidence=IDA

GO:0000178 "exosome (RNase complex)" evidence=IDA;NAS

GO:0004532 "exoribonuclease activity" evidence=IDA

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0043928 "exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

FB|FBgn0032346 Csl4 "Csl4" [Drosophila melanogaster (taxid:7227)]

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 51/144 (35%), Positives = 79/144 (54%)

Query:     1 MVVKEEEMVLVTPGEVLGKATE-VKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQR 59
             M  +++E V+  PGE L +  + +  G G Y  + NG +YAS +G++       DS D+ 
Sbjct:     1 MSEQQDETVVCLPGERLCRTEDSIVLGIGTY--EQNGYIYASKSGIVNI----EDSGDKC 54

Query:    60 PTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRA 119
               V V     H  +P  G VV ARV     + A   I CV    +   + G++R++DVR 
Sbjct:    55 QVVSVHKPGFHLTIPATGDVVTARVLVTTPKFAKCAIFCVRNVLLESSYRGLLRKEDVRE 114

Query:   120 TEIDKVDMHLSFRPGDIVRASVVS 143
             TE D+VD++ SFRPGD++ A V++
Sbjct:   115 TEKDRVDIYKSFRPGDVILARVIN 138

GO:0006397 "mRNA processing" evidence=ISS

GO:0000177 "cytoplasmic exosome (RNase complex)" evidence=ISS

GO:0000175 "3'-5'-exoribonuclease activity" evidence=ISS

GO:0000176 "nuclear exosome (RNase complex)" evidence=ISS;IDA

GO:0035327 "transcriptionally active chromatin" evidence=IDA

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0010468 "regulation of gene expression" evidence=IMP

UNIPROTKB|Q5E9E9 EXOSC1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 50/131 (38%), Positives = 73/131 (55%)

Query:    13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
             PGE L    E   G G Y  +H G +++SL G L   S         P + V        
Sbjct:    10 PGERLCNLEEGSPGSGTYT-RH-GYIFSSLAGCLTKTS----ENGALPVISVMRETESQL 63

Query:    73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
             +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ SFR
Sbjct:    64 LPDVGAIVTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIRKEDVRATEKDKVEIYKSFR 123

Query:   133 PGDIVRASVVS 143
             PGDIV A V+S
Sbjct:   124 PGDIVLAKVIS 134

GO:0005730 "nucleolus" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0000178 "exosome (RNase complex)" evidence=IEA

UNIPROTKB|E2RT56 EXOSC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 212 (79.7 bits), Expect = 2.5e-17, P = 2.5e-17
 Identities = 50/131 (38%), Positives = 73/131 (55%)

Query:    13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
             PGE L    E   G G Y  +H G +++SL G L   S         P + V        
Sbjct:    22 PGERLCNLEEGSPGSGTYT-RH-GYIFSSLAGCLTKSS----ENGALPVISVMRETESQL 75

Query:    73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
             +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ SFR
Sbjct:    76 LPDVGTIVTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIRKEDVRATEKDKVEIYKSFR 135

Query:   133 PGDIVRASVVS 143
             PGDIV A V+S
Sbjct:   136 PGDIVLAKVIS 146

GO:0003723 "RNA binding" evidence=IEA

GO:0000178 "exosome (RNase complex)" evidence=IEA

MGI|MGI:1913833 Exosc1 "exosome component 1" [Mus musculus (taxid:10090)]

 Score = 212 (79.7 bits), Expect = 2.5e-17, P = 2.5e-17
 Identities = 51/131 (38%), Positives = 73/131 (55%)

Query:    13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
             PGE L    E   G G Y  +H G +++SL G L   S         P V V        
Sbjct:    10 PGERLCNLEEGSPGSGTYT-RH-GYIFSSLAGCLMKTS----ENGAVPVVSVMRETESQL 63

Query:    73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
             +P+ G+VV  +V+ + +R A   I+ VG+  ++  F G IR++D+RATE DKV+++ SFR
Sbjct:    64 LPDVGAVVTCKVSSINSRFAKVHILYVGSTPLKNAFRGTIRKEDIRATEKDKVEIYKSFR 123

Query:   133 PGDIVRASVVS 143
             PGDIV A V+S
Sbjct:   124 PGDIVLAKVIS 134

GO:0000178 "exosome (RNase complex)" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0006396 "RNA processing" evidence=ISO

UNIPROTKB|F1S8Y4 EXOSC1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 202 (76.2 bits), Expect = 2.9e-16, P = 2.9e-16
 Identities = 50/132 (37%), Positives = 73/132 (55%)

Query:    13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
             PGE L    E   G G Y  +H G +++SL G L   S         P + V        
Sbjct:    10 PGERLCNLEEGSPGSGTYT-RH-GYIFSSLAGCLTKSS----ENGALPVISVMRETDSQL 63

Query:    73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQ-QDVRATEIDKVDMHLSF 131
             +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR+ +DVRATE DKV+++ SF
Sbjct:    64 LPDVGAIVTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIRRKEDVRATEKDKVEIYKSF 123

Query:   132 RPGDIVRASVVS 143
             RPGDIV A V+S
Sbjct:   124 RPGDIVLAKVIS 135

GO:0005730 "nucleolus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000178 "exosome (RNase complex)" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	grail3.0016041401	SubName- Full=Putative uncharacterized protein; (199 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	estExt_fgenesh4_pm.C_LG_XIV0164	hypothetical protein (241 aa)			•	•	•	•	•		0.950
	eugene3.00031704	hypothetical protein (320 aa)			•	•	•	•	•		0.926
	estExt_Genewise1_v1.C_LG_XII0359	SubName- Full=Putative uncharacterized protein; (242 aa)				•	•	•	•		0.901
	estExt_fgenesh4_pm.C_LG_XIV0472	hypothetical protein (288 aa)			•	•	•	•	•		0.882
	estExt_fgenesh4_pg.C_LG_III0702	hypothetical protein (935 aa)				•	•	•	•		0.793
	gw1.I.838.1	hypothetical protein (302 aa)			•	•	•	•	•		0.735
	gw1.IX.3706.1	annotation not avaliable (298 aa)			•	•	•	•	•		0.730
	gw1.XVIII.1197.1	hypothetical protein (232 aa)				•	•	•	•		0.671
	eugene3.00060466	hypothetical protein (318 aa)			•	•	•	•	•		0.644
	estExt_Genewise1_v1.C_LG_XVIII2468	hypothetical protein (213 aa)	•								0.638

---

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	146
pfam10447	72	pfam10447, EXOSC1, Exosome component EXOSC1/CSL4	4e-32
cd05791	92	cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-bindi	1e-29
COG1096	188	COG1096, COG1096, Predicted RNA-binding protein (c	6e-15
PRK09521	189	PRK09521, PRK09521, exosome complex RNA-binding pr	3e-11
pfam14382	39	pfam14382, ECR1_N, Exosome complex exonuclease RRP	6e-09
PRK04163	235	PRK04163, PRK04163, exosome complex RNA-binding pr	2e-06
cd04454	82	cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1	5e-06
COG1097	239	COG1097, RRP4, RNA-binding protein Rrp4 and relate	6e-05

>gnl|CDD|192591 pfam10447, EXOSC1, Exosome component EXOSC1/CSL4

 Score =  108 bits (272), Expect = 4e-32
 Identities = 39/71 (54%), Positives = 54/71 (76%)

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
           +P+ G +V+ARVT+V  R A  +I+ VG  +++E F GIIR+QDVRATE D+V ++  FR
Sbjct: 1   LPKVGDIVLARVTRVTPRQAYCEILAVGGTALKETFKGIIRKQDVRATEKDRVKIYECFR 60

Query: 133 PGDIVRASVVS 143
           PGDIVRA V+S
Sbjct: 61  PGDIVRAKVIS 71

This family of proteins are components of the exosome 3'->5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions. Length = 72

>gnl|CDD|240217 cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-binding domain

 Score =  102 bits (257), Expect = 1e-29
 Identities = 41/72 (56%), Positives = 57/72 (79%)

Query: 72  PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSF 131
            +P+ GS+VIARVT++  R A  DI+CVG + ++E F G+IR++D+RATE DKV+M+  F
Sbjct: 2   VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCF 61

Query: 132 RPGDIVRASVVS 143
           RPGDIVRA V+S
Sbjct: 62  RPGDIVRAKVIS 73

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". Length = 92

>gnl|CDD|224021 COG1096, COG1096, Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

 Score = 67.7 bits (166), Expect = 6e-15
 Identities = 44/144 (30%), Positives = 65/144 (45%), Gaps = 13/144 (9%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
             ++   V PG+VL    E   G+G Y     G + A+ TG++R      D  D+   + 
Sbjct: 1   MVKDGTFVLPGDVLAVIEEFLPGEGTYE--EGGEIRAAATGVVR-----RD--DKNRVIS 51

Query: 64  VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREK--FSGIIRQQDVRATE 121
           V   K   P+P+ G +V  RVT V  + A   I+ V  K        +  I    VR   
Sbjct: 52  VKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGY 111

Query: 122 IDKVDMHLSFRPGDIVRASVVSFM 145
           ++K+    +FR GDIVRA V+S  
Sbjct: 112 VEKLSD--AFRIGDIVRARVISTG 133

Length = 188

>gnl|CDD|236547 PRK09521, PRK09521, exosome complex RNA-binding protein Csl4; Provisional

 Score = 57.7 bits (140), Expect = 3e-11
 Identities = 39/145 (26%), Positives = 60/145 (41%), Gaps = 15/145 (10%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
             ++  LV PG+ L    E   G+G Y    NG VYAS+ G +          D    + 
Sbjct: 1   MVKQGDLVLPGDYLAVIEEYLPGEGTYE--DNGEVYASVVGKVFI-------DDINRKIS 51

Query: 64  VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCV--GAKSVREKFSGIIRQQDVRATE 121
           V   K   P+ + G +V  RV  V  + A   I+ +    + +       I    V    
Sbjct: 52  VIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGY 111

Query: 122 IDKV-DMHLSFRPGDIVRASVVSFM 145
           ++ + D    F+ GDIVRA V+S+ 
Sbjct: 112 VESLTDA---FKIGDIVRAKVISYT 133

Length = 189

>gnl|CDD|206550 pfam14382, ECR1_N, Exosome complex exonuclease RRP4 N-terminal region

 Score = 48.5 bits (117), Expect = 6e-09
 Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 2/39 (5%)

Query: 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRT 48
          +V PGE LG A+E   G G YV   +G +YAS+ G++  
Sbjct: 1  IVVPGERLGTASEYMPGHGTYV--EDGNIYASVAGVVSI 37

ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology. Length = 39

>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4; Provisional

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 35/146 (23%), Positives = 61/146 (41%), Gaps = 23/146 (15%)

Query: 1   MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRP 60
           M +  E+  +V PG++L +  E KAG+G Y    NG +Y+++ GL+          D+  
Sbjct: 1   MKIFVEDRKIVVPGDLLAEG-EFKAGRGTYKE--NGKIYSTVVGLVD------IKDDKVR 51

Query: 61  TVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV--R 118
            + + G      +P+ G +VI +VT V       DI           +   +   +V  R
Sbjct: 52  VIPLEGKY----IPKVGDLVIGKVTDVTFSGWEVDI--------NSPYKAYLPVSEVLGR 99

Query: 119 ATEIDKVDMHLSFRPGDIVRASVVSF 144
              ++  D+      GD + A V   
Sbjct: 100 PVNVEGTDLRKYLDIGDYIIAKVKDV 125

Length = 235

>gnl|CDD|239901 cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain

 Score = 42.2 bits (99), Expect = 5e-06
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 10/71 (14%)

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
           +P+ G +VI  VT+V +R    DI+            G  R +D  ATE DK ++  S +
Sbjct: 3   LPDVGDIVIGIVTEVNSRFWKVDIL----------SRGTARLEDSSATEKDKKEIRKSLQ 52

Query: 133 PGDIVRASVVS 143
           PGD++ A V+S
Sbjct: 53  PGDLILAKVIS 63

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". Length = 82

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

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 33/137 (24%), Positives = 52/137 (37%), Gaps = 22/137 (16%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
           +V PG+++      K G G Y     G +Y+S+ GLL               + + G   
Sbjct: 10  IVLPGDLVLAEGSYKLGHGTYF--EGGKIYSSVVGLLDV------KGKLVRVIPLEGRY- 60

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV--RATEIDKVDM 127
              +PE G VVI ++ +V       DI           +  ++   D   R  E  + D+
Sbjct: 61  ---IPEVGDVVIGKIIEVGPSGWKVDI--------GSPYPALLSLSDFLRRKFENAEKDL 109

Query: 128 HLSFRPGDIVRASVVSF 144
                 GD+V A VV  
Sbjct: 110 RPFLNVGDLVYAKVVDV 126

Length = 239

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	146
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	100.0
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	99.97
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	99.97
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	99.96
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	99.95
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	99.93
KOG3013	301	consensus Exosomal 3'-5' exoribonuclease complex,	99.92
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	99.91
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.56
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	99.54
PF14382	39	ECR1_N: Exosome complex exonuclease RRP4 N-termina	99.48
KOG1004	230	consensus Exosomal 3'-5' exoribonuclease complex s	99.43
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.38
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.11
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	99.1
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.1
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.06
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.01
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.0
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.98
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.93
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.93
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	98.88
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.85
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	98.84
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.84
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.83
PRK08582	139	hypothetical protein; Provisional	98.8
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	98.79
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.78
PRK07252	120	hypothetical protein; Provisional	98.76
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.75
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.74
PRK08059	123	general stress protein 13; Validated	98.73
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.69
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	98.69
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.68
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.68
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	98.67
PRK05807	136	hypothetical protein; Provisional	98.67
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.61
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.57
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	98.56
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	98.56
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	98.5
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.5
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.45
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	98.42
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.4
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.38
PRK07400	318	30S ribosomal protein S1; Reviewed	98.35
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	98.34
PHA02945	88	interferon resistance protein; Provisional	98.34
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.29
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.28
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.27
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.22
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.19
PRK07400	318	30S ribosomal protein S1; Reviewed	98.16
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.11
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	98.09
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	98.08
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	97.99
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	97.99
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	97.95
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	97.94
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	97.94
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	97.93
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	97.91
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	97.9
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	97.88
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	97.87
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	97.84
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.84
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	97.82
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	97.81
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	97.77
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	97.75
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	97.68
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	97.61
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	97.55
COG2183	780	Tex Transcriptional accessory protein [Transcripti	97.49
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.37
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.34
PRK09202	470	nusA transcription elongation factor NusA; Validat	97.3
PRK12327	362	nusA transcription elongation factor NusA; Provisi	97.08
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.06
TIGR01953	341	NusA transcription termination factor NusA. This m	96.94
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.64
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	96.26
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	96.23
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	96.15
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.09
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.83
PRK11642	813	exoribonuclease R; Provisional	95.47
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	95.27
PRK11712	489	ribonuclease G; Provisional	95.01
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	94.91
PRK10811	1068	rne ribonuclease E; Reviewed	94.91
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	94.87
PF01016	81	Ribosomal_L27: Ribosomal L27 protein; InterPro: IP	94.46
CHL00121	86	rpl27 ribosomal protein L27; Reviewed	94.0
PRK05435	82	rpmA 50S ribosomal protein L27; Validated	93.87
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	93.63
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	90.91
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	90.88
TIGR00062	83	L27 ribosomal protein L27. Eubacterial, chloroplas	90.86
PF01959	354	DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); Inte	90.02
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	89.8
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	89.29
PRK02290	344	3-dehydroquinate synthase; Provisional	88.92
KOG4600	144	consensus Mitochondrial ribosomal protein MRP7 (L2	87.88
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	86.37
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	85.54
KOG2916	304	consensus Translation initiation factor 2, alpha s	84.08
PRK05054	644	exoribonuclease II; Provisional	83.68

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

Probab=100.00  E-value=2.2e-33  Score=214.24  Aligned_cols=129  Identities=32%  Similarity=0.471  Sum_probs=121.9

Q ss_pred             cCCcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 032149            6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT   85 (146)
Q Consensus         6 ~~~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~   85 (146)
                      +++++|+|||.|+.+|||++|.|||+.  +|.|+|+.+|.+.+       |+++..++|.|.+..+.+|+.||+|+|+|+
T Consensus         3 ~~g~~v~PGd~~a~~EE~~~G~gt~~~--~g~i~Aa~~G~~~~-------d~~n~~~~V~p~~~~~~~~K~GdiV~grV~   73 (188)
T COG1096           3 KDGTFVLPGDVLAVIEEFLPGEGTYEE--GGEIRAAATGVVRR-------DDKNRVISVKPGKKTPPLPKGGDIVYGRVT   73 (188)
T ss_pred             ccCcEEcCcceeeeeeeeecCCCeEeE--CCEEEEeecccEEE-------cccceEEEeccCCCCCCCCCCCCEEEEEEe
Confidence            468999999999999999999999999  99999999999999       567889999999877999999999999999


Q ss_pred             EEecceEEEEEEeecc--cccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           86 KVMTRMASADIMCVGA--KSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        86 ~v~~~~~~v~I~~v~~--~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +++.+.|.|+|.++++  +.+.+++.|.||+|+++..+..  +++++|++||+|+|+|+|++
T Consensus        74 ~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~--~~~d~f~~GDivrA~Vis~~  133 (188)
T COG1096          74 DVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVE--KLSDAFRIGDIVRARVISTG  133 (188)
T ss_pred             eccceEEEEEEEEEecccccCCCCceeeEEEEeccccccc--ccccccccccEEEEEEEecC
Confidence            9999999999999999  4588899999999999999988  89999999999999999975

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

Probab=99.97  E-value=1.1e-31  Score=202.27  Aligned_cols=132  Identities=42%  Similarity=0.635  Sum_probs=115.6

Q ss_pred             CcEEecCCccCCCC-CeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 032149            8 MVLVTPGEVLGKAT-EVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK   86 (146)
Q Consensus         8 ~~iV~PGd~l~~~~-~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~   86 (146)
                      ..+++|||++|..+ ++..|.|||+.  +|.|+||.+|...++.    ..+++++.++........+|..||||+++|++
T Consensus         5 ~~~~lpG~~~c~~e~~~~~g~Gtye~--~~yI~aS~ag~~~~~~----~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~   78 (193)
T KOG3409|consen    5 ETLVLPGEVVCRAEGEYRMGEGTYER--NGYIFASVAGVNFRDN----LVQKIEVVSVEKQLFNELLPFVGAIVTARVSR   78 (193)
T ss_pred             eEEEcccceeeecccccccccceeec--CCeEEeccccceeecC----CccceeeeeecccchhhcCCccCcEEEEEEEe
Confidence            57999999999876 49999999999  9999999999554421    13334455555443467899999999999999


Q ss_pred             EecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           87 VMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        87 v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++.++|.|+|+++++.+|...|+|+||++|+|++++|++++..+|+|||+|+|+|+|++
T Consensus        79 i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~  137 (193)
T KOG3409|consen   79 INLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLG  137 (193)
T ss_pred             eccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecC
Confidence            99999999999999999999999999999999999999999999999999999999965

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=99.97  E-value=1.1e-30  Score=201.44  Aligned_cols=128  Identities=30%  Similarity=0.439  Sum_probs=117.2

Q ss_pred             CCcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 032149            7 EMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK   86 (146)
Q Consensus         7 ~~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~   86 (146)
                      .+++|+|||.|+..++|++|+|||++  +|.||||++|.+++       |..++.|+|.|.....+.|++||+|+|+|++
T Consensus         4 ~~~~V~PGe~l~~~~e~~~G~Gty~~--~~~i~as~~G~~~i-------d~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~   74 (189)
T PRK09521          4 QGDLVLPGDYLAVIEEYLPGEGTYED--NGEVYASVVGKVFI-------DDINRKISVIPFKKTPPLLKKGDIVYGRVVD   74 (189)
T ss_pred             cCCEECCCCccccccceEcCCCEEee--CCEEEEEeeEEEEE-------cCCCCEEEEecCcCCCCCCCCCCEEEEEEEE
Confidence            46799999999998999999999999  99999999999999       3346799999987668999999999999999


Q ss_pred             EecceEEEEEEeec--ccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           87 VMTRMASADIMCVG--AKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        87 v~~~~~~v~I~~v~--~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +.++.|+|+|.+++  +++++.++.|++|.+|++..+.+  +|.++|++||+|+|+|+++.
T Consensus        75 i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~--~~~~~~~~GD~V~akV~~i~  133 (189)
T PRK09521         75 VKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVE--SLTDAFKIGDIVRAKVISYT  133 (189)
T ss_pred             EcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhh--hHHhccCCCCEEEEEEEecC
Confidence            99999999999887  67788889999999999877666  89999999999999999873

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=99.96  E-value=4.5e-29  Score=198.55  Aligned_cols=117  Identities=27%  Similarity=0.451  Sum_probs=106.5

Q ss_pred             CcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEE
Q 032149            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV   87 (146)
Q Consensus         8 ~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v   87 (146)
                      +++|+|||.|+ .++|.+|+|||++  +|.|+||++|.+...         ++.++|.|.++ +|+|++||+|+|+|+++
T Consensus         8 ~~~V~PGd~l~-~~~~~~G~Gty~~--~g~i~As~~G~~~~~---------~~~i~V~p~~~-~y~P~vGDiViG~V~~i   74 (235)
T PRK04163          8 RKIVVPGDLLA-EGEFKAGRGTYKE--NGKIYSTVVGLVDIK---------DDKVRVIPLEG-KYIPKVGDLVIGKVTDV   74 (235)
T ss_pred             CcEECCCCCcC-cCCeecCCceEEe--CCEEEEEEeEEEEEE---------CCEEEEEECCC-cccCCCCCEEEEEEEEE
Confidence            58999999997 5889999999999  999999999999984         25999999875 59999999999999999


Q ss_pred             ecceEEEEEEeecccccccceeeEEeccccccccc--cccccccCCCCCCEEEEEEEEee
Q 032149           88 MTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        88 ~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~--d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +++.|+|+|        ..++.|+||.++++..+.  |+.+|+++|++||+|+|||+++.
T Consensus        75 ~~~~~~vdI--------~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~  126 (235)
T PRK04163         75 TFSGWEVDI--------NSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVD  126 (235)
T ss_pred             eCceEEEEe--------CCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEEC
Confidence            999999999        678999999999986643  66799999999999999999874

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

Probab=99.95  E-value=9.3e-28  Score=189.66  Aligned_cols=120  Identities=28%  Similarity=0.415  Sum_probs=109.4

Q ss_pred             cCCcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 032149            6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT   85 (146)
Q Consensus         6 ~~~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~   85 (146)
                      ..+++|+|||.|...+.+..|+|||..  +++||||++|.+++.         ++.+.|.|+++ +|+|++||+|||+|+
T Consensus         6 ~~~~iV~PGd~vl~~~~~~~G~Gty~~--~~~iyssv~G~~~~~---------~~~v~VIpl~g-~YiP~~gD~VIG~I~   73 (239)
T COG1097           6 SMRKIVLPGDLVLAEGSYKLGHGTYFE--GGKIYSSVVGLLDVK---------GKLVRVIPLEG-RYIPEVGDVVIGKII   73 (239)
T ss_pred             cccceecCCCccCCCCCEecCCCcEec--CCEEEEEEEeEEEEe---------CCEEEEEeCCC-cccCCCCCEEEEEEE
Confidence            457999999977777899999999998  999999999999995         46899999975 999999999999999


Q ss_pred             EEecceEEEEEEeecccccccceeeEEecccc--ccccccccccccCCCCCCEEEEEEEEee
Q 032149           86 KVMTRMASADIMCVGAKSVREKFSGIIRQQDV--RATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        86 ~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi--~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .+.++.|.|||        +++|.++|+.|++  |..+.++.+|+++|++||+|+|||.+++
T Consensus        74 ~v~~~~W~VDI--------~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd  127 (239)
T COG1097          74 EVGPSGWKVDI--------GSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVD  127 (239)
T ss_pred             EEcccceEEEc--------CCccceEeehhhhhcccccccccccccccccCCEEEEEEEEcc
Confidence            99999999999        8999999999999  3445557799999999999999999875

>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=99.93  E-value=1.1e-25  Score=152.74  Aligned_cols=72  Identities=60%  Similarity=0.955  Sum_probs=52.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEee----------cccccccceeeEEeccccccccccccccccCCCCCCEEEEEEE
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCV----------GAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVV  142 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v----------~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vi  142 (146)
                      +|++||+|+|+|+++++++|.|+|+++          .+.++..+|+|+||++|+|+++.|+++|.+||+|||+|+|+|+
T Consensus         1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi   80 (82)
T PF10447_consen    1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI   80 (82)
T ss_dssp             ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred             CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence            599999999999999999999999999          6778889999999999999999999999999999999999999


Q ss_pred             Ee
Q 032149          143 SF  144 (146)
Q Consensus       143 s~  144 (146)
                      |+
T Consensus        81 Sl   82 (82)
T PF10447_consen   81 SL   82 (82)
T ss_dssp             EE
T ss_pred             eC
Confidence            96

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.

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

Probab=99.92  E-value=9.3e-26  Score=179.38  Aligned_cols=123  Identities=28%  Similarity=0.487  Sum_probs=108.1

Q ss_pred             CCcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 032149            7 EMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK   86 (146)
Q Consensus         7 ~~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~   86 (146)
                      ..++|+||+.+...+.|+.|+|||..  ||.|+||++|.+++.         |+.++|+|++ .+|.|++||+|.|||+.
T Consensus        28 ~~~ivtPG~~V~~d~~fmRGHGTy~~--d~~i~ssvaG~v~rv---------NkLi~V~plk-~rY~pEvGDvVVgRV~e   95 (301)
T KOG3013|consen   28 HSTIVTPGELVTDDPGFMRGHGTYVR--DGEIYSSVAGVVQRV---------NKLISVKPLK-SRYAPEVGDVVVGRVIE   95 (301)
T ss_pred             CceeecCCccccCchhhhhcccceec--CCeEEEeecchhhhh---------cceEEEeehh-hhcCCccCCEEEEEeee
Confidence            46799999999998899999999999  999999999999885         5899999997 78999999999999999


Q ss_pred             EecceEEEEEEeeccccccc---cee-eEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           87 VMTRMASADIMCVGAKSVRE---KFS-GIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        87 v~~~~~~v~I~~v~~~~l~~---~~~-g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |.+++|+|++.+-.++.|..   ... |++|    |..+.|+..|+++|+.||+|.|+|++++
T Consensus        96 Vq~KRWkvd~nsk~d~vL~LsSvNLPGg~~R----Rk~~~DEl~MR~fl~egDLi~AEVQ~v~  154 (301)
T KOG3013|consen   96 VQQKRWKVDLNSKQDAVLMLSSVNLPGGIQR----RKSEEDELQMRSFLKEGDLIVAEVQNVF  154 (301)
T ss_pred             eecceeEEecccccceEEEeecccCCchhhh----ccchhhHHHHHHHhhccCeehHHHHHhc
Confidence            99999999998777765543   223 3443    6778899999999999999999998764

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

Probab=99.91  E-value=4.4e-24  Score=147.73  Aligned_cols=74  Identities=55%  Similarity=0.947  Sum_probs=72.3

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+|++||+|+|+|++++.++|.|+|+++++++++++|+|+||+||+++++.++.+|++||++||+|+|||+|++
T Consensus         2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~   75 (92)
T cd05791           2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLG   75 (92)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999986

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".

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

Probab=99.56  E-value=2e-14  Score=96.49  Aligned_cols=65  Identities=26%  Similarity=0.442  Sum_probs=58.9

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +|+|++||+|+|+|+++.++.|+|+|        ...++|++|.+++...+..  ++.+.|++||+|+|+|+++.
T Consensus         1 ~y~p~~GdiV~G~V~~v~~~~~~V~i--------~~~~~g~l~~~~~~~~~~~--~~~~~~~~GD~i~~~V~~~~   65 (82)
T cd04454           1 RYLPDVGDIVIGIVTEVNSRFWKVDI--------LSRGTARLEDSSATEKDKK--EIRKSLQPGDLILAKVISLG   65 (82)
T ss_pred             CCCCCCCCEEEEEEEEEcCCEEEEEe--------CCCceEEeechhccCcchH--HHHhcCCCCCEEEEEEEEeC
Confidence            48999999999999999999999999        6779999999999765444  89999999999999999874

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".

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

Probab=99.54  E-value=2.9e-14  Score=97.54  Aligned_cols=64  Identities=22%  Similarity=0.181  Sum_probs=55.4

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +|+|++||+|+|+|+++..+.|+|+|        ++++.|+|+.+++...   ..++++.|++||+|+|||.++.
T Consensus         1 rY~P~~gD~VIG~V~~~~~~~~~VdI--------~s~~~a~L~~~~f~ga---tk~~rp~L~~GDlV~ArV~~~~   64 (86)
T cd05790           1 RYVPAKGDHVIGIVVAKAGDFFKVDI--------GGSEPASLSYLAFEGA---TKRNRPNLNVGDLVYARVVKAN   64 (86)
T ss_pred             CCcCCCCCEEEEEEEEEcCCeEEEEc--------CCCcceEechHHcccc---cccccccCCCCCEEEEEEEecC
Confidence            59999999999999999999999999        7888999998765321   2267999999999999998863

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".

>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C

Probab=99.48  E-value=2.5e-14  Score=84.21  Aligned_cols=38  Identities=39%  Similarity=0.773  Sum_probs=34.1

Q ss_pred             EEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEc
Q 032149           10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTL   49 (146)
Q Consensus        10 iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~   49 (146)
                      +|+|||+|+.+++|++|+|||++  +|+||||++|.+++.
T Consensus         1 iV~PG~~l~~~~e~~~G~GTY~~--~g~I~asv~G~v~~~   38 (39)
T PF14382_consen    1 IVVPGDRLGSSEEYMPGHGTYVR--DGNIYASVAGTVKID   38 (39)
T ss_dssp             EE-TT-EEEETTTSEESTTEEEE--TTEEEESSSEEEEEE
T ss_pred             CCCCCCEeecCCCEecCCCEEEe--CCEEEEEeeEEEEEc
Confidence            69999999999999999999999  999999999999873

>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]

Probab=99.43  E-value=2.5e-12  Score=100.27  Aligned_cols=118  Identities=23%  Similarity=0.249  Sum_probs=89.0

Q ss_pred             cEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 032149            9 VLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK   86 (146)
Q Consensus         9 ~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~   86 (146)
                      ++.+|||.+..  +.+-.+|+|.+.+  ++.+.++.+|.+...++-   ....++.+|... +++|+|.+||.|||+|+.
T Consensus         2 ~~~~pg~~~~~~~~~sv~~G~g~~~~--g~~~~~~~~G~~~~~~~g---k~~~~v~~vds~-~kRYiP~~~D~VIGiV~~   75 (230)
T KOG1004|consen    2 TFYFPGDSIPRPRLCSVVLGPGLRRR--GQERLVTKCGRLRHKEPG---KGGGGVYWVDSQ-QKRYIPVKGDHVIGIVTS   75 (230)
T ss_pred             ceecCCcccccCccCceeecCCcccc--CceEEeccccceeeccCC---cccceeEEEecc-cceecCCCCCEEEEEEEe
Confidence            57899998764  3458999999998  999999999988775410   111225677764 689999999999999999


Q ss_pred             EecceEEEEEEeecccccc-cceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           87 VMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        87 v~~~~~~v~I~~v~~~~l~-~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      -..+.++|||..-+-+.|+ ..|+|.        +.    .-++.|..||+|+|||...
T Consensus        76 ~~gd~ykVDigg~~~a~L~~laFe~A--------tk----rNrPnl~vGdliyakv~~a  122 (230)
T KOG1004|consen   76 KSGDIYKVDIGGSEPASLSYLAFEGA--------TK----RNRPNLQVGDLIYAKVVDA  122 (230)
T ss_pred             ccCceEEEecCCCCeeeeeeccccCc--------cc----cCCCccccccEEEEEEEec
Confidence            9999999999543333333 234442        22    4489999999999999864

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

Probab=99.38  E-value=2.1e-12  Score=87.17  Aligned_cols=67  Identities=30%  Similarity=0.441  Sum_probs=57.6

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccc--cccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT--EIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~--~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +|.|++||+|.|+|+++.++.|+|+|        ...+.|+||.+|+...  .....++.+.|++||.|.|+|+++.
T Consensus         1 ~y~p~~GdiV~g~V~~i~~~g~~v~i--------~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~   69 (86)
T cd05789           1 RYIPEVGDVVIGRVTEVGFKRWKVDI--------NSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVD   69 (86)
T ss_pred             CCcCCCCCEEEEEEEEECCCEEEEEC--------CCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEEC
Confidence            48899999999999999999999999        6789999999998631  1122378899999999999999874

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".

>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=99.11  E-value=3.2e-10  Score=74.59  Aligned_cols=61  Identities=25%  Similarity=0.378  Sum_probs=54.2

Q ss_pred             CCCCEEEEEEEEEec-ceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           75 EPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        75 ~~GdiViG~V~~v~~-~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++|++|.|+|+++.+ ..+++++        .....|++|++|++..+..  ++.+.|++||+|+|+|+++.
T Consensus         2 ~~G~iv~G~V~~i~~~~g~~v~l--------~~~~~Glvhis~~s~~~~~--~~~~~~~~Gd~v~~kV~~~~   63 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQL--------PFGKTGLVSIFHLSDSYTE--NPLEGFKPGKIVRCCILSKK   63 (72)
T ss_pred             CCCCEEEEEEEEeeCCcEEEEEC--------CCCCEEEEEHHHhcCcccC--CHHHhCCCCCEEEEEEEEec
Confidence            689999999999987 5899998        6789999999999877666  67899999999999999874

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

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

Probab=99.10  E-value=5e-10  Score=72.93  Aligned_cols=61  Identities=21%  Similarity=0.263  Sum_probs=53.4

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |++|.|+|+++.++.++|++        ...+.|.+|.++++..+.+..++.++|++||.|+|+|+++.
T Consensus         1 G~iV~g~V~~i~~~gi~v~l--------~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d   61 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQL--------ADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGH   61 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEe--------CCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEe
Confidence            89999999999999999998        57799999999998654223378999999999999999874

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=99.10  E-value=5.2e-10  Score=72.44  Aligned_cols=59  Identities=25%  Similarity=0.271  Sum_probs=53.4

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ||+|.|+|+++.++.|+|++        ...+.|++|.+++...+.+  ++.++|++||.++|+|+++.
T Consensus         1 G~iv~g~V~~i~~~~~~v~l--------~~~~~g~l~~~e~~~~~~~--~~~~~~~~Gd~i~~~i~~~~   59 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDI--------GYKSEGIIPISEFSDDPIE--NGEDEVKVGDEVEVYVLRVE   59 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEe--------CCCceEEEEHHHhCccccC--CHhHcCCCCCEEEEEEEEEE
Confidence            89999999999999999999        4568999999999876666  78999999999999999864

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

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

Probab=99.06  E-value=2.8e-10  Score=82.24  Aligned_cols=62  Identities=16%  Similarity=0.283  Sum_probs=58.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +++|+++.|+||+|++..|||++        ...-+|++|+|++...++.  ++.+.+++||.|.++|+++.
T Consensus         3 ~kvG~~l~GkItgI~~yGAFV~l--------~~g~tGLVHISEIa~~fVk--dI~d~L~vG~eV~vKVl~id   64 (129)
T COG1098           3 MKVGSKLKGKITGITPYGAFVEL--------EGGKTGLVHISEIADGFVK--DIHDHLKVGQEVKVKVLDID   64 (129)
T ss_pred             ccccceEEEEEEeeEecceEEEe--------cCCCcceEEehHhhhhhHH--hHHHHhcCCCEEEEEEEeec
Confidence            68999999999999999999999        6778899999999999999  99999999999999999874

>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=99.01  E-value=2e-09  Score=71.29  Aligned_cols=63  Identities=16%  Similarity=0.162  Sum_probs=54.4

Q ss_pred             CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccc-ccccccCCCCCCEEEEEEEEee
Q 032149           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-KVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d-~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++||+|.|+|+++++..++|++        .....|++|.+++...... ..++.+.|++||.|.|+|+++.
T Consensus         2 k~G~~V~g~V~~i~~~G~fV~l--------~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id   65 (74)
T cd05705           2 KEGQLLRGYVSSVTKQGVFFRL--------SSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVN   65 (74)
T ss_pred             CCCCEEEEEEEEEeCCcEEEEe--------CCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEE
Confidence            6899999999999999999998        6679999999999876533 2236799999999999999874

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.

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

Probab=99.00  E-value=2.5e-09  Score=70.00  Aligned_cols=64  Identities=17%  Similarity=0.271  Sum_probs=54.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+.|+++.|+|+++.+..|++++...      ....|++|.++++.....  ++.+.|++||.|+|+|+++.
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~------~~~~gll~~s~l~~~~~~--~~~~~~~~Gd~v~vkv~~~d   64 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEY------GNIEGMILLSELSRRRIR--SIRKLVKVGRKEVVKVIRVD   64 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCC------CCeEEEEEhHHcCCcccC--CHHHeeCCCCEEEEEEEEEE
Confidence            67899999999999999999999211      138999999999866555  78999999999999999864

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

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

Probab=98.98  E-value=4.5e-09  Score=68.55  Aligned_cols=61  Identities=30%  Similarity=0.371  Sum_probs=53.8

Q ss_pred             CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++|++|.|+|+++.+..++|++        ....+|++|.+++...+..  +..+.|++||.|+|+|+++.
T Consensus         2 ~~G~iv~g~V~~v~~~gi~v~l--------~~~~~g~v~~s~l~~~~~~--~~~~~~~~Gd~v~~~V~~~d   62 (73)
T cd05706           2 KVGDILPGRVTKVNDRYVLVQL--------GNKVTGPSFITDALDDYSE--ALPYKFKKNDIVRACVLSVD   62 (73)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEe--------CCCcEEEEEhhhccCcccc--ccccccCCCCEEEEEEEEEe
Confidence            6899999999999999999998        6679999999999765433  56789999999999999874

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

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

Probab=98.93  E-value=6.5e-09  Score=67.33  Aligned_cols=59  Identities=25%  Similarity=0.468  Sum_probs=53.1

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |++|.|+|+++.+..|+|++        .....|++|.+++...+.+  ++.+.|++||.++|+|+++.
T Consensus         1 G~~v~g~V~~v~~~g~~v~l--------~~~~~g~i~~~~~~~~~~~--~~~~~~~~Gd~v~~~v~~~d   59 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKL--------GDGVEGFLRAAELSRDRVE--DATERFKVGDEVEAKITNVD   59 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEe--------CCCCEEEEEHHHCCCcccc--CHHHccCCCCEEEEEEEEEe
Confidence            79999999999999999999        4678999999999876655  78899999999999999874

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.

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

Probab=98.93  E-value=6.1e-09  Score=67.19  Aligned_cols=59  Identities=19%  Similarity=0.319  Sum_probs=52.8

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |++|.|+|+++.+..++|++        .....|++|.+++......  +..+.|++||.|+|+|+++.
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l--------~~~~~G~v~~s~l~~~~~~--~~~~~~~~Gd~v~~~v~~~d   59 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTL--------GRGVDARVRVSELSDSYLK--DWKKRFKVGQLVKGKIVSID   59 (68)
T ss_pred             CCEEEEEEEEEECccEEEEe--------CCCCEEEEEHHHCCchhhc--CHhhccCCCCEEEEEEEEEe
Confidence            79999999999999999999        5569999999999765555  78899999999999999875

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.

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

Probab=98.88  E-value=5.1e-09  Score=73.32  Aligned_cols=63  Identities=19%  Similarity=0.322  Sum_probs=54.0

Q ss_pred             CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc-----------------cccccccCCCCCCEE
Q 032149           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-----------------DKVDMHLSFRPGDIV  137 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~-----------------d~~~~~~~~~~GDiV  137 (146)
                      ++|++|.|+|+++.+..+++++        .....|++|.+|+...+.                 +..++.+.|++||+|
T Consensus         2 ~~G~vV~G~V~~v~~~gl~v~L--------~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V   73 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISL--------PNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLV   73 (100)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEC--------CCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEE
Confidence            6899999999999999999988        667999999999975431                 123588999999999


Q ss_pred             EEEEEEee
Q 032149          138 RASVVSFM  145 (146)
Q Consensus       138 ~A~Vis~~  145 (146)
                      +|+|+++.
T Consensus        74 ~~kVi~~d   81 (100)
T cd05693          74 RCKVVSLD   81 (100)
T ss_pred             EEEEEEcc
Confidence            99999875

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.

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

Probab=98.85  E-value=1.8e-08  Score=65.76  Aligned_cols=62  Identities=26%  Similarity=0.337  Sum_probs=53.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++|++|.|+|+++++..|+|++.       .....|++|.++++.....  ++.+.|++||.|+|+|+++.
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~-------~~~~~g~i~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd   62 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDID-------GTNVSGLCHKSEISDNRVA--DASKLFRVGDKVRAKVLKID   62 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEEC-------CCCeEEEEEHHHCCCCccC--CHhHeecCCCEEEEEEEEEe
Confidence            46999999999999999999992       1368999999999765544  67889999999999999874

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.

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

Probab=98.84  E-value=3e-08  Score=64.63  Aligned_cols=62  Identities=24%  Similarity=0.338  Sum_probs=56.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |++|+++.|+|+++.+..++|++        .....|++|.+++.....+  +..+.|++||.|.|+|+++.
T Consensus         2 ~~~G~iv~g~V~~v~~~g~~V~l--------~~~~~g~ip~~~l~~~~~~--~~~~~~~~G~~v~v~v~~vd   63 (74)
T PF00575_consen    2 LKEGDIVEGKVTSVEDFGVFVDL--------GNGIEGFIPISELSDDRID--DPSEVYKIGQTVRVKVIKVD   63 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEE--------STSSEEEEEGGGSSSSEES--SSHGTCETTCEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEECCEEEEEE--------CCcEEEEEEeehhcCcccc--ccccccCCCCEEEEEEEEEE
Confidence            68999999999999999999999        6789999999999876555  78999999999999999874

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 ....

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

Probab=98.84  E-value=2.1e-08  Score=63.65  Aligned_cols=59  Identities=25%  Similarity=0.375  Sum_probs=51.8

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+++.|+|+++.+..|+|++        ...+.|++|.++++.....  ++.+.|++||.|.++|+++.
T Consensus         1 G~~~~g~V~~i~~~g~~v~i--------~~~~~g~l~~~~l~~~~~~--~~~~~~~~Gd~v~v~v~~~~   59 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVEL--------GGGISGLVHISQIAHKRVK--DVKDVLKEGDKVKVKVLSID   59 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEE--------CCCCEEEEEhHHcCCcccC--CHHHccCCCCEEEEEEEEEC
Confidence            79999999999999999999        5679999999998765544  66788999999999998864

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.

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

Probab=98.83  E-value=2.4e-08  Score=65.58  Aligned_cols=63  Identities=17%  Similarity=0.187  Sum_probs=54.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+.|+++.|+|+++.+..++|++.       .....|++|.+++.....+  +..+.|++||.|+++|+++.
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~-------~~~~eGlvh~sel~~~~~~--~~~~~~~~Gd~v~vkv~~vd   63 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIP-------GCRKQGLVHKSHMSSCRVD--DPSEVVDVGEKVWVKVIGRE   63 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEEC-------CCCeEEEEEchhhCCCccc--CHhhEECCCCEEEEEEEEEC
Confidence            578999999999999999999981       1236899999999876666  88899999999999999874

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.

>PRK08582 hypothetical protein; Provisional

Probab=98.80  E-value=3.5e-08  Score=73.02  Aligned_cols=62  Identities=23%  Similarity=0.310  Sum_probs=55.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +++|++|.|+|+++++..++|+|        .....|++|.+++...+..  ++.+.|++||.|.|+|+++.
T Consensus         3 ~kvG~iv~G~V~~I~~fG~fV~L--------~~~~~GlVhiSels~~~v~--~~~~~l~vGD~VkvkV~~id   64 (139)
T PRK08582          3 IEVGSKLQGKVTGITNFGAFVEL--------PEGKTGLVHISEVADNYVK--DINDHLKVGDEVEVKVLNVE   64 (139)
T ss_pred             CcCCCEEEEEEEEEECCeEEEEE--------CCCCEEEEEeeccCccccc--ccccccCCCCEEEEEEEEEC
Confidence            57899999999999999999999        5679999999999866655  67899999999999999874

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

Probab=98.79  E-value=3.2e-08  Score=65.24  Aligned_cols=61  Identities=21%  Similarity=0.170  Sum_probs=52.8

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ||+|.|+|+++.+..++|++        .....|++|.+++........+..+.|++||.|.|+|+++.
T Consensus         1 G~~V~g~V~~i~~~g~~V~l--------~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id   61 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTI--------SPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVD   61 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEe--------CCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEe
Confidence            89999999999999999998        66799999999997543223378999999999999999874

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.

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

Probab=98.78  E-value=3.9e-08  Score=62.17  Aligned_cols=61  Identities=26%  Similarity=0.344  Sum_probs=53.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++|+++.|+|+++.+..++|++        ...+.|++|.+++......  ++.+.|++||.|+|+|.++.
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i--------~~~~~g~l~~~~~~~~~~~--~~~~~~~~G~~v~~~V~~~~   61 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDL--------GNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLSVD   61 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEe--------CCCCEEEEEHHHCCccccC--CHHHeecCCCEEEEEEEEEe
Confidence            4699999999999999999999        5579999999998866544  66788999999999999864

>PRK07252 hypothetical protein; Provisional

Probab=98.76  E-value=5.5e-08  Score=70.29  Aligned_cols=61  Identities=21%  Similarity=0.335  Sum_probs=54.0

Q ss_pred             CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++|+++.|+|+++.+..|+|+|        .....|++|.++++.....  +..+.|++||.|.|+|+++.
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei--------~~~~~GllhiseLs~~~~~--~~~~~~~vGD~V~VkI~~iD   62 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVAL--------ENGTTGLIHISEIKTGFID--NIHQLLKVGEEVLVQVVDFD   62 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEE--------CCCCEEEEEHHHcCCcccc--ChhhccCCCCEEEEEEEEEe
Confidence            5799999999999999999999        5668999999999865554  67788999999999999874

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

Probab=98.75  E-value=5.6e-08  Score=61.75  Aligned_cols=59  Identities=20%  Similarity=0.234  Sum_probs=51.1

Q ss_pred             CCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        76 ~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +|+++.|+|+++.+..|+|++        . ...|++|.+++...+..  ++.+.|++||.|+|+|+++.
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l--------~-~~~g~l~~~e~~~~~~~--~~~~~~~~Gd~v~v~i~~vd   59 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDL--------G-GVDGLLHISDMSWGRVK--HPSEVVNVGDEVEVKVLKID   59 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEE--------C-CeEEEEEhHHCCCcccc--CHhHEECCCCEEEEEEEEEE
Confidence            489999999999999999998        3 48899999998754444  67788999999999999874

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.

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

Probab=98.74  E-value=5.7e-08  Score=62.69  Aligned_cols=59  Identities=20%  Similarity=0.303  Sum_probs=52.2

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+++.|+|+++.+..++|++        .....|++|.+++......  +..+.|++||.+.++|+++.
T Consensus         1 g~~~~g~V~~v~~~G~~V~l--------~~~~~gli~~s~l~~~~~~--~~~~~~~~G~~i~v~v~~~d   59 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSF--------YNNVKGFLPKSELSEAFIK--DPEEHFRVGQVVKVKVLSCD   59 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEE--------CCCCEEEEEHHHcChhhcC--CHHHcccCCCEEEEEEEEEc
Confidence            89999999999999999999        4568999999999765555  67889999999999999864

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.

>PRK08059 general stress protein 13; Validated

Probab=98.73  E-value=6.3e-08  Score=69.98  Aligned_cols=62  Identities=27%  Similarity=0.345  Sum_probs=55.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +++|++|.|+|+++.+..|+|+|        ...+.|++|.++++.....  ++.+.|++||.|.|+|+++.
T Consensus         5 ~k~G~iv~G~V~~i~~~G~fV~i--------~~~~~Gli~~sel~~~~~~--~~~~~~~vGD~I~vkI~~id   66 (123)
T PRK08059          5 YEVGSVVTGKVTGIQPYGAFVAL--------DEETQGLVHISEITHGFVK--DIHDFLSVGDEVKVKVLSVD   66 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEE--------CCCCEEEEEHHHCCccccc--CHHHcCCCCCEEEEEEEEEE
Confidence            57899999999999999999999        5679999999999765554  67889999999999999873

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

Probab=98.69  E-value=1e-07  Score=60.30  Aligned_cols=59  Identities=29%  Similarity=0.259  Sum_probs=51.7

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+++.|+|+++.+..|+|++        .....|++|.++++.....  ++.+.|++||.++|+|+++.
T Consensus         1 g~~~~g~V~~i~~~G~fv~l--------~~~~~g~~~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd   59 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDI--------GVKQDGLIHISKMADRFVS--HPSDVVSVGDIVEVKVISID   59 (68)
T ss_pred             CCEEEEEEEEEecccEEEEc--------CCCCEEEEEHHHCCCcccc--CHHHhcCCCCEEEEEEEEEE
Confidence            78999999999999999999        5568999999999765555  67788999999999999874

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.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=98.69  E-value=6.2e-08  Score=80.41  Aligned_cols=65  Identities=17%  Similarity=0.306  Sum_probs=57.6

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccc-cceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~-~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      -.|++||+|.|+|++|.+..++|+|.       . ....|+||.|++......  ++++.|++||.|.++|+++.
T Consensus        13 ~~P~~GdvV~g~V~~I~d~GafV~L~-------EY~gvEGlIhiSElS~~ri~--~i~d~vkvGd~v~vkVl~VD   78 (319)
T PTZ00248         13 KFPEEDDLVMVKVVRITEMGAYVSLL-------EYDDIEGMILMSELSKRRIR--SINKLIRVGRHEVVVVLRVD   78 (319)
T ss_pred             hCCCCCCEEEEEEEEEeCCeEEEEec-------CCCCcEEEEEHHHhcccccC--CHHHhcCCCCEEEEEEEEEe
Confidence            45899999999999999999999992       1 258999999999876666  99999999999999999874

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

Probab=98.68  E-value=9.9e-08  Score=77.38  Aligned_cols=66  Identities=20%  Similarity=0.220  Sum_probs=56.8

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      -.|++||+|.|+|+++.+..|+|++...      ....|++|.+++......  ++++.|++||.|.|+|+++.
T Consensus         4 ~~P~~GdiV~G~V~~I~~~G~fV~L~e~------~gieGlI~iSEls~~~i~--~i~~~~kvGd~V~vkVi~VD   69 (262)
T PRK03987          4 EWPEEGELVVGTVKEVKDFGAFVTLDEY------PGKEGFIHISEVASGWVK--NIRDHVKEGQKVVCKVIRVD   69 (262)
T ss_pred             CCCCCCCEEEEEEEEEECCEEEEEECCC------CCcEEEEEHHHcCccccc--CHHHhCCCCCEEEEEEEEEe
Confidence            4699999999999999999999999311      157999999999766555  78899999999999999875

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

Probab=98.68  E-value=1.3e-07  Score=61.03  Aligned_cols=59  Identities=19%  Similarity=0.340  Sum_probs=51.9

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+++.|+|+++.+..++|++        .....|++|.+++......  +..+.|++||.+.++|+++.
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l--------~~~v~g~i~~~~l~~~~~~--~~~~~~~~Gd~i~~~V~~id   59 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKL--------SDHIKGLVPPMHLADVRLK--HPEKKFKPGLKVKCRVLSVE   59 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEe--------cCCcEEEEEHHHCCCcccc--CHHHcCCCCCEEEEEEEEEE
Confidence            78999999999999999999        5669999999998765444  67789999999999999874

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.

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

Probab=98.67  E-value=1.2e-07  Score=63.51  Aligned_cols=62  Identities=21%  Similarity=0.285  Sum_probs=55.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +++|+++.|+|+++.+..++|++        .....|++|.++++.....  ++.+.|++||.|+++|+++.
T Consensus        12 ~~~G~i~~g~V~~v~~~G~fv~l--------~~~~~g~v~~~el~~~~~~--~~~~~~~~Gd~v~vkV~~id   73 (83)
T cd04461          12 LKPGMVVHGYVRNITPYGVFVEF--------LGGLTGLAPKSYISDEFVT--DPSFGFKKGQSVTAKVTSVD   73 (83)
T ss_pred             CCCCCEEEEEEEEEeeceEEEEc--------CCCCEEEEEHHHCCccccc--CHHHhcCCCCEEEEEEEEEc
Confidence            68999999999999999999999        4568999999999765554  78899999999999999864

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.

>PRK05807 hypothetical protein; Provisional

Probab=98.67  E-value=1.5e-07  Score=69.32  Aligned_cols=61  Identities=20%  Similarity=0.316  Sum_probs=54.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|++|.|+|+++++..|+|++        . ..+|++|++++...+..  +..+.|++||.|.++|+++.
T Consensus         3 ~~vG~vv~G~Vt~i~~~GafV~L--------~-~~~Glvhiseis~~~v~--~~~~~~kvGd~V~VkV~~id   63 (136)
T PRK05807          3 LKAGSILEGTVVNITNFGAFVEV--------E-GKTGLVHISEVADTYVK--DIREHLKEQDKVKVKVISID   63 (136)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEhhhccccccc--CccccCCCCCEEEEEEEEEC
Confidence            36899999999999999999998        2 35899999999877766  77899999999999999874

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

Probab=98.61  E-value=2.4e-07  Score=63.39  Aligned_cols=63  Identities=21%  Similarity=0.284  Sum_probs=52.0

Q ss_pred             CCCCCEEEEEEEEEecc--eEEEEEEeecccccccceeeEEecccccccc-ccccccccCCCCCCEEEEEEEEe
Q 032149           74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE-IDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~--~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~-~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      +++|+++.|+|+++.+.  .|+|++        .....|+||.+++.... ....+..+.|++||.|.++|+..
T Consensus         5 ~~~G~iy~g~V~~i~~~~~GaFV~l--------~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~   70 (88)
T cd04453           5 PIVGNIYLGRVKKIVPGLQAAFVDI--------GLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKE   70 (88)
T ss_pred             CCCCCEEEEEEEEeccCCcEEEEEe--------CCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEe
Confidence            58999999999999996  999999        45679999999985411 12226688999999999999874

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

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

Probab=98.57  E-value=4.1e-07  Score=57.82  Aligned_cols=59  Identities=17%  Similarity=0.291  Sum_probs=50.8

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+++.|+|+++.+..|+|++        .....|++|.++++.....  +..+.|++||.|+++|.++.
T Consensus         1 g~~~~g~V~~v~~~G~~v~l--------~~~~~g~l~~~~l~~~~~~--~~~~~~~~Gd~v~v~v~~~d   59 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEI--------LPGKDGLVHISELSDERVE--KVEDVLKVGDEVKVKVIEVD   59 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEe--------CCCCEEEEEhHHcCCcccc--CHHHccCCCCEEEEEEEEEC
Confidence            78999999999999999999        5568999999999755444  55688999999999999864

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.

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

Probab=98.56  E-value=5.3e-07  Score=58.23  Aligned_cols=57  Identities=25%  Similarity=0.387  Sum_probs=49.0

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |++|.|+|+++.++.++|++        ...+.|++|.+++.... .  . .+.|++||.|.|+|+.+.
T Consensus         1 G~~V~g~V~~i~~~G~~v~l--------~~~v~g~v~~~~l~~~~-~--~-~~~~~~G~~i~~kVi~id   57 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDF--------LSSFTGTVDFLHLDPEK-S--S-KSTYKEGQKVRARILYVD   57 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEE--------cCCceEEEEHHHcCCcc-C--c-ccCcCCCCEEEEEEEEEe
Confidence            89999999999999999998        45699999999985332 2  2 788999999999999875

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.

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

Probab=98.56  E-value=4.7e-07  Score=59.21  Aligned_cols=59  Identities=20%  Similarity=0.363  Sum_probs=50.8

Q ss_pred             CCEEE-EEEEEE-ecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVI-ARVTKV-MTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiVi-G~V~~v-~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+++- |+|+++ .+..++|++        .....|++|.+++.....+  ...+.|++||.+.|+|+++.
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l--------~~gv~G~i~~s~l~~~~~~--~~~~~~~vG~~v~~kV~~id   61 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFEL--------KDGLLGFVHISHLSDDKVP--SDTGPFKAGTTHKARIIGYS   61 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEe--------CCCCEEEEEHHHCCcchhc--CcccccCCCCEEEEEEEEEe
Confidence            67888 999999 689999999        5568999999999755555  67889999999999999874

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.

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

Probab=98.50  E-value=3.1e-07  Score=80.79  Aligned_cols=61  Identities=25%  Similarity=0.310  Sum_probs=57.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|++|.|.|+++++..|+|+|         ..+.|++|++|+.....+  .+++.|++||.|+++|+++.
T Consensus       190 l~~G~vV~G~V~~It~~GafVdi---------gGvdGLlHiseiS~~rv~--~P~~vvkvGd~VkvkVi~~D  250 (541)
T COG0539         190 LEVGEVVEGVVKNITDYGAFVDI---------GGVDGLLHISEISWKRVD--HPSEVVKVGDEVKVKVISLD  250 (541)
T ss_pred             CCCCceEEEEEEEeecCcEEEEe---------cCeeeEEehhhccccccC--CHHHhcccCCEEEEEEEEEc
Confidence            68999999999999999999999         449999999999988888  99999999999999999975

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

Probab=98.50  E-value=6.7e-07  Score=57.29  Aligned_cols=59  Identities=15%  Similarity=0.268  Sum_probs=50.0

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccc-ccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRA-TEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~-~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+++.|+|+++++..++|++        .....|++|.+++.. ....  +..+.|++||.|+|+|+++.
T Consensus         1 G~~~~g~V~~i~~~G~fv~l--------~~~~~Glv~~~~l~~~~~~~--~~~~~~~~G~~v~v~v~~id   60 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGL--------DGGIDGLVHISDISWTQRVR--HPSEIYKKGQEVEAVVLNID   60 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEe--------CCCCEEEEEHHHCCCccccC--ChhhEECCCCEEEEEEEEEE
Confidence            78999999999999999999        456899999999873 2223  56788999999999999874

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.45  E-value=1.6e-07  Score=85.01  Aligned_cols=89  Identities=17%  Similarity=0.238  Sum_probs=71.0

Q ss_pred             CCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEec
Q 032149           35 NGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQ  114 (146)
Q Consensus        35 ~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~  114 (146)
                      +|.++++..+.....       +.+..|....     ..|++|+++.|+|+++.+..++|+|        .....|++|+
T Consensus       589 dG~V~i~~~~~~~~~-------~a~~~I~~~~-----~~~~~G~i~~G~V~~I~~~GafVei--------~~g~~GllHi  648 (684)
T TIGR03591       589 DGTVKIAASDGEAAE-------AAIKMIEGIT-----AEPEVGKIYEGKVVRIMDFGAFVEI--------LPGKDGLVHI  648 (684)
T ss_pred             CeEEEEEECcHHHHH-------HHHHHHHhhh-----cccccCcEEEEEEEEEeCCEEEEEE--------CCCcEEEEEH
Confidence            788888887766552       1123444332     2389999999999999999999999        4468999999


Q ss_pred             cccccccccccccccCCCCCCEEEEEEEEee
Q 032149          115 QDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus       115 sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+++....+  +..+.|++||.|+++|+++.
T Consensus       649 Sei~~~~v~--~~~~~~kvGD~V~VkVi~id  677 (684)
T TIGR03591       649 SEIANERVE--KVEDVLKEGDEVKVKVLEID  677 (684)
T ss_pred             HHcCCCccc--ChhhccCCCCEEEEEEEEEC
Confidence            999776666  78999999999999999875

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).

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

Probab=98.42  E-value=2.1e-06  Score=56.78  Aligned_cols=55  Identities=18%  Similarity=0.199  Sum_probs=48.4

Q ss_pred             CCCCEEEEEEEEEecceEEEEEEeecccccc-cceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~-~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +.|++|.|.|.++.+..+++++        . ..+.|++|.+++...        +.|++||.+.|+|+++.
T Consensus         3 ~~G~~v~g~V~si~d~G~~v~~--------g~~gv~Gfl~~~~~~~~--------~~~~~Gq~v~~~V~~vd   58 (74)
T cd05694           3 VEGMVLSGCVSSVEDHGYILDI--------GIPGTTGFLPKKDAGNF--------SKLKVGQLLLCVVEKVK   58 (74)
T ss_pred             CCCCEEEEEEEEEeCCEEEEEe--------CCCCcEEEEEHHHCCcc--------cccCCCCEEEEEEEEEE
Confidence            6799999999999999999998        4 368999999887532        88999999999999874

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.

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

Probab=98.40  E-value=1.1e-06  Score=54.47  Aligned_cols=55  Identities=16%  Similarity=0.305  Sum_probs=47.2

Q ss_pred             EEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           80 VIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        80 ViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      +.|+|+++.+..|+|++        .....|++|.+++......  ++.+.|++||.|+|+|+++
T Consensus         1 v~g~V~~v~~~g~~v~l--------~~~~~g~~~~~~~~~~~~~--~~~~~~~~G~~v~~~v~~~   55 (65)
T cd00164           1 VTGKVVSITKFGVFVEL--------EDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEV   55 (65)
T ss_pred             CEEEEEEEEeeeEEEEe--------cCCCEEEEEHHHCCCcccc--CHhhEeCCCCEEEEEEEEE
Confidence            47999999999999999        4568999999998755443  5778899999999999986

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=98.38  E-value=3.1e-07  Score=83.26  Aligned_cols=89  Identities=17%  Similarity=0.249  Sum_probs=71.7

Q ss_pred             CCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEec
Q 032149           35 NGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQ  114 (146)
Q Consensus        35 ~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~  114 (146)
                      +|.++++..+.....       ..+..|+..+.     .|++|+++.|+|+++.+..++|+|        .....|++|+
T Consensus       592 ~G~v~i~~~~~~~~~-------~a~~~I~~~~~-----~~~vG~v~~G~V~~I~~fGafVei--------~~~~~Gllhi  651 (693)
T PRK11824        592 DGTVKIAATDGEAAE-------AAKERIEGITA-----EPEVGEIYEGKVVRIVDFGAFVEI--------LPGKDGLVHI  651 (693)
T ss_pred             CceEEEEcccHHHHH-------HHHHHHHHhcc-----cCcCCeEEEEEEEEEECCeEEEEE--------CCCCEEEEEe
Confidence            788888888877662       12334444432     278999999999999999999999        4568999999


Q ss_pred             cccccccccccccccCCCCCCEEEEEEEEee
Q 032149          115 QDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus       115 sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++++.....  +..+.|++||.|+++|+++.
T Consensus       652 Sels~~~v~--~~~~v~kvGD~V~VkV~~iD  680 (693)
T PRK11824        652 SEIADERVE--KVEDVLKEGDEVKVKVLEID  680 (693)
T ss_pred             eeccCcccc--CccceeCCCCEEEEEEEEEC
Confidence            999866666  77899999999999999874

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=98.35  E-value=2.1e-06  Score=71.35  Aligned_cols=62  Identities=23%  Similarity=0.329  Sum_probs=54.9

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      -+++|++|.|+|+++++..++|++         ....|++|.+++......  ++.+.|++||.|+|+|+++.
T Consensus       193 ~~k~G~vv~G~V~~I~~~G~fV~i---------~gv~Gllhisels~~~~~--~~~~~~~vGd~VkvkVl~iD  254 (318)
T PRK07400        193 RLEVGEVVVGTVRGIKPYGAFIDI---------GGVSGLLHISEISHEHIE--TPHSVFNVNDEMKVMIIDLD  254 (318)
T ss_pred             cCCCCCEEEEEEEEEECCeEEEEE---------CCEEEEEEHHHccccccc--ChhhccCCCCEEEEEEEEEe
Confidence            368999999999999999999998         246799999999876655  78899999999999999874

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

Probab=98.34  E-value=3.8e-06  Score=54.39  Aligned_cols=62  Identities=16%  Similarity=0.256  Sum_probs=51.3

Q ss_pred             CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .+|+++.|+|+++++..++|++        ....+|++|.+++...+ ...+..+.|+.||.|+++|+++.
T Consensus         2 ~~g~~~~g~V~~i~~~G~fv~l--------~~~~~Gl~~~~~l~~~~-~~~~~~~~~~~Gd~v~v~v~~id   63 (72)
T cd05689           2 PEGTRLFGKVTNLTDYGCFVEL--------EEGVEGLVHVSEMDWTN-KNIHPSKVVSLGDEVEVMVLDID   63 (72)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEc--------CCCCEEEEEEEeccCcc-cccCcccEeCCCCEEEEEEEEee
Confidence            4699999999999999999999        45689999999986321 12256688999999999999864

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.

>PHA02945 interferon resistance protein; Provisional

Probab=98.34  E-value=2.8e-06  Score=58.11  Aligned_cols=62  Identities=15%  Similarity=0.166  Sum_probs=52.1

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEecccc--ccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDV--RATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi--~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      -.|++|++|+|+|+. .+..++|.+.       .. ..+|+||.|++  .+.-..  + ++.+ .|..|.|||+.+.
T Consensus         7 ~~P~~GelvigtV~~-~d~ga~v~L~-------EY~g~eg~i~~seveva~~wvK--~-rd~l-~GqkvV~KVirVd   71 (88)
T PHA02945          7 SLPNVGDVLKGKVYE-NGYALYIDLF-------DYPHSEAILAESVQMHMNRYFK--Y-RDKL-VGKTVKVKVIRVD   71 (88)
T ss_pred             cCCCCCcEEEEEEEe-cCceEEEEec-------ccCCcEEEEEeehhhhccceEe--e-eeEe-cCCEEEEEEEEEC
Confidence            359999999999999 9999999983       22 47899999955  665555  5 9999 9999999999864

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

Probab=98.29  E-value=5e-06  Score=54.99  Aligned_cols=61  Identities=15%  Similarity=0.238  Sum_probs=50.1

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc-cccccccCCCCCCEEEEEEEEe
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~-d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      |+++.|+|+++.+..++|+|...     .....|++|.+++..... .  +..+.|++||.|+++|.++
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~-----~~~~~gll~~s~l~~~~~~~--~~~~~~~~Gd~v~v~v~~v   62 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGL-----KGRKEGLVHISQLSFEGRVA--NPSDVVKRGQKVKVKVISI   62 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCC-----CCCcEEEEEhHhccCCCCcC--ChhheeCCCCEEEEEEEEE
Confidence            78999999999999999999200     025789999999975543 4  6788999999999999886

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.

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

Probab=98.28  E-value=1.5e-06  Score=70.06  Aligned_cols=66  Identities=21%  Similarity=0.265  Sum_probs=58.9

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +-.|..|++|+|+|.+|.+..|+|.+.       -+ ...|++|.|++...-+.  +++++++.|..+.|+|+++.
T Consensus         6 ~~~PeeGEiVv~tV~~V~~~GAyv~L~-------EY~g~Eg~ihiSEvas~wVk--nIrd~vkegqkvV~kVlrVd   72 (269)
T COG1093           6 REYPEEGEIVVGTVKQVADYGAYVELD-------EYPGKEGFIHISEVASGWVK--NIRDYVKEGQKVVAKVLRVD   72 (269)
T ss_pred             cCCCCCCcEEEEEEEEeeccccEEEee-------ccCCeeeeEEHHHHHHHHHH--HHHHHhhcCCeEEEEEEEEc
Confidence            457999999999999999999999983       23 37899999999888778  99999999999999999874

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.27  E-value=3e-06  Score=76.89  Aligned_cols=65  Identities=14%  Similarity=0.197  Sum_probs=55.1

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccc--ccccccccccCCCCCCEEEEEEEEee
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRA--TEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~--~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .|++|+++.|+|+++.+..++|+|        .....|++|+|++..  +.....++.+.|++||.|.++|+++.
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel--------~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID  710 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSL--------LPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADID  710 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEe--------cCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEEC
Confidence            489999999999999999999999        456899999999852  22222388999999999999999874

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.

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

Probab=98.22  E-value=9.2e-06  Score=52.40  Aligned_cols=54  Identities=24%  Similarity=0.391  Sum_probs=46.5

Q ss_pred             CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +.|++|.|+|.++..+.++|+|        .. ..|+|+.++...        .+.|++||.|.+.|.++.
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdi--------g~-~eg~lp~~e~~~--------~~~~~~Gd~v~v~v~~v~   55 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDL--------GK-VEAILPKKEQIP--------GESYRPGDRIKAYVLEVR   55 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEc--------CC-eEEEeeHHHCCC--------CCcCCCCCEEEEEEEEEe
Confidence            5799999999999999999998        44 899999888742        456899999999998863

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.

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

Probab=98.19  E-value=2.2e-05  Score=51.98  Aligned_cols=53  Identities=21%  Similarity=0.324  Sum_probs=47.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      ++.|+.+.|+|+++++..+++++        .....|++|.+++          .+.|+.||.+.++|.++
T Consensus        14 ~~~G~~~~g~V~~i~~~G~fV~l--------~~~~~Glv~~se~----------~~~~~iGd~v~v~I~~i   66 (77)
T cd04473          14 LEVGKLYKGKVNGVAKYGVFVDL--------NDHVRGLIHRSNL----------LRDYEVGDEVIVQVTDI   66 (77)
T ss_pred             CCCCCEEEEEEEeEecceEEEEE--------CCCcEEEEEchhc----------cCcCCCCCEEEEEEEEE
Confidence            68999999999999999999999        5569999998774          45699999999999886

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.

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=98.16  E-value=8.3e-06  Score=67.76  Aligned_cols=63  Identities=19%  Similarity=0.216  Sum_probs=56.3

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      +-.++|++|.|+|+++..+.++|+|        .....|++|.+|+...+..  ++.+.|++||.|.++|++.
T Consensus        27 ~~~~~G~iv~G~V~~i~~~g~~Vdi--------g~k~~g~lp~sEis~~~~~--~~~~~~~~G~~v~~~Vi~~   89 (318)
T PRK07400         27 YHFKPGDIVNGTVFSLEPRGALIDI--------GAKTAAFMPIQEMSINRVE--GPEEVLQPNETREFFILSD   89 (318)
T ss_pred             hhcCCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcccccc--CHHHccCCCCEEEEEEEEE
Confidence            3369999999999999999999999        6678999999999876666  7889999999999999975

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

Probab=98.11  E-value=2.6e-05  Score=59.86  Aligned_cols=65  Identities=25%  Similarity=0.300  Sum_probs=52.2

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccc--c-------cccccCCCCCCEEEEEEE
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID--K-------VDMHLSFRPGDIVRASVV  142 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d--~-------~~~~~~~~~GDiV~A~Vi  142 (146)
                      +.|.+|+++.|+|+++....+++++         .+++|+++.+++......  .       .+....|+.||.|++||.
T Consensus        77 f~P~~GEVv~g~V~~v~~~Gi~V~l---------g~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~  147 (187)
T PRK08563         77 FKPELQEVVEGEVVEVVEFGAFVRI---------GPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIV  147 (187)
T ss_pred             EeccCCCEEEEEEEEEEccEEEEEE---------eCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEE
Confidence            4489999999999999999999998         368999999988643211  0       134567899999999998


Q ss_pred             Eee
Q 032149          143 SFM  145 (146)
Q Consensus       143 s~~  145 (146)
                      ++.
T Consensus       148 ~v~  150 (187)
T PRK08563        148 AVS  150 (187)
T ss_pred             EEE
Confidence            864

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=98.09  E-value=1.1e-05  Score=70.42  Aligned_cols=62  Identities=19%  Similarity=0.296  Sum_probs=55.5

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|++|.|+|+++.+..++|+|        .....|++|.+++......  ++.+.|++||.|+|+|+++.
T Consensus       200 l~~G~iv~G~V~~v~~~G~fV~l--------~~gv~g~v~~sels~~~~~--~~~~~~~vGd~i~vkVl~id  261 (491)
T PRK13806        200 VKEGDVVEGTVTRLAPFGAFVEL--------APGVEGMVHISELSWSRVQ--KADEAVSVGDTVRVKVLGIE  261 (491)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEc--------CCCcEEEEEHHHCCCcccc--ChhHhcCCCCEEEEEEEEEe
Confidence            68999999999999999999998        4568999999999876656  78899999999999999764

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=98.08  E-value=1.2e-05  Score=70.39  Aligned_cols=62  Identities=18%  Similarity=0.201  Sum_probs=54.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ..+|++|.|+|+++++..++|++        .....|++|.+++......  +..+.|++||.|.|+|+++.
T Consensus       377 ~~vG~~v~G~V~~i~~~G~FV~l--------~~gv~Gli~~se~s~~~~~--~~~~~~~~Gd~v~~~V~~id  438 (491)
T PRK13806        377 FAPGTTVTGTVEKRAQFGLFVNL--------APGVTGLLPASVISRAGKP--ATYEKLKPGDSVTLVVEEID  438 (491)
T ss_pred             CCCCCEEEEEEEEEecCceEEEc--------CCCcEEEEEHHHcCccccc--chhhcCCCCCEEEEEEEEEe
Confidence            35799999999999999999999        5579999999999865554  77899999999999999874

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.99  E-value=2.3e-05  Score=68.60  Aligned_cols=61  Identities=18%  Similarity=0.210  Sum_probs=54.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|++|.|+|+++++..++|+|        . ...|++|.+++.....+  ++.+.|++||.|.++|+++.
T Consensus       206 lk~G~iv~G~V~~i~~~G~FVdl--------g-gv~Glv~~Sels~~~v~--~~~~~~kvGd~V~vkVl~iD  266 (486)
T PRK07899        206 LQKGQVRKGVVSSIVNFGAFVDL--------G-GVDGLVHVSELSWKHID--HPSEVVEVGQEVTVEVLDVD  266 (486)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHCCCcccC--CHHHhcCCCCEEEEEEEEEE
Confidence            46899999999999999999999        3 48899999999876666  78899999999999999864

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

Probab=97.99  E-value=4.8e-05  Score=48.67  Aligned_cols=56  Identities=18%  Similarity=0.290  Sum_probs=46.1

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |++|.|+|+++.+..++|++         ....|++|.+++......  +..+  .+||.+.|+|+++.
T Consensus         1 G~iv~g~V~~v~~~G~~v~l---------~g~~gfip~s~~~~~~~~--~~~~--~vG~~i~~~i~~vd   56 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI---------EGVRAFLPASQVDLRPVE--DLDE--YVGKELKFKIIEID   56 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE---------CCEEEEEEHHHCCCcccC--ChHH--hCCCEEEEEEEEEe
Confidence            78999999999999999997         358999999998755443  3333  38999999999874

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.

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.95  E-value=2.6e-05  Score=68.89  Aligned_cols=62  Identities=26%  Similarity=0.439  Sum_probs=55.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|++|.|+|+++.+..++|.+        .....|++|.+++......  ++.+.|++||.|+|+|+++.
T Consensus       458 ~~~G~vV~G~V~~v~~~G~fV~l--------~~gi~g~i~~se~s~~~~~--~~~~~~~~Gd~v~~~V~~vd  519 (565)
T PRK06299        458 HKKGSIVTGTVTEVKDKGAFVEL--------EDGVEGLIRASELSRDRVE--DATEVLKVGDEVEAKVINID  519 (565)
T ss_pred             cCCCCEEEEEEEEEecCceEEec--------CCCcEEEEEHHHhcchhcc--CccccCCCCCEEEEEEEEEc
Confidence            37899999999999999999998        4578999999999877666  88999999999999999864

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

Probab=97.94  E-value=1.9e-05  Score=60.87  Aligned_cols=64  Identities=30%  Similarity=0.340  Sum_probs=52.8

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccc-----ccc----cccCCCCCCEEEEEEE
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-----KVD----MHLSFRPGDIVRASVV  142 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d-----~~~----~~~~~~~GDiV~A~Vi  142 (146)
                      +.|..|.+|-|.|+++....++|.|         .|+.|++|.+++...+.+     ...    -...|+.||.|||||+
T Consensus        77 fkP~~gEVV~GeVv~~~~~G~fV~i---------gp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv  147 (183)
T COG1095          77 FKPFRGEVVEGEVVEVVEFGAFVRI---------GPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIV  147 (183)
T ss_pred             EEeccccEEEEEEEEEeecceEEEe---------ccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEE
Confidence            4588999999999999999999999         699999999999754321     112    2338999999999999


Q ss_pred             Ee
Q 032149          143 SF  144 (146)
Q Consensus       143 s~  144 (146)
                      +.
T Consensus       148 ~~  149 (183)
T COG1095         148 GV  149 (183)
T ss_pred             EE
Confidence            75

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.94  E-value=3.5e-05  Score=65.11  Aligned_cols=61  Identities=20%  Similarity=0.250  Sum_probs=53.5

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|++|.|+|+++.+..++|++        . ...|++|.+++.....+  ++.+.|++||.|.|+|+++.
T Consensus       190 ~~~G~~v~g~V~~v~~~G~fV~l--------~-~v~g~v~~sels~~~~~--~~~~~~~vGd~i~~~Vl~vd  250 (390)
T PRK06676        190 LKEGDVVEGTVARLTDFGAFVDI--------G-GVDGLVHISELSHERVE--KPSEVVSVGQEVEVKVLSID  250 (390)
T ss_pred             CCCCCEEEEEEEEEecceEEEEe--------C-CeEEEEEHHHcCccccC--CHHHhcCCCCEEEEEEEEEe
Confidence            58999999999999999999998        2 47899999999865555  77889999999999999863

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

Probab=97.93  E-value=4.4e-05  Score=58.35  Aligned_cols=65  Identities=25%  Similarity=0.342  Sum_probs=52.2

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc--ccc-------ccccCCCCCCEEEEEEE
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DKV-------DMHLSFRPGDIVRASVV  142 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~--d~~-------~~~~~~~~GDiV~A~Vi  142 (146)
                      +.|.+|+++.|+|+++++..+++++         .+++|+++.+++...+.  |..       +....|+.||.|++||.
T Consensus        77 f~p~~gEvv~G~V~~v~~~GifV~l---------g~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~  147 (179)
T TIGR00448        77 FKPELGEIVEGEVIEIVEFGAFVSL---------GPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIV  147 (179)
T ss_pred             EeccCCCEEEEEEEEEEeeEEEEEe---------CCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEE
Confidence            4488999999999999999999998         46999999998863321  111       23468999999999999


Q ss_pred             Eee
Q 032149          143 SFM  145 (146)
Q Consensus       143 s~~  145 (146)
                      ++.
T Consensus       148 ~v~  150 (179)
T TIGR00448       148 ALS  150 (179)
T ss_pred             EEE
Confidence            863

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

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.91  E-value=4.2e-05  Score=66.99  Aligned_cols=61  Identities=26%  Similarity=0.221  Sum_probs=53.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      .+.||+|.|+|+++..+.++|+|        .....|+|+.+++......  ++.+.|++||.|.|+|+++
T Consensus        33 ~~~GdiV~G~V~~v~~~gv~VdI--------g~k~eG~Ip~~Els~~~~~--~~~~~~~vGd~Ie~~V~~~   93 (486)
T PRK07899         33 FNDGDIVEGTVVKVDRDEVLLDI--------GYKTEGVIPSRELSIKHDV--DPNEVVEVGDEVEALVLQK   93 (486)
T ss_pred             CCCCCEEEEEEEEEECCcEEEEE--------CCCcEEEEEHHHhcccccC--ChhhcCCCCCEEEEEEEEE
Confidence            58999999999999999999999        6678999999998764433  6788899999999999975

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=97.90  E-value=3.5e-05  Score=71.55  Aligned_cols=63  Identities=19%  Similarity=0.172  Sum_probs=53.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ..+|++|.|+|+++.+..++|++        .....|++|.+|+... .+..++.+.|++||.|.|+|+++.
T Consensus       576 ~~vG~iV~G~V~~I~~fG~fVeL--------~~gveGLvhiSEls~~-~~~~~p~~~~kvGd~V~vkVl~iD  638 (863)
T PRK12269        576 FGVNDVVKGRVTKIADFGAFIEL--------AEGIEGLAHISEFSWV-KKTSKPSDMVKIGDEVECMILGYD  638 (863)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEe--------cCCceeeeEHHHhcCc-cccCCHHHcCCCCCEEEEEEEEEe
Confidence            57899999999999999999999        5578999999999742 122277889999999999999874

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

Probab=97.88  E-value=9.4e-05  Score=48.69  Aligned_cols=62  Identities=18%  Similarity=0.203  Sum_probs=48.6

Q ss_pred             CCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccccc--cc-------cccccCCCCCCEEEEEEEEee
Q 032149           76 PGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEI--DK-------VDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        76 ~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~~~--d~-------~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +|+++.|+|+++++..++|++        .. ...|++|.+++.....  |.       ......|++||.|+++|+++.
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l--------~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd   72 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVEL--------DNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVD   72 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEe--------cCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEec
Confidence            389999999999999999999        33 5889999998863210  10       133578999999999999864

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.

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

Probab=97.87  E-value=3.5e-05  Score=68.05  Aligned_cols=62  Identities=19%  Similarity=0.206  Sum_probs=57.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ..+|+.+.|+|+++++..|+++|        .....|++|+|++......  ...+.++.||.|.++|+++.
T Consensus       275 ~~~g~~v~G~Vt~i~~~GafVei--------~~GvEGlvhvSEisw~~~~--~P~evv~~Gq~V~V~Vl~id  336 (541)
T COG0539         275 YPVGDKVEGKVTNLTDYGAFVEI--------EEGVEGLVHVSEISWTKKN--VPSEVVKVGQEVEVKVLDID  336 (541)
T ss_pred             cCCCCEEEEEEEEeecCcEEEEe--------cCCccceeechhhcccccC--CHHHhcccCCEEEEEEEeeC
Confidence            47899999999999999999999        6889999999999988777  59999999999999999864

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.84  E-value=7.2e-05  Score=63.19  Aligned_cols=62  Identities=15%  Similarity=0.212  Sum_probs=53.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|+++.|+|+++.+..++|++        .....|++|.+++......  +..+.|++||.|.|+|+++.
T Consensus       275 ~~~G~~v~g~V~~i~~~G~fV~l--------~~gi~Glv~~se~~~~~~~--~~~~~~~~Gd~v~v~V~~id  336 (390)
T PRK06676        275 LPEGDVIEGTVKRLTDFGAFVEV--------LPGVEGLVHISQISHKHIA--TPSEVLEEGQEVKVKVLEVN  336 (390)
T ss_pred             hcCCcEEEEEEEEEeCceEEEEE--------CCCCeEEEEhHHcCccccC--ChhhccCCCCEEEEEEEEEE
Confidence            57899999999999999999998        4568999999998755444  67788999999999999874

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.84  E-value=4.4e-05  Score=70.81  Aligned_cols=63  Identities=14%  Similarity=0.256  Sum_probs=55.1

Q ss_pred             CCCCCCEEE-EEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           73 VPEPGSVVI-ARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        73 ~P~~GdiVi-G~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .|++|+++. |+|++|.+..+||+|        ....+|++|+|++......  +..+.|++||.|.++|+++.
T Consensus       750 ~~~vG~iy~~g~V~~I~~FGaFVeL--------~~g~EGLVHISeLs~~rv~--~~~dv~kvGD~V~VkVi~ID  813 (891)
T PLN00207        750 VPTVGDIYRNCEIKSIAPYGAFVEI--------APGREGLCHISELSSNWLA--KPEDAFKVGDRIDVKLIEVN  813 (891)
T ss_pred             CcCCCcEEECcEEEEEeccEEEEEe--------CCCCEEEEEhhhcCCcccc--CHHHhcCCCCEEEEEEEEEC
Confidence            389999995 699999999999999        4457999999999866555  77899999999999999874

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.82  E-value=7.8e-05  Score=65.88  Aligned_cols=61  Identities=23%  Similarity=0.301  Sum_probs=54.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|+++-|+|+++.+..++|++        . ...|++|.+++......  ++.+.|++||.|.|+|+++.
T Consensus       199 l~~G~iv~g~V~~v~~~G~~V~i--------~-g~~glv~~se~s~~~~~--~~~~~~kvG~~v~v~V~~~d  259 (565)
T PRK06299        199 LEEGQVVEGVVKNITDYGAFVDL--------G-GVDGLLHITDISWKRVN--HPSEVVNVGDEVKVKVLKFD  259 (565)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEE--------C-CEEEEEEHHHhcccccC--CHhhcCCCCCEEEEEEEEEe
Confidence            68999999999999999999999        4 68999999999766555  78899999999999999863

>TIGR00717 rpsA ribosomal protein S1

Probab=97.81  E-value=6.8e-05  Score=65.39  Aligned_cols=62  Identities=27%  Similarity=0.336  Sum_probs=55.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|++|.|+|+++++..++|.+        ...+.|++|.+++.....+  ++.+.|++||.|.|+|+++.
T Consensus       444 ~~~G~~v~g~V~~v~~~G~fV~l--------~~~~~Glv~~s~l~~~~~~--~~~~~~~~Gd~v~~~V~~id  505 (516)
T TIGR00717       444 YKVGSVVKGKVTEIKDFGAFVEL--------PGGVEGLIRNSELSENRDE--DKTDEIKVGDEVEAKVVDID  505 (516)
T ss_pred             cCcceEEEEEEEEEecceEEEEc--------CCCeEEEEEHHHcCccccc--cccccCCCCCEEEEEEEEEe
Confidence            36899999999999999999998        5669999999999876655  78999999999999999863

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=97.77  E-value=9.2e-05  Score=66.77  Aligned_cols=61  Identities=18%  Similarity=0.281  Sum_probs=53.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|++|.|+|+++.+..++|++         ....|++|.++++.....  ++.+.|++||.|.|+|+++.
T Consensus       475 l~~G~iV~g~V~~v~~~G~fV~l---------~gv~Gll~~sels~~~~~--~~~~~~~vGd~V~vkV~~id  535 (647)
T PRK00087        475 LEEGDVVEGEVKRLTDFGAFVDI---------GGVDGLLHVSEISWGRVE--KPSDVLKVGDEIKVYILDID  535 (647)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEE---------CCEEEEEEHHHcCccccC--CHHHhcCCCCEEEEEEEEEE
Confidence            47899999999999999999998         347899999999865555  77889999999999999874

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

Probab=97.75  E-value=0.00016  Score=49.95  Aligned_cols=59  Identities=24%  Similarity=0.305  Sum_probs=46.0

Q ss_pred             CEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccccc---------ccccCCCCCCEEEEEEEEee
Q 032149           78 SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKV---------DMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        78 diViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~---------~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +++.|+|+++.+..++|++        . +..|++|.++++..+....         .....|++||.|+++|.++.
T Consensus         1 ~vv~g~V~~i~~~GifV~l--------~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd   68 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRI--------G-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVS   68 (99)
T ss_pred             CEEEEEEEEEEeccEEEEE--------c-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEe
Confidence            4789999999999999999        2 4789999988864432210         12467899999999998874

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.

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

Probab=97.68  E-value=0.00015  Score=65.33  Aligned_cols=61  Identities=18%  Similarity=0.321  Sum_probs=54.2

Q ss_pred             CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++|++|.|+|+++++..++|++        .....|++|.++++.....  ++.+.|++||.|+|+|+++.
T Consensus       561 ~~G~~v~g~V~~i~~~G~fV~l--------~~~i~Gli~~sel~~~~~~--~~~~~~kvGd~V~vkV~~id  621 (647)
T PRK00087        561 PVGSIVLGKVVRIAPFGAFVEL--------EPGVDGLVHISQISWKRID--KPEDVLSEGEEVKAKILEVD  621 (647)
T ss_pred             cCCeEEEEEEEEEECCeEEEEE--------CCCCEEEEEhhhcCccccC--CHhhcCCCCCEEEEEEEEEe
Confidence            6899999999999999999998        5579999999999865555  77889999999999999874

>TIGR00717 rpsA ribosomal protein S1

Probab=97.61  E-value=0.00025  Score=61.90  Aligned_cols=62  Identities=19%  Similarity=0.247  Sum_probs=53.3

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      -.++|++|.|+|+++.+..++|++        . ...|++|.+++......  ++.+.|++||.|.|+|+++.
T Consensus       184 ~l~~G~~v~g~V~~i~~~G~~V~l--------~-g~~g~lp~~e~s~~~~~--~~~~~~~vG~~v~v~Vl~~d  245 (516)
T TIGR00717       184 NLKEGDVVKGVVKNITDFGAFVDL--------G-GVDGLLHITDMSWKRVK--HPSEYVKVGQEVKVKVIKFD  245 (516)
T ss_pred             hccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHcCCCCCC--CHHHhccCCCEEEEEEEEEE
Confidence            368999999999999999999998        3 47899999998765555  67888999999999998764

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

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=97.55  E-value=0.00028  Score=65.62  Aligned_cols=61  Identities=15%  Similarity=0.168  Sum_probs=53.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|++|.|+|.++.+..++|++         ....|++|.+++......  ++.+.|++|+.|.|+|+++.
T Consensus       491 l~~G~~V~G~Vk~i~~~G~fVdl---------~Gv~Gfvp~SeiS~~~v~--~~~~~~kvGq~v~vkVi~iD  551 (863)
T PRK12269        491 VHIEDSVSGVVKSFTSFGAFIDL---------GGFDGLLHVNDMSWGHVA--RPREFVKKGQTIELKVIRLD  551 (863)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEE---------CCEEEEEEchhccccccC--CHHHhccCCCEEEEEEEEEe
Confidence            57899999999999999999998         357899999999876655  77899999999999999874

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=97.49  E-value=0.00022  Score=65.14  Aligned_cols=62  Identities=23%  Similarity=0.324  Sum_probs=57.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|.++.|.|+.+.+..++|+|        +-...|++|+|+.......  +..+.+++||+|.++|+++.
T Consensus       656 Lk~Gm~leg~Vrnv~~fgafVdI--------gv~qDglvHis~ls~~fv~--~P~~vv~vGdiV~v~V~~vD  717 (780)
T COG2183         656 LKPGMILEGTVRNVVDFGAFVDI--------GVHQDGLVHISQLSDKFVK--DPNEVVKVGDIVKVKVIEVD  717 (780)
T ss_pred             ccCCCEEEEEEEEeeeccceEEe--------ccccceeeeHHHhhhhhcC--ChHHhcccCCEEEEEEEEEe
Confidence            59999999999999999999999        7788999999999887777  77999999999999999874

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

Probab=97.37  E-value=0.00081  Score=51.57  Aligned_cols=64  Identities=19%  Similarity=0.155  Sum_probs=50.0

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccc-cc---c--c----ccccCCCCCCEEEEEE
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE-ID---K--V----DMHLSFRPGDIVRASV  141 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~-~d---~--~----~~~~~~~~GDiV~A~V  141 (146)
                      +.|-.|+++.|+|+++....+++++         .++++.+|.+++.... -|   .  .    +-...++.||.||+||
T Consensus        77 FrPf~gEVv~g~V~~v~~~G~~v~~---------Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV  147 (176)
T PTZ00162         77 FKPFKDEVLDAIVTDVNKLGFFAQA---------GPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRL  147 (176)
T ss_pred             EecCCCCEEEEEEEEEecceEEEEe---------eCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEE
Confidence            4489999999999999999999998         6788888888885211 01   1  1    1245789999999999


Q ss_pred             EEe
Q 032149          142 VSF  144 (146)
Q Consensus       142 is~  144 (146)
                      .++
T Consensus       148 ~~v  150 (176)
T PTZ00162        148 QGV  150 (176)
T ss_pred             EEE
Confidence            875

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

Probab=97.34  E-value=0.0013  Score=44.83  Aligned_cols=60  Identities=20%  Similarity=0.156  Sum_probs=41.8

Q ss_pred             CCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc----cc--c---ccccCCCCCCEEEEEEEEe
Q 032149           76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI----DK--V---DMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        76 ~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~----d~--~---~~~~~~~~GDiV~A~Vis~  144 (146)
                      +|+++.|+|+++....+++++.         |..++++.+++.+...    ..  .   +-...+++||.||+||+++
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G---------pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v   69 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG---------PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGT   69 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc---------CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEE
Confidence            4899999999999999999994         4444444444431110    00  0   1245689999999999875

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=97.30  E-value=0.00068  Score=59.25  Aligned_cols=56  Identities=25%  Similarity=0.340  Sum_probs=49.2

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      |..+.|++|.|+|.++....++|++         ....|+||.++..        ..+.|++||.|+|.|+++
T Consensus       130 yk~~~GeIV~G~V~ri~~~giiVDL---------ggvea~LP~sE~i--------p~E~~~~GdrIka~I~~V  185 (470)
T PRK09202        130 YKDRVGEIITGVVKRVERGNIIVDL---------GRAEAILPRKEQI--------PRENFRPGDRVRAYVYEV  185 (470)
T ss_pred             HHhhcCCEEEEEEEEEecCCEEEEE---------CCeEEEecHHHcC--------CCccCCCCCEEEEEEEEE
Confidence            4567999999999999999999998         4589999988863        477899999999999986

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=97.08  E-value=0.0016  Score=55.24  Aligned_cols=58  Identities=16%  Similarity=0.251  Sum_probs=48.7

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .|..+.|++|.|+|.++..+.|+|++        . ...|+||.++..        ..+.|++||.|+|.|.++.
T Consensus       129 ef~~k~GeiV~G~V~~~~~~~~~Vdl--------g-~vEa~LP~~E~i--------p~e~~~~Gd~Ika~V~~V~  186 (362)
T PRK12327        129 EFSEREGDIVTGVVQRRDNRFVYVNL--------G-KIEAVLPPAEQI--------PGETYKHGDRIKVYVVKVE  186 (362)
T ss_pred             HHHHhcCCEEEEEEEEEeCCcEEEEe--------C-CeEEEecHHHcC--------CCCCCCCCCEEEEEEEEEe
Confidence            35679999999999999999999998        3 388999965542        2677999999999999864

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.06  E-value=0.002  Score=55.55  Aligned_cols=62  Identities=24%  Similarity=0.337  Sum_probs=50.0

Q ss_pred             CCCCCEEEEEEEEEecc--eEEEEEEeecccccccceeeEEecccccccc----------ccccccccCCCCCCEEEEEE
Q 032149           74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE----------IDKVDMHLSFRPGDIVRASV  141 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~--~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~----------~d~~~~~~~~~~GDiV~A~V  141 (146)
                      +.+|++..|+|+++.+.  .|||+|        ...-.|+||.+|+....          ...-++.+.+++||.|.++|
T Consensus        23 ~~vGnIY~GrV~~i~p~l~aAFVdi--------G~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV   94 (414)
T TIGR00757        23 QLKGNIYKGRVTRILPSLQAAFVDI--------GLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQV   94 (414)
T ss_pred             CCCCCEEEEEEeeecCCCceEEEEc--------CCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEE
Confidence            46899999999999998  899999        66778999999985321          01114567899999999999


Q ss_pred             EE
Q 032149          142 VS  143 (146)
Q Consensus       142 is  143 (146)
                      ..
T Consensus        95 ~K   96 (414)
T TIGR00757        95 VK   96 (414)
T ss_pred             ee
Confidence            75

The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.

>TIGR01953 NusA transcription termination factor NusA

Probab=96.94  E-value=0.0027  Score=53.42  Aligned_cols=58  Identities=22%  Similarity=0.312  Sum_probs=47.7

Q ss_pred             CCCCCCCCEEEEEEEEEecce-EEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRM-ASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~-~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .|..+.|++|.|+|.++..+. |+|+|         ....|+|+.++...        .+.|++||.++|.|.++.
T Consensus       126 ey~~k~GeiV~G~V~~v~~~g~v~Vdi---------G~~ea~LP~~E~ip--------~E~~~~Gd~ik~~V~~V~  184 (341)
T TIGR01953       126 EFSSKEGEIISGTVKRVNRRGNLYVEL---------GKTEGILPKKEQIP--------GEKFRIGDRIKAYVYEVR  184 (341)
T ss_pred             HHHhhcCCEEEEEEEEEecCCcEEEEE---------CCeEEEecHHHcCC--------CcCCCCCCEEEEEEEEEE
Confidence            355689999999999998865 79998         35899999877643        445999999999999864

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.

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

Probab=96.64  E-value=0.0046  Score=56.01  Aligned_cols=63  Identities=16%  Similarity=0.256  Sum_probs=56.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      -+++|.+-.|+|+++.+..++|.+        ...-.|++|+|++....++  +..+.++.||.|+.||+++.
T Consensus       616 e~evg~iy~G~V~ri~~fGaFv~l--------~~gkdgl~hiS~~~~~rv~--kv~dvlk~Gd~v~Vkv~~iD  678 (692)
T COG1185         616 EVEVGEVYEGTVVRIVDFGAFVEL--------LPGKDGLVHISQLAKERVE--KVEDVLKEGDEVKVKVIEID  678 (692)
T ss_pred             hcccccEEEEEEEEEeecceEEEe--------cCCcceeEEehhhhhhhhh--cccceeecCceEEEEEeeec
Confidence            389999999999999999999999        4667899999999877666  77899999999999999874

>TIGR02063 RNase_R ribonuclease R

Probab=96.26  E-value=0.018  Score=52.60  Aligned_cols=64  Identities=17%  Similarity=0.215  Sum_probs=50.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccccc--cc-------cccccCCCCCCEEEEEEEE
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEI--DK-------VDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~~~--d~-------~~~~~~~~~GDiV~A~Vis  143 (146)
                      .++|.++.|+|+++++..++|++        .. ...|++|.+++...+.  +.       ......|++||.|.++|.+
T Consensus       625 ~~iG~~~~g~V~~v~~fGifV~L--------~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~  696 (709)
T TIGR02063       625 EKIGEEFEGVISGVTSFGLFVEL--------ENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVK  696 (709)
T ss_pred             ccCCcEEEEEEEEEEeCCEEEEe--------cCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEE
Confidence            67899999999999999999999        33 5899999999863211  10       1224679999999999998


Q ss_pred             ee
Q 032149          144 FM  145 (146)
Q Consensus       144 ~~  145 (146)
                      +.
T Consensus       697 vd  698 (709)
T TIGR02063       697 AD  698 (709)
T ss_pred             Ee
Confidence            74

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.

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

Probab=96.23  E-value=0.007  Score=58.57  Aligned_cols=67  Identities=21%  Similarity=0.134  Sum_probs=59.4

Q ss_pred             CCCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        70 ~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      ..+-.++|++|.|.|+++.+++..|..        ...+.|-+|++++......-.++.+.|++||-|.|||+.-
T Consensus       879 ~~~~~~igsiv~a~v~svKp~~L~v~l--------~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~  945 (1710)
T KOG1070|consen  879 STEDLSIGSIVRAYVKSVKPDQLNVLL--------AANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGG  945 (1710)
T ss_pred             cccceeeeeEEEEEEeeecccceEEec--------cccccCceehHHhhccccccCChhhhcccCCeEEEEEEcC
Confidence            456679999999999999999999997        7789999999999877766668999999999999999853

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=96.15  E-value=0.022  Score=38.78  Aligned_cols=63  Identities=13%  Similarity=0.190  Sum_probs=52.0

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEe-ccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR-QQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~-~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ..|++||+|. .|..+++..+.|.++       ....+|+|- .++++....+  ++...+ +|-.+.++|+.+.
T Consensus        12 ~~P~v~dvv~-~Vv~i~d~~~YV~Ll-------eY~iegmIl~~selsr~rir--si~kll-VGk~e~v~ViRVD   75 (86)
T PHA02858         12 VFPNINEVTK-GIVFVKDNIFYVKLI-------DYGLEALIVNYVNVNADRAE--KLKKKL-VGKTINVQVIRTD   75 (86)
T ss_pred             ecCCCCeEEE-EEEEEeccEEEEEEe-------cCccceEEecHHHHhHHHHH--hhhhhh-cCCeeEEEEEEEC
Confidence            3599999999 899999999999994       445778877 7777665555  788888 9999999999764

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.09  E-value=0.017  Score=49.22  Aligned_cols=57  Identities=18%  Similarity=0.289  Sum_probs=46.9

Q ss_pred             CCCCCCCCEEEEEEEEEec-ceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           71 GPVPEPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~-~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      .|..++|++|.|+|.++.. ..+++++         ....|+|+.++.-        ..+.|++||.|+|-|..+
T Consensus       133 ey~~~~Geiv~g~V~r~~~~~~i~vdl---------g~~ea~LP~~eqi--------p~E~~~~Gdrik~~i~~V  190 (374)
T PRK12328        133 KYKKKVGKIVFGTVVRVDNEENTFIEI---------DEIRAVLPMKNRI--------KGEKFKVGDVVKAVLKRV  190 (374)
T ss_pred             HHHHhcCcEEEEEEEEEecCCCEEEEc---------CCeEEEeCHHHcC--------CCCcCCCCCEEEEEEEEE
Confidence            4678999999999999986 4588887         3588999876543        367799999999999876

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.83  E-value=0.026  Score=49.05  Aligned_cols=62  Identities=8%  Similarity=0.075  Sum_probs=48.3

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      .|..++|++|.|+|.++..+.+++++.+    .+.. ...|+|+.++.        -..+.|++||.|+|-|..+
T Consensus       147 ef~~~~GeIV~G~V~r~e~~~viv~l~~----~~g~~~~EaiLP~~Eq--------ip~E~y~~Gdrika~i~~V  209 (449)
T PRK12329        147 EFQDLEDTVLTARVLRFERQSVIMAVSS----GFGQPEVEAELPKREQ--------LPNDNYRANATFKVFLKEV  209 (449)
T ss_pred             HHHHhcCcEEEEEEEEEcCCCEEEEecc----cCCCcceEEEecHHHc--------CCCCcCCCCCEEEEEEEEe
Confidence            4668999999999999999989988721    0111 37899987654        3367899999999999876

>PRK11642 exoribonuclease R; Provisional

Probab=95.47  E-value=0.06  Score=50.17  Aligned_cols=64  Identities=17%  Similarity=0.231  Sum_probs=50.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccc-c-cccc-------ccccCCCCCCEEEEEEEE
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRAT-E-IDKV-------DMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~-~-~d~~-------~~~~~~~~GDiV~A~Vis  143 (146)
                      .++|+++.|+|++|++..++|++        .. ...|++|.+++... + .+..       .....|+.||.|.++|.+
T Consensus       641 ~~iGe~f~G~Is~V~~fGifVeL--------~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~  712 (813)
T PRK11642        641 DQVGNVFKGVISSVTGFGFFVRL--------DDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEA  712 (813)
T ss_pred             ccCCcEEEEEEEEeecCceEEEE--------CCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEE
Confidence            46899999999999999999999        43 48899999988632 1 1110       234679999999999987


Q ss_pred             ee
Q 032149          144 FM  145 (146)
Q Consensus       144 ~~  145 (146)
                      +.
T Consensus       713 vD  714 (813)
T PRK11642        713 VN  714 (813)
T ss_pred             ee
Confidence            64

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

Probab=95.27  E-value=0.081  Score=48.04  Aligned_cols=64  Identities=14%  Similarity=0.192  Sum_probs=50.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccc-cceeeEEecccccccc--ccc-------cccccCCCCCCEEEEEEEE
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATE--IDK-------VDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~-~~~~g~l~~sdi~~~~--~d~-------~~~~~~~~~GDiV~A~Vis  143 (146)
                      .++|...-|+|+++++..++|++        . ....|++|.+++....  -|+       ......|++||.|+.+|++
T Consensus       570 ~~iG~~~~g~I~~v~~~GifV~L--------~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~  641 (654)
T TIGR00358       570 DKVGTEFSGEISSVTRFGMFVRL--------DDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTE  641 (654)
T ss_pred             hCCCcEEEEEEEeEEcCcEEEEe--------cCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEE
Confidence            46799999999999999999999        4 4589999999886431  111       1223679999999999998


Q ss_pred             ee
Q 032149          144 FM  145 (146)
Q Consensus       144 ~~  145 (146)
                      +.
T Consensus       642 vd  643 (654)
T TIGR00358       642 VN  643 (654)
T ss_pred             Ee
Confidence            74

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.

>PRK11712 ribonuclease G; Provisional

Probab=95.01  E-value=0.069  Score=47.08  Aligned_cols=62  Identities=21%  Similarity=0.231  Sum_probs=47.8

Q ss_pred             CCCCCEEEEEEEEEecc--eEEEEEEeecccccccceeeEEecccccccc-------c---cccccccCCCCCCEEEEEE
Q 032149           74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE-------I---DKVDMHLSFRPGDIVRASV  141 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~--~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~-------~---d~~~~~~~~~~GDiV~A~V  141 (146)
                      ..+|+|-.|+|.+|-+.  .|||+|        ...-.|.||.+|+.+..       .   ....+.+.+++||.|..+|
T Consensus        36 ~~vGnIY~G~V~~v~pg~~AAFVdI--------G~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV  107 (489)
T PRK11712         36 GIVGNIYKGRVSRVLPGMQAAFVDI--------GLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQV  107 (489)
T ss_pred             cccccEEEEEEeecCCCCceeEEee--------CCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEE
Confidence            46799999999999874  499999        67788999999884210       0   0113566799999999999


Q ss_pred             EE
Q 032149          142 VS  143 (146)
Q Consensus       142 is  143 (146)
                      ..
T Consensus       108 ~K  109 (489)
T PRK11712        108 VK  109 (489)
T ss_pred             Ee
Confidence            75

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

Probab=94.91  E-value=0.053  Score=51.76  Aligned_cols=65  Identities=18%  Similarity=0.241  Sum_probs=53.2

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      -..|.+|.++|++++.+...| +    ...+.....|.|+.+++......  .+.+-+++|+.|.|||+++.
T Consensus       983 ~~~g~iV~~~V~~vt~rr~~C-v----~v~ld~G~~g~i~~~~~Sd~~v~--~p~~~v~vgq~v~~kvi~id 1047 (1299)
T KOG1856|consen  983 FYEGAIVPVTVTKVTHRRGIC-V----RVRLDCGVTGFILAKNLSDRDVR--RPENRVKVGQTVYCKVIKID 1047 (1299)
T ss_pred             hccCceEEEeeeEEEecccce-e----EEEecCCCceeeeccccChhhcc--CHHHhhccCceEEEEeeeee
Confidence            367999999999999999666 1    11236788999999998875555  88999999999999999874

>PRK10811 rne ribonuclease E; Reviewed

Probab=94.91  E-value=0.082  Score=49.98  Aligned_cols=62  Identities=11%  Similarity=0.215  Sum_probs=48.1

Q ss_pred             CCCCCEEEEEEEEEecce--EEEEEEeecccccccceeeEEecccccccc-cc------ccccccCCCCCCEEEEEEEE
Q 032149           74 PEPGSVVIARVTKVMTRM--ASADIMCVGAKSVREKFSGIIRQQDVRATE-ID------KVDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~--~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~-~d------~~~~~~~~~~GDiV~A~Vis  143 (146)
                      +.+|+|-.|+|.+|-+..  |||+|        ...-.|+|+.+|+.... ..      .-...+.+++||.|..+|..
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDI--------G~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~K  106 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDK  106 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEe--------cCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEee
Confidence            468999999999997754  99999        67788999999884221 11      11346779999999999975

>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=94.87  E-value=0.099  Score=34.59  Aligned_cols=59  Identities=17%  Similarity=0.195  Sum_probs=46.3

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEE-EEEEE
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIV-RASVV  142 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV-~A~Vi  142 (146)
                      |++|.|+|..-+.+...|++.       .+...|+|+.....+.......+..++++||.+ .+=|+
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~-------~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL   60 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAIL-------PEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL   60 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEec-------CCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE
Confidence            789999999999999999993       457888888777665444444688899999988 55444

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.

>PF01016 Ribosomal_L27: Ribosomal L27 protein; InterPro: IPR001684 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=94.46  E-value=0.069  Score=36.12  Aligned_cols=47  Identities=17%  Similarity=0.321  Sum_probs=38.8

Q ss_pred             ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcC
Q 032149            3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLS   50 (146)
Q Consensus         3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~   50 (146)
                      +|.-..+.|.||+.|..  -..|-||.++..-. |..|||..-|.+.+..
T Consensus        22 vK~~~G~~V~~G~IivRQRgtk~hPG~NVg~Gr-D~TLfAl~~G~V~f~~   70 (81)
T PF01016_consen   22 VKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGR-DHTLFALVDGRVKFTK   70 (81)
T ss_dssp             ESSSTTCEESSTSEEEEBSSSSSEEBTTEEEET-TSEEEESSSCEEEEEE
T ss_pred             EEEeCCEEEcCCCEEEEeCCCcCcCCCCEEECC-CCcEEEecCEEEEEEE
Confidence            34556789999998863  35799999999865 8999999999998854

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 [, ]. L27 is a protein from the large (50S) subunit; it is essential for ribosome function, but its exact role is unclear. It belongs to a family of ribosomal proteins, examples of which are found in bacteria, chloroplasts of plants and red algae and the mitochondria of fungi (e.g. MRP7 from yeast mitochondria). The schematic relationship between these groups of proteins is shown below. Bacterial L27 Nxxxxxxxxx Algal L27 Nxxxxxxxxx Plant L27 tttttNxxxxxxxxxxxxx Yeast MRP7 tttNxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 't': transit peptide. 'N': N-terminal of mature protein. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZJQ_T 2ZJP_T 3PIP_T 3DLL_T 3PIO_T 1Y69_U 3CF5_T 2ZJR_T 1VSA_U 3PYT_W ....

>CHL00121 rpl27 ribosomal protein L27; Reviewed

Probab=94.00  E-value=0.12  Score=35.20  Aligned_cols=59  Identities=20%  Similarity=0.268  Sum_probs=43.5

Q ss_pred             cccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecC
Q 032149            4 KEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (146)
Q Consensus         4 ~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~   67 (146)
                      |.-..+.|.||+.|..  ...|-||.++-.-. |..|||...|.+.+...    ..++..|+|.|.
T Consensus        24 K~~~gq~V~~G~IivRQRGtk~hPG~NVg~Gr-D~TlfAl~~G~V~f~~~----~~~~~~vsv~~~   84 (86)
T CHL00121         24 KRFGGEKVSAGNILIRQRGTKFKPGLNVGCGK-DFTLYALIDGFVKFKKK----NKKQKSINVINI   84 (86)
T ss_pred             EEcCCEEEcCCcEEEEcCCCeECCCCcccccC-CceEEEccceEEEEEEe----CCCCEEEEEeec
Confidence            4456789999998864  34699999887643 99999999999988531    223456777764

>PRK05435 rpmA 50S ribosomal protein L27; Validated

Probab=93.87  E-value=0.19  Score=33.96  Aligned_cols=47  Identities=19%  Similarity=0.288  Sum_probs=37.8

Q ss_pred             ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcC
Q 032149            3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLS   50 (146)
Q Consensus         3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~   50 (146)
                      +|.-..+.|.||..|..  ...|.||.++-.-. |..|||...|.+.+..
T Consensus        23 vK~~~g~~V~~G~IivRQRGtk~~PG~nVg~Gr-D~TlfA~~~G~V~f~~   71 (82)
T PRK05435         23 VKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGK-DHTLFALVDGVVKFER   71 (82)
T ss_pred             eEecCCEEEcCCcEEEEeCCCeECCCCCEeecC-CceEEEecceEEEEEE
Confidence            34456789999998863  34699999999853 9999999999998853

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

Probab=93.63  E-value=0.24  Score=48.49  Aligned_cols=62  Identities=16%  Similarity=0.165  Sum_probs=55.9

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .+.||+|.|.|..+..+..++.+        ...+.|..++++...+...  .-+..|.+|++|.++|.++.
T Consensus      1160 lk~g~iv~G~V~nv~~~glfi~l--------s~~v~a~v~is~~~ds~~k--~w~k~~~~gklv~~rv~~ve 1221 (1710)
T KOG1070|consen 1160 LKIGDIVRGFVKNVETKGLFIAL--------SRKVEAFVPISGLSDSFEK--EWEKHLPVGKLVTGRVLSVE 1221 (1710)
T ss_pred             cccCceeEEEEEEecCCcEEEEE--------ccceEEEEEccccccchhh--hhhccCCccceeeeEEEEee
Confidence            48899999999999999999998        7889999999998877766  77889999999999999863

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=90.91  E-value=1.2  Score=27.92  Aligned_cols=48  Identities=19%  Similarity=0.099  Sum_probs=25.3

Q ss_pred             CCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEE
Q 032149           76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASV  141 (146)
Q Consensus        76 ~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~V  141 (146)
                      +|+++..+|++.++..|+++-        ...-.-+|+.++.          .+-+++||.|.+-|
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~--------~~~~~vlLp~~e~----------~~~~~~Gd~v~VFv   48 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDD--------GEGKEVLLPKSEV----------PEPLKVGDEVEVFV   48 (61)
T ss_dssp             --------EEEE-SSEEEEEE--------TT-EEEEEEGGG----------------TTSEEEEEE
T ss_pred             CCCCcceEEEEEeCCEEEEEC--------CCCCEEEechHHc----------CCCCCCCCEEEEEE
Confidence            589999999999999999986        4456677776544          34478899887654

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

Probab=90.88  E-value=1  Score=37.01  Aligned_cols=50  Identities=18%  Similarity=0.215  Sum_probs=33.6

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      +..|-|.|-+......++-+        ...+.|+||.|++          ....+.|+.+.|||+.+
T Consensus       156 nq~v~~tVYr~~~~G~fv~~--------e~~~~GfIh~sEr----------~~~prlG~~l~~rVi~~  205 (287)
T COG2996         156 NQEVDATVYRLLESGTFVIT--------ENGYLGFIHKSER----------FAEPRLGERLTARVIGV  205 (287)
T ss_pred             cCeeeeEEEEEeccceEEEE--------cCCeEEEEcchhh----------cccccCCceEEEEEEEE
Confidence            44445555554444444433        4678899998765          45569999999999975

>TIGR00062 L27 ribosomal protein L27

Probab=90.86  E-value=0.53  Score=31.93  Aligned_cols=47  Identities=19%  Similarity=0.326  Sum_probs=37.6

Q ss_pred             ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcC
Q 032149            3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLS   50 (146)
Q Consensus         3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~   50 (146)
                      +|.-..+.|.||+.|..  ...|-||.++-.-. |..|||...|.+....
T Consensus        23 vK~~~gq~V~~G~IivRQRGtk~hPG~nVg~Gr-D~TlfAl~~G~V~f~~   71 (83)
T TIGR00062        23 VKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGK-DHTLFALSDGVVKFEK   71 (83)
T ss_pred             eEecCCEEEcCCcEEEEcCCceECCCCcccccC-CCeEEEecceEEEEEE
Confidence            34456789999998864  34699999998753 9999999999998853

Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.

>PF01959 DHQS: 3-dehydroquinate synthase (EC 4

Probab=90.02  E-value=3.8  Score=34.85  Aligned_cols=93  Identities=15%  Similarity=0.345  Sum_probs=63.7

Q ss_pred             EEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEec
Q 032149           10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMT   89 (146)
Q Consensus        10 iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v~~   89 (146)
                      +..||+.=...+|+.+|.-+..-..+|+-+....|++++.        +++.+.|+-..        +.   -++.-+-+
T Consensus       246 v~~pg~kT~YLSEL~sG~~VlvVd~~G~tR~~~VGRvKIE--------~RPLllIeA~~--------~g---~~~svilQ  306 (354)
T PF01959_consen  246 VLMPGGKTRYLSELRSGDEVLVVDADGRTRTAIVGRVKIE--------RRPLLLIEAEA--------DG---KRISVILQ  306 (354)
T ss_pred             EEcCCCceeehhhhcCCCEEEEEeCCCCEEEEEeeEEEEe--------ecceEEEEEEe--------CC---eEEEEEEe
Confidence            4678998777788999999887666999999999999995        36677777431        22   23334567


Q ss_pred             ceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 032149           90 RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        90 ~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis  143 (146)
                      +-|.+.+..-++.+        ++              --.++|||.|.+++..
T Consensus       307 naetIRlv~p~G~~--------vs--------------Vt~Lk~GD~vL~~~~~  338 (354)
T PF01959_consen  307 NAETIRLVGPDGEP--------VS--------------VTELKPGDEVLVYLEE  338 (354)
T ss_pred             cCcEEEEECCCCCE--------ee--------------eeecCCCCEEEEEecC
Confidence            77888884322211        11              2346889988887653

6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process

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

Probab=89.80  E-value=1.4  Score=33.62  Aligned_cols=67  Identities=21%  Similarity=0.098  Sum_probs=43.5

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccc------cceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR------EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~------~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      ..|-.|++|-|.|+.+....+++++...+-..++      ..|.   +-++-.....+  +++ ....|+.||-+|+..
T Consensus        77 FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~---p~~n~P~f~~~--d~s-~I~~~~~VR~kiigt  149 (170)
T KOG3298|consen   77 FKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFD---PGENPPNFQTE--DES-VIQKGVEVRLKIIGT  149 (170)
T ss_pred             EeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccC---CCCCCCccccc--ccc-eeeeCcEEEEEEEEE
Confidence            4588899999999999999999999655432221      1222   22221111112  333 688999999999864

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

Probab=89.29  E-value=0.64  Score=41.97  Aligned_cols=60  Identities=8%  Similarity=0.156  Sum_probs=48.3

Q ss_pred             CCCCCEE-----EEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 032149           74 PEPGSVV-----IARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        74 P~~GdiV-----iG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis  143 (146)
                      ++++|+.     .|+|+.+++..++|++        ....+|++|.+|.......  +.++.+.+|+-|-.+-+.
T Consensus       661 ~~~~~l~~g~vy~~tIt~~rd~G~~V~l--------~p~~~~Llh~sqL~~e~ia--kpsd~levGq~I~vk~ie  725 (760)
T KOG1067|consen  661 DQVQDLEFGGVYTATITEIRDTGVMVEL--------YPMQQGLLHNSQLDQEKIA--KPSDLLEVGQEIQVKYIE  725 (760)
T ss_pred             ccccceEeeeEEEEEEeeecccceEEEe--------cCCchhhccchhccccccc--ChHHHHhhcceeEEEEEe
Confidence            4555554     6899999999999999        3357799999999877666  788889999999877553

>PRK02290 3-dehydroquinate synthase; Provisional

Probab=88.92  E-value=5.1  Score=33.99  Aligned_cols=93  Identities=17%  Similarity=0.367  Sum_probs=62.3

Q ss_pred             EEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEec
Q 032149           10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMT   89 (146)
Q Consensus        10 iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v~~   89 (146)
                      +..||+.=...+|+.+|.-+-.-..+|+-+..+.|++++.        +++.+-|+-..       -|    -++.-+-+
T Consensus       236 v~~pgg~T~YLsEL~sG~eVlvVd~~G~tR~~~VGRvKIE--------~RPL~lIeAe~-------~g----~~~~viLQ  296 (344)
T PRK02290        236 VRVPGDKTRYLSELRSGDEVLVVDADGNTREAIVGRVKIE--------KRPLLLIEAEY-------GG----KRIRTILQ  296 (344)
T ss_pred             EEcCCCcchhhHhhcCCCEEEEEeCCCCEEEEEeeEEEEe--------eccEEEEEEEe-------CC----eEEEEEEe
Confidence            4679998877788999998887666999999999999995        35666666421       12    22333456


Q ss_pred             ceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 032149           90 RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        90 ~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis  143 (146)
                      +-|.+.+..-+++        .++              --.++|||.|.+++..
T Consensus       297 naetIrlv~~dG~--------~vs--------------Vt~Lk~GD~VL~~~~~  328 (344)
T PRK02290        297 NAETIRLVTPDGK--------PVS--------------VVDLKPGDEVLGYLEE  328 (344)
T ss_pred             cCcEEEEECCCCC--------Eee--------------eeecCCCCEEEEEecC
Confidence            7788887422221        111              2235888888887643

>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]

Probab=87.88  E-value=1.4  Score=32.54  Aligned_cols=63  Identities=22%  Similarity=0.279  Sum_probs=46.1

Q ss_pred             ccccCCcEEecCCccCCC--CCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCC
Q 032149            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK   68 (146)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~--~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~   68 (146)
                      +|.+.++.|.||+.|...  ..|-||.++=.-. |..|||-.-|.++.......-  .++.|.|.|..
T Consensus        50 vKk~egq~V~~G~IIvrQRgtkfHPG~nVGiGK-DhtifaL~eG~Vrf~k~~~~~--~Rk~i~V~~~~  114 (144)
T KOG4600|consen   50 VKKYEGQSVIPGNIIVRQRGTKFHPGDNVGIGK-DHTIFALEEGRVRFEKSKITP--PRKWIGVDPRG  114 (144)
T ss_pred             ceecCCeeeecccEEEEecccccCCCcccccCC-cceEEEeeccEEEEEEccCCC--CcceEEEeecC
Confidence            466778999999998753  3577877666543 889999999999986533222  35788888753

>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=86.37  E-value=4.2  Score=29.36  Aligned_cols=69  Identities=17%  Similarity=0.154  Sum_probs=37.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccc-----cccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKS-----VREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~-----l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      |-+|.++.|+|.+.+.+...|.+.-.++--     |..+ ...=+.+++=-..- ..+-.-+|..|+.||=||.+.
T Consensus         1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~p-s~fd~~~~~W~W~~-~~~~~l~~d~ge~IRFRV~~~   74 (122)
T PF08292_consen    1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEP-SRFDEEEQAWVWEY-DEEQELFFDIGEEIRFRVESE   74 (122)
T ss_dssp             --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TT-EEEECCCTEEEEEE-SSSEEEEE-TT-EEEEEEEEE
T ss_pred             CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCC-CccCccCCEEEEEC-CCCceeEccCCCEEEEEEeEE
Confidence            668999999999999999999985554411     1100 00001111100001 014456679999999999875

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

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

Probab=85.54  E-value=1.4  Score=38.83  Aligned_cols=62  Identities=21%  Similarity=0.299  Sum_probs=49.0

Q ss_pred             CCCCCEEEEEEEEEecce--EEEEEEeecccccccceeeEEecccccccccc--ccccccCCCCCCEEEEEEEE
Q 032149           74 PEPGSVVIARVTKVMTRM--ASADIMCVGAKSVREKFSGIIRQQDVRATEID--KVDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~--~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d--~~~~~~~~~~GDiV~A~Vis  143 (146)
                      -.+|++-.|+|++|-+..  |||||        ...-.|+||.+++.+....  ..++...++.|+.+..+|..
T Consensus        35 ~~~gniy~grv~~i~p~~~aafvdi--------g~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~k  100 (487)
T COG1530          35 QIVGNIYKGRVTRVLPSLEAAFVDI--------GLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVK  100 (487)
T ss_pred             eeecCceEEEecccCccchhheeec--------cCCccceEEecccchhhhhcccccceeeecCCceEEEEEEe
Confidence            367999999999998865  99999        5677899999998762222  11356799999999988875

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

Probab=84.08  E-value=1.1  Score=36.74  Aligned_cols=66  Identities=17%  Similarity=0.245  Sum_probs=48.2

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      .-.|+++++|++.|..|..-.|.|.++-.+      ...|++--|+.+.....  ++....++|-.=.+-|+.+
T Consensus        11 ~kyPev~e~VmvnV~sIaemGayv~LlEYn------niEGmiLlsELSrRRIR--SI~klirVGr~E~vvVlrV   76 (304)
T KOG2916|consen   11 NKYPEVEEIVMVNVRSIAEMGAYVKLLEYN------NIEGMILLSELSRRRIR--SIQKLIRVGRNEPVVVLRV   76 (304)
T ss_pred             ccCCCcccEEEEEeeEehhccceEeeeecC------CcccchhhhHHHHHHHH--HHHHHHhcCCcceEEEEEE
Confidence            346999999999999999999999996443      35677777776655555  6666677776555555544

>PRK05054 exoribonuclease II; Provisional

Probab=83.68  E-value=5.3  Score=36.44  Aligned_cols=65  Identities=11%  Similarity=0.248  Sum_probs=47.3

Q ss_pred             CCCCC--EEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccc---cc---c--cccc--ccCCCCCCEEEEEE
Q 032149           74 PEPGS--VVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT---EI---D--KVDM--HLSFRPGDIVRASV  141 (146)
Q Consensus        74 P~~Gd--iViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~---~~---d--~~~~--~~~~~~GDiV~A~V  141 (146)
                      .++|+  ..-|.|++++....+|+|.       .....|++|.+.+...   +.   +  ...+  ...|+.||-|+.+|
T Consensus       557 ~~~G~~~~f~g~I~~v~~~G~fV~l~-------~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v  629 (644)
T PRK05054        557 DKAGTDTRFAAEIIDISRGGMRVRLL-------ENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTL  629 (644)
T ss_pred             hccCCCeEEEEEEEeeecCcEEEEEe-------CCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEE
Confidence            35665  9999999999999999993       3457899998877431   10   1  1111  24699999999999


Q ss_pred             EEee
Q 032149          142 VSFM  145 (146)
Q Consensus       142 is~~  145 (146)
                      .++.
T Consensus       630 ~~vd  633 (644)
T PRK05054        630 AEVR  633 (644)
T ss_pred             EEEc
Confidence            9864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	146
2nn6_I	209	Structure Of The Human Rna Exosome Composed Of Rrp4		5e-18
4ifd_I	301	Crystal Structure Of An 11-subunit Eukaryotic Exoso		2e-08

>pdb|2NN6|I Chain I, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 209

Iteration: 1
 Score = 86.7 bits (213), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 50/132 (37%), Positives = 72/132 (54%), Gaps = 6/132 (4%)
Query: 13  PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
           PGE L    E   G G Y    +G +++SL G L   S         P V V        
Sbjct: 24  PGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 77
Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
           +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ SFR
Sbjct: 78  LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFR 137
Query: 133 PGDIVRASVVSF 144
           PGDIV A V+S 
Sbjct: 138 PGDIVLAKVISL 149

>pdb|4IFD|I Chain I, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 301

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 36/126 (28%), Positives = 56/126 (44%), Gaps = 34/126 (26%)
Query: 53  PDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAK---------- 102
           P +   R T +   +     +P+ G +V+ RVT++  + A+ +I+ V  K          
Sbjct: 121 PGTEKGRKTNKYANNDFANNLPKEGDIVLTRVTRLSLQRANVEILAVEDKPSPIDSGIGS 180
Query: 103 ------------------------SVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVR 138
                                    + E F GIIR QDVR+T+ D+V +   F+PGDIVR
Sbjct: 181 NGSGIVAAGGGSGAATFSVSQASSDLGETFRGIIRSQDVRSTDRDRVKVIECFKPGDIVR 240
Query: 139 ASVVSF 144
           A V+S 
Sbjct: 241 AQVLSL 246

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	146
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	5e-34
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	1e-22
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	3e-19
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	6e-19
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	7e-12
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	5e-11

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 Length = 209

 Score =  117 bits (293), Expect = 5e-34
 Identities = 49/135 (36%), Positives = 71/135 (52%), Gaps = 6/135 (4%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
              PGE L    E   G G Y    +G +++SL G L             P V V     
Sbjct: 21  YCIPGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMK----SSENGALPVVSVVRETE 74

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHL 129
              +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ 
Sbjct: 75  SQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYK 134

Query: 130 SFRPGDIVRASVVSF 144
           SFRPGDIV A V+S 
Sbjct: 135 SFRPGDIVLAKVISL 149

>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 = 87.4 bits (216), Expect = 1e-22
 Identities = 29/138 (21%), Positives = 51/138 (36%), Gaps = 16/138 (11%)

Query: 8   MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH 67
           M  V PG+ +G A E   G+G Y     G ++A++ G L             P       
Sbjct: 1   MRFVMPGDRIGSAEEYVKGEGVYE--EGGELFAAVAGKLIIKDRVAKVESISPI------ 52

Query: 68  KAHGPVPEPGSVVIARVTKVMTRMASADIMCV--GAKSVREKFSGIIRQQDVRATEIDKV 125
               P    G VV+ RV  +   +A  ++       +    +  GI+   +V    + ++
Sbjct: 53  ----PEIVKGDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEI 108

Query: 126 DMHLSFRPGDIVRASVVS 143
                    DI++A V+ 
Sbjct: 109 SEA--VGYLDILKARVIG 124

>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 Length = 308

 Score = 80.6 bits (198), Expect = 3e-19
 Identities = 26/141 (18%), Positives = 53/141 (37%), Gaps = 12/141 (8%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
           ++ +  LV PG+ +   T    G G Y+      + AS+ G +               + 
Sbjct: 35  RDTKKHLVVPGDTITTDTGFMRGHGTYM--GEEKLIASVAGSVE---------RVNKLIC 83

Query: 64  VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID 123
           V   K    + E G +V+ R+T+V  +    +        +      +   +  R +  D
Sbjct: 84  VKALKTR-YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAED 142

Query: 124 KVDMHLSFRPGDIVRASVVSF 144
           ++ M    + GD++ A V + 
Sbjct: 143 ELAMRGFLQEGDLISAEVQAV 163

>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 Length = 251

 Score = 79.0 bits (194), Expect = 6e-19
 Identities = 27/144 (18%), Positives = 48/144 (33%), Gaps = 19/144 (13%)

Query: 3   VKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTV 62
           +  +   +V PGE+L    E +     Y+ K N   Y+++ GL            +    
Sbjct: 11  IVLQPRSIVVPGELLA-EGEFQIPWSPYILKINSKYYSTVVGLFD---------VKDTQF 60

Query: 63  EVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV-RATE 121
           EV   +     P+   +VI  V  V       DI           +   +   ++   + 
Sbjct: 61  EVIPLEGSFYYPKINDIVIGLVEDVEIYGWVVDIKA--------PYKAYLPASNLLGRSI 112

Query: 122 IDKVDMHLSFRPGDIVRASVVSFM 145
               D+      GD V A + +F 
Sbjct: 113 NVGEDLRRYLDVGDYVIARIENFD 136

>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 Length = 235

 Score = 59.7 bits (144), Expect = 7e-12
 Identities = 35/144 (24%), Positives = 52/144 (36%), Gaps = 21/144 (14%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
           ++    +V PGE L +  E       YV  + G+  A++ GLLR                
Sbjct: 5   RQLAGRIVVPGEPLPEEVEAS---PPYVIDYKGVKRATVVGLLRE-------KGDGGGRA 54

Query: 64  VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV--RATE 121
               K    VP+ G VVI  +  V       DI           +  ++  QD   R   
Sbjct: 55  FVKLKEI-YVPQAGDVVIGLIQSVGIMNWFVDINS--------PYVAVLSVQDFLGRPFN 105

Query: 122 IDKVDMHLSFRPGDIVRASVVSFM 145
               DM    + GD ++A VV+F 
Sbjct: 106 PAVDDMQSLLKVGDYIKAKVVAFD 129

>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 Length = 229

 Score = 57.4 bits (138), Expect = 5e-11
 Identities = 31/135 (22%), Positives = 47/135 (34%), Gaps = 22/135 (16%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
           +V PG++L       AG G YV    G VYA + GL                V V   K 
Sbjct: 4   IVLPGDLLSTN-PRAAGYGTYV--EGGKVYAKIIGLFDQ---------TETHVRVIPLKG 51

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHL 129
               P  G VVI  + +V     + DI           +   +   +    + +K   + 
Sbjct: 52  R-YTPSVGDVVIGIIREVAANGWAVDIYS--------PYQAFLPVSENPEMKPNK-KPNE 101

Query: 130 SFRPGDIVRASVVSF 144
               GD + A V++ 
Sbjct: 102 VLDIGDAIIAKVLNI 116

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	146
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	100.0
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	100.0
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	99.96
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	99.96
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	99.95
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	99.95
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	99.95
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	99.54
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.03
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.02
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	98.98
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	98.97
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	98.97
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	98.97
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	98.95
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	98.93
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	98.77
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	98.73
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	98.68
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.58
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.54
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.43
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.39
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.38
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.22
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	98.12
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.1
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.09
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.04
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	98.01
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	97.9
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	97.83
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	97.81
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	97.78
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	97.78
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.68
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.65
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	97.63
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.53
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.42
2bh8_A	101	1B11; transcription, molecular evolution, unique a	96.15
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	95.89
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	95.72
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	95.25
3v2d_0	85	50S ribosomal protein L27; ribosome associated inh	93.65
3r8s_W	76	50S ribosomal protein L27; protein biosynthesis, R	92.48
2zjr_T	91	50S ribosomal protein L27; ribosome, large ribosom	91.57
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	91.29
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	90.05
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	89.71
1y71_A	130	Kinase-associated protein B; structural genomics,	87.67
2ftc_O	69	L27MT, MRP-L27, mitochondrial 39S ribosomal protei	86.74

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

Probab=100.00  E-value=4.1e-33  Score=212.44  Aligned_cols=122  Identities=23%  Similarity=0.378  Sum_probs=113.9

Q ss_pred             CcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEE
Q 032149            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV   87 (146)
Q Consensus         8 ~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v   87 (146)
                      |++|+|||.|+.+++|.+|+|||++  +|+|+||++|.+++.         ++.++|.|.++.+|.|+ ||+|+|+|+++
T Consensus         1 m~iV~PGd~l~~~~~~~~G~Gty~~--~~~i~as~~G~v~~~---------~~~v~V~~~~~~~y~p~-GdiV~G~V~~V   68 (179)
T 3m7n_A            1 MRFVMPGDRIGSAEEYVKGEGVYEE--GGELFAAVAGKLIIK---------DRVAKVESISPIPEIVK-GDVVLGRVVDL   68 (179)
T ss_dssp             CCEECTTCEEEETTTSEECTTEEEE--TTEEEESSSEEEEEE---------TTEEEEEESSCCCCCCT-TCEEEEEEEEE
T ss_pred             CeEEcCCCCCCCCCCEeccCCEEEe--CCEEEEEEEEEEEEe---------CCEEEEEECCCCcccCC-CCEEEEEEEEE
Confidence            5799999999998999999999999  999999999999984         47999999877789999 99999999999


Q ss_pred             ecceEEEEEEee--cccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 032149           88 MTRMASADIMCV--GAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        88 ~~~~~~v~I~~v--~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis  143 (146)
                      ++++|+|+|.++  +++++..+++|+||+||++..+.+  +|+++|++||+|+|+|++
T Consensus        69 ~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~--~~~~~~~~GD~V~akVi~  124 (179)
T 3m7n_A           69 RNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVK--EISEAVGYLDILKARVIG  124 (179)
T ss_dssp             CSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCS--SGGGTCCTTCEEEEEEEE
T ss_pred             eCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhh--CHhhcCCCCCEEEEEEEC
Confidence            999999999998  557788899999999999988877  999999999999999997

>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=100.00  E-value=7.2e-34  Score=221.48  Aligned_cols=133  Identities=38%  Similarity=0.617  Sum_probs=118.6

Q ss_pred             CCcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 032149            7 EMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK   86 (146)
Q Consensus         7 ~~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~   86 (146)
                      ++++|+|||.|+..++|++|+|||++  +|+||||++|.+.+..    .+..+++++|.|.++.+|.|++||+|+|+|++
T Consensus        18 ~~~iV~PGd~l~~~~~~~~G~Gty~~--~g~I~Asv~G~v~~~~----~~~~~~vi~V~p~~~~~y~p~vGDvV~G~V~~   91 (209)
T 2nn6_I           18 PVRYCIPGERLCNLEEGSPGSGTYTR--HGYIFSSLAGCLMKSS----ENGALPVVSVVRETESQLLPDVGAIVTCKVSS   91 (209)
T ss_dssp             --CCCCTTCEEEETTTCCCSSSCEEE--TTEEECCSCSCBCCCB----CTTSSBC-CBCCSCCCCCCCCTTCEEEEEEEE
T ss_pred             CCcEEcCCCCCCCCCCeeecCCEEEE--CCEEEEEEEEEEEEec----cCCcccEEEEecCCCCcCCCCCCCEEEEEEEE
Confidence            46799999999988899999999999  9999999999987631    12234679999987667999999999999999


Q ss_pred             EecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           87 VMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        87 v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +++++|+|+|.+++++.|..+|+|+||+||++.++.++.+|+++|++||+|+|+|+++.
T Consensus        92 v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~  150 (209)
T 2nn6_I           92 INSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLG  150 (209)
T ss_dssp             ECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEE
T ss_pred             EECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEe
Confidence            99999999999999999999999999999999999988999999999999999999975

>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C

Probab=99.96  E-value=1.2e-28  Score=196.58  Aligned_cols=119  Identities=22%  Similarity=0.267  Sum_probs=107.9

Q ss_pred             CCcEEecCCccCCCCCeeeCC--cEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 032149            7 EMVLVTPGEVLGKATEVKAGK--GAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV   84 (146)
Q Consensus         7 ~~~iV~PGd~l~~~~~~~~G~--Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V   84 (146)
                      ++++|+|||.|+. ++|.+|+  |||.+  +|+||||++|.+...         ++.++|.|.++.+|.|++||+|+|+|
T Consensus        15 ~~~iV~PGd~l~~-~~~~~G~~~Gty~~--~g~i~as~~G~v~~~---------~~~v~V~p~~~~~y~p~~GDiV~G~V   82 (251)
T 2je6_I           15 PRSIVVPGELLAE-GEFQIPWSPYILKI--NSKYYSTVVGLFDVK---------DTQFEVIPLEGSFYYPKINDIVIGLV   82 (251)
T ss_dssp             SSCEECTTCEEEE-ECCCCCCCTTEEEE--TTEEEECSSEEEEEE---------TTEEEEEESCCSCCCCCTTCEEEEEE
T ss_pred             CCcEEcCCCCCcc-CCeeeCCCCCEEEE--CCEEEEEEEEEEEEe---------CCEEEEEECCCcccCCCCCCEEEEEE
Confidence            3689999999996 6799999  99999  999999999999884         25899999977689999999999999


Q ss_pred             EEEecceEEEEEEeecccccccceeeEEeccccccccccc-cccccCCCCCCEEEEEEEEee
Q 032149           85 TKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDK-VDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        85 ~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~-~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++++++.|+|+|        ..+++|+||.++++..+.+. .+|+++|++||+|+|+|+++.
T Consensus        83 ~~v~~~ga~VdI--------~~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~  136 (251)
T 2je6_I           83 EDVEIYGWVVDI--------KAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFD  136 (251)
T ss_dssp             EEECSSEEEEEC--------SSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEE
T ss_pred             EEEeCceEEEEc--------CCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEEC
Confidence            999999999998        67899999999998766544 699999999999999999975

>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=99.96  E-value=3.1e-28  Score=191.92  Aligned_cols=116  Identities=26%  Similarity=0.359  Sum_probs=103.7

Q ss_pred             CcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEE
Q 032149            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV   87 (146)
Q Consensus         8 ~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v   87 (146)
                      +++|+|||.|+. ++|++|+|||.+  +|+|+||++|.+...         ++.++|.|.+ .+|.|++||+|+|+|+++
T Consensus         2 ~~iV~PGd~l~~-~~~~~G~Gty~~--~g~i~as~~G~v~~~---------~~~v~V~p~~-~~y~p~~GDiV~G~V~~v   68 (229)
T 2ba0_A            2 RKIVLPGDLLST-NPRAAGYGTYVE--GGKVYAKIIGLFDQT---------ETHVRVIPLK-GRYTPSVGDVVIGIIREV   68 (229)
T ss_dssp             CCEECTTCEEES-CTTSBCTTEEEE--TTEEEECSSEEEEEC---------SSCEEEEECS-SSCCCCTTCEEEEEEEEE
T ss_pred             CCEEcCCCCccc-CCeEecCCEEEe--CCEEEEEEEEEEEEe---------CCEEEEEeCC-CcccCCCCCEEEEEEEEE
Confidence            579999999985 679999999999  999999999999884         2479999986 579999999999999999


Q ss_pred             ecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           88 MTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        88 ~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++++|+|+|        ..+++|+||.++++. ..+..+|+++|++||+|+|||+++.
T Consensus        69 ~~~~a~V~I--------~~~~~g~l~isev~~-~~~~~~~~~~l~~GD~V~arVi~v~  117 (229)
T 2ba0_A           69 AANGWAVDI--------YSPYQAFLPVSENPE-MKPNKKPNEVLDIGDAIIAKVLNID  117 (229)
T ss_dssp             CSSEEEEEC--------SSSSCEEEEGGGCTT-CCTTSCGGGTCCTTCEEEEEEEEEC
T ss_pred             eCCeEEEEe--------CCCeEEEEEHHHccc-cccccchhcccCCCCEEEEEEEEEC
Confidence            999999998        778999999999983 2234589999999999999999974

>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=99.95  E-value=3.4e-28  Score=192.24  Aligned_cols=119  Identities=26%  Similarity=0.275  Sum_probs=61.2

Q ss_pred             CcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEE
Q 032149            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV   87 (146)
Q Consensus         8 ~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v   87 (146)
                      +++|+|||.|+. ++|.+|+|||.+  +|.|+||++|.+...       +++..++|.|.+ .+|.|++||+|+|+|+++
T Consensus         9 ~~iV~PGd~l~~-~~~~~G~Gty~~--~~~I~Asv~G~v~~~-------~~~~~vsV~p~~-~~y~p~~GDiV~G~V~~v   77 (235)
T 2z0s_A            9 GRIVVPGEPLPE-EVEASPPYVIDY--KGVKRATVVGLLREK-------GDGGGRAFVKLK-EIYVPQAGDVVIGLIQSV   77 (235)
T ss_dssp             --------------------------------------------------------------CCCCCCTTCCEEEEEEEE
T ss_pred             CcEEeCCCCccc-CceEcCCCEEEE--CCEEEEEEeEEEEEe-------CCccEEEEEeCC-CccCCCCCCEEEEEEEEE
Confidence            479999999986 669999999999  999999999998773       234589999985 569999999999999999


Q ss_pred             ecceEEEEEEeecccccccceeeEEecccccc--ccccccccccCCCCCCEEEEEEEEee
Q 032149           88 MTRMASADIMCVGAKSVREKFSGIIRQQDVRA--TEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        88 ~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~--~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++++|+|+|        ..+++|+||.+|+..  .+.+..+|+++|++||+|+|+|+++.
T Consensus        78 ~~~~~~V~I--------~~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~  129 (235)
T 2z0s_A           78 GIMNWFVDI--------NSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFD  129 (235)
T ss_dssp             CSSEEEEEC--------SSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEEC
T ss_pred             eCCeEEEEe--------CCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEEC
Confidence            999999998        778999999999964  33455699999999999999999974

>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=99.95  E-value=5.7e-28  Score=197.59  Aligned_cols=124  Identities=22%  Similarity=0.352  Sum_probs=95.7

Q ss_pred             cCCcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 032149            6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT   85 (146)
Q Consensus         6 ~~~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~   85 (146)
                      ..+++|+|||.|+..++|++|+|||++  +|+||||++|.++..         ++.++|.|.+ .+|+|++||+|+|+|+
T Consensus        37 ~~~~iVlPGd~L~~~~~~~~G~Gty~~--~g~I~Asv~G~v~~~---------~~~vsV~p~~-~rY~P~vGDvViG~Vt  104 (308)
T 2nn6_H           37 TKKHLVVPGDTITTDTGFMRGHGTYMG--EEKLIASVAGSVERV---------NKLICVKALK-TRYIGEVGDIVVGRIT  104 (308)
T ss_dssp             ---CBCCTTCBCCCCTTCCBCTTEEEC--SSSEEECSSEEEEEE---------TTEEEEEESS-CCCCCCSSBCCCEEEE
T ss_pred             CCCcEEeCCCCCCCCCCEeecCCeEEE--CCEEEEEEEEEEEec---------CCEEEEeeCC-CccCCCCCCEEEEEEE
Confidence            356899999999988999999999999  999999999999874         4699999986 5799999999999999


Q ss_pred             EEecceEEEEEEeeccccccc---ce-eeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           86 KVMTRMASADIMCVGAKSVRE---KF-SGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        86 ~v~~~~~~v~I~~v~~~~l~~---~~-~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++++++|+|+|.+..+..+..   .| .|++|.++.    .|..+|+++|++||+|+|||++++
T Consensus       105 ~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~----~D~~~m~~~l~vGDlV~ArVisv~  164 (308)
T 2nn6_H          105 EVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSA----EDELAMRGFLQEGDLISAEVQAVF  164 (308)
T ss_dssp             EEETTEEEEECSSSSCEEEESSCCC-----------------CHHHHHHSCSSCEECCEEEEEE
T ss_pred             EEeCceEEEEECCCcCCceechhhccccceeecccc----hhhhhhhccCCCCCEEEEEEEEcC
Confidence            999999999996544432221   23 355554433    344689999999999999999975

>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=99.95  E-value=1.4e-27  Score=193.68  Aligned_cols=121  Identities=21%  Similarity=0.207  Sum_probs=92.9

Q ss_pred             CcEEecCCccCCCC-----------------------Ceee--CCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeE
Q 032149            8 MVLVTPGEVLGKAT-----------------------EVKA--GKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTV   62 (146)
Q Consensus         8 ~~iV~PGd~l~~~~-----------------------~~~~--G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i   62 (146)
                      +++|+|||.|+..+                       +|++  |+|||+.  ++.|+||++|.++..+...  ....+.+
T Consensus        39 ~~iVlPGD~L~~~~~~~~~~~g~~~~~~l~~~~~~~~~~~~~~G~Gty~~--~~~I~as~aG~l~~~~~~~--~~~~~~v  114 (289)
T 2nn6_G           39 GQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRC--GDRLLVTKCGRLRHKEPGS--GSGGGVY  114 (289)
T ss_dssp             SSBCCSSEEECCSCSCCEECSSEEECC-------------------------CCCEEECSCCEEEEECCTT--TSSCCEE
T ss_pred             CcEEeCCCCcCccccccccccccccccccccccccCcceEEccCCCeEEE--CCEEEEEEeEeEEeccCCc--cCccceE
Confidence            57899999999765                       7999  9999999  9999999999998853100  0011489


Q ss_pred             EEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccc-cccccccccccCCCCCCEEEEEE
Q 032149           63 EVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVR-ATEIDKVDMHLSFRPGDIVRASV  141 (146)
Q Consensus        63 ~V~p~~~~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~-~~~~d~~~~~~~~~~GDiV~A~V  141 (146)
                      +|.|.+ .+|+|++||+|+|+|++++.++|+|+|        ..++.|+||.++++ ++  .  +|+++|++||+|+|||
T Consensus       115 ~V~~~~-~rYiP~vGDiVIG~Vt~v~~~~~~VdI--------~s~~~a~L~~~~f~Gat--k--~~r~~f~~GDlV~ArV  181 (289)
T 2nn6_G          115 WVDSQQ-KRYVPVKGDHVIGIVTAKSGDIFKVDV--------GGSEPASLSYLSFEGAT--K--RNRPNVQVGDLIYGQF  181 (289)
T ss_dssp             EEECCC-SSCCCCSSEEEEEEEEEEETTEEEEEC--------SSSSCCCEESCSSSCCS--S--CSSSSSCTTCEEEEEE
T ss_pred             EEEecC-CCCCCCCCCEEEEEEEEEeCcEEEEEE--------CCCceeEEehhhcCcch--h--hhhhhcCCCCEEEEEE
Confidence            999986 689999999999999999999999999        57899999999887 33  3  7999999999999999


Q ss_pred             EEee
Q 032149          142 VSFM  145 (146)
Q Consensus       142 is~~  145 (146)
                      ++++
T Consensus       182 ~s~~  185 (289)
T 2nn6_G          182 VVAN  185 (289)
T ss_dssp             EECC
T ss_pred             EEcC
Confidence            9975

>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=99.54  E-value=2.2e-14  Score=108.69  Aligned_cols=65  Identities=14%  Similarity=0.139  Sum_probs=57.7

Q ss_pred             CCCCCCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        70 ~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++|+|++||+|+|+|+++.++.|+|+|        .. ++.|+||.+++.. ..  .+|+++|++||+|+|||+++.
T Consensus         1 krY~P~~gDvViG~V~~v~~~~~~VdI--------~~~~~~a~L~~s~~~g-~~--k~~r~~l~~GDlV~ArV~~~~   66 (175)
T 2ja9_A            1 KRYIPSVNDFVIGVIIGTFSDSYKVSL--------QNFSSSVSLSYMAFPN-AS--KKNRPTLQVGDLVYARVCTAE   66 (175)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEES--------STTSCCEEEETTSSTT-CC--SSSCCCCCTTCEEEEEEEECC
T ss_pred             CCccCCCcCEEEEEEEEEECcEEEEEE--------CCCCccEEEEHHHCCc-hh--hhhhccCCCCCEEEEEEEEec
Confidence            379999999999999999999999999        66 8999999998862 22  379999999999999999874

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

Probab=99.03  E-value=1.8e-09  Score=77.74  Aligned_cols=62  Identities=24%  Similarity=0.297  Sum_probs=56.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +++|++|.|+|+++++..|+|+|        .....|++|++++...+..  ++.+.|++||.|.|+|+++.
T Consensus         5 ~~vG~iv~G~V~~i~~~G~FV~l--------~~~~~Glihisel~~~~~~--~~~~~~~vGd~V~vkV~~vd   66 (130)
T 2k4k_A            5 FEVGSVYTGKVTGLQAYGAFVAL--------DEETQGLVHISEVTHGFVK--DINEHLSVGDEVQVKVLAVD   66 (130)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE--------ETTEEEEEEGGGTSSSCCS--CGGGTCCTTCEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEE--------CCCcEEEEEHHHCCccccc--CccccCCCCCEEEEEEEEEe
Confidence            68999999999999999999999        5679999999999876666  78999999999999999874

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

Probab=99.02  E-value=2e-09  Score=71.03  Aligned_cols=58  Identities=21%  Similarity=0.349  Sum_probs=51.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +++|+++.|+|+++.+..|+|+|        .....|++|.+++.....      +.|++||.|+|+|+++.
T Consensus         3 ~~~G~iv~G~V~~v~~~G~fV~l--------~~~~~Gllh~sel~~~~~------~~~~~Gd~V~v~V~~vd   60 (80)
T 2k52_A            3 VEPGKFYKGVVTRIEKYGAFINL--------NEQVRGLLRPRDMISLRL------ENLNVGDEIIVQAIDVR   60 (80)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE--------ETTEEEEECGGGCSSCCG------GGCCTTCEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEE--------CCCCEEEEEHHHCCcccc------eeeCCCCEEEEEEEEEE
Confidence            68999999999999999999999        557999999999864321      78999999999999874

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

Probab=98.98  E-value=1.8e-09  Score=74.63  Aligned_cols=64  Identities=19%  Similarity=0.374  Sum_probs=54.8

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeeccccccc---ceeeEEecccc-ccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE---KFSGIIRQQDV-RATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~---~~~g~l~~sdi-~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ..+++|+++.|+|+++.+..|+|+|        ..   ...|++|++++ ......  ++.+.|++||.|+++|+++.
T Consensus         8 ~~~~vG~i~~G~V~~v~~fG~FV~l--------~~~~~~~~Glvhisel~~~~~~~--~~~~~~~~Gd~V~VkV~~vd   75 (103)
T 2eqs_A            8 EEPTIGDIYNGKVTSIMQFGCFVQL--------EGLRKRWEGLVHISELRREGRVA--NVADVVSKGQRVKVKVLSFT   75 (103)
T ss_dssp             SSCCTTCEEEEEEEEECSSCEEEEE--------CSSSSCCEEEECGGGTSSSSCCC--CHHHHCCTTCEEEEEEEEEE
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEE--------cCCCCCeEEEEEHHHCCCCcccC--CcccEeCCCCEEEEEEEEEE
Confidence            3479999999999999999999999        43   68999999999 333344  77889999999999999864

>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=98.97  E-value=1.7e-09  Score=76.87  Aligned_cols=66  Identities=15%  Similarity=0.168  Sum_probs=57.2

Q ss_pred             CCCCCCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        70 ~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      -.+.|++|+++.|+|++|.+..|+|+|        .. ...|++|++++...+.+  ++.+.|++||.|+|+|+++.
T Consensus        16 ~~~~~~vG~iv~G~V~~I~~fGaFV~l--------~g~~~~Glvhisel~~~~~~--~~~~~~~~Gd~V~VkV~~vd   82 (119)
T 2cqo_A           16 MENLPALYTIFQGEVAMVTDYGAFIKI--------PGCRKQGLVHRTHMSSCRVD--KPSEIVDVGDKVWVKLIGRE   82 (119)
T ss_dssp             SCCSCCTTCEEEEEEEEEETTEEEEEC--------TTCSSCEEEEHHHHCSSCCS--CHHHHCCTTCEEEEEEEEEE
T ss_pred             hhcccCCCCEEEEEEEEEeCceEEEEE--------CCCcEEEEEEHHHCCccccc--ChhhcCCCCCEEEEEEEEEe
Confidence            346689999999999999999999998        33 36999999999766655  78899999999999999874

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

Probab=98.97  E-value=1.6e-09  Score=75.49  Aligned_cols=65  Identities=22%  Similarity=0.374  Sum_probs=57.4

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ...+++|++|.|+|+++.+..|+|+|        .....|++|.+++.....+  ++.+.|++||.|.|+|+++.
T Consensus        26 ~~~~~~G~iv~G~V~~v~~~G~fV~l--------~~~~~Gll~~sel~~~~~~--~~~~~~~vGd~V~v~V~~vd   90 (109)
T 2khj_A           26 VALNKKGAIVTGKVTAVDAKGATVEL--------ADGVEGYLRASEASRDRVE--DATLVLSVGDEVEAKFTGVD   90 (109)
T ss_dssp             TTTCCSSSEEEEEEEEECSSCEEEEC--------STTCBCCBCTTCCCSSSSS--SGGGSCCTTCEEEEEEEEEE
T ss_pred             hhcCCCCCEEEEEEEEEECCeEEEEE--------CCCCEEEEEHHHcCccccc--ChhhccCCCCEEEEEEEEEE
Confidence            34589999999999999999999999        5578999999999766555  78899999999999999874

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

Probab=98.97  E-value=4.6e-09  Score=73.89  Aligned_cols=75  Identities=17%  Similarity=0.150  Sum_probs=58.7

Q ss_pred             eEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccc-cccccccccCCCCCCEEEE
Q 032149           61 TVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT-EIDKVDMHLSFRPGDIVRA  139 (146)
Q Consensus        61 ~i~V~p~~~~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~-~~d~~~~~~~~~~GDiV~A  139 (146)
                      ...+.|......-+++|+++.|+|+++++..|+|+|        .....|++|.+++... ...  ++.+.|++||.|++
T Consensus        15 ~~~~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l--------~~~~~Glvhisel~~~~~~~--~~~~~~~vGd~V~v   84 (115)
T 2khi_A           15 VPRGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEI--------EEGVEGLVHVSEMDWTNKNI--HPSKVVNVGDVVEV   84 (115)
T ss_dssp             ------CCCSSCSSCSSCEEEEEEEEEETTEEEEEC--------STTCEEEEETTSSSCSSTTC--SSTTTCCTTCEEEE
T ss_pred             hcccCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEE--------CCCCEEEEEHHHCCcccccc--CcccEECCCCEEEE
Confidence            455667655556789999999999999999999998        5579999999998642 233  67889999999999


Q ss_pred             EEEEee
Q 032149          140 SVVSFM  145 (146)
Q Consensus       140 ~Vis~~  145 (146)
                      +|+++.
T Consensus        85 kV~~vd   90 (115)
T 2khi_A           85 MVLDID   90 (115)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            999874

>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=98.95  E-value=3.2e-09  Score=80.65  Aligned_cols=66  Identities=18%  Similarity=0.232  Sum_probs=47.5

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ..|++|++|.|+|+++++..|+|+|..      .....|++|+|++......  ++++.|++||.|.++|+++.
T Consensus        11 ~~p~~G~iv~G~V~~I~~fGaFV~L~e------~~g~eGLvhiSels~~~v~--~~~~~~~vGd~V~VkVl~vD   76 (182)
T 1kl9_A           11 KFPEVEDVVMVNVRSIAEMGAYVSLLE------YNNIEGMILLSELSRRRIR--SINKLIRIGRNECVVVIRVD   76 (182)
T ss_dssp             SSCCTTCEEEEEEEEECSSEEEEEETT------TTTEEEEEEGGGC--------------CTTCEEEEEEEEEE
T ss_pred             cCCCCCCEEEEEEEEEeccEEEEEEcc------CCCcEEEEEHHHCCCcccC--CHHHhcCCCCEEEEEEEEEE
Confidence            457999999999999999999999810      1358999999999876666  88999999999999999874

>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=98.93  E-value=5.4e-09  Score=78.90  Aligned_cols=64  Identities=19%  Similarity=0.258  Sum_probs=51.1

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccc--cceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~--~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ..|++|++|.|+|+++++..|+|+|        .  ....|++|+|++......  ++++.|++||.|.|+|+++.
T Consensus        11 ~~p~~G~iv~G~V~~i~~fGaFV~L--------~e~~gveGLvhiSels~~~v~--~~~~~~~vGd~V~vkVl~vd   76 (175)
T 2a19_A           11 KYPEIDDIVMVNVQQIAEMGAYVKL--------LEYDNIEGMILLSELSRRRIR--SIQKLIRVGKNDVAVVLRVD   76 (175)
T ss_dssp             SSCCTTCEEEEEEEEEETTEEEEEE--------TTTTTCEEEEECC----------CCCCCCCTTSEEEEEEEEEE
T ss_pred             cCCCCCCEEEEEEEEEecceEEEEE--------cCCCCcEEEEEHHHcCCcccC--CHHHcCCCCCEEEEEEEEEE
Confidence            5688999999999999999999999        3  458999999999876666  88999999999999999874

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

Probab=98.77  E-value=4.1e-08  Score=78.88  Aligned_cols=65  Identities=20%  Similarity=0.271  Sum_probs=57.4

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccc--cceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~--~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ...|++||+|.|+|+++.+..|+|+|        .  ....|++|.|++......  ++.+.|++||.|.++|+++.
T Consensus         6 ~~~p~~Gdiv~G~V~~I~~fGaFV~L--------~e~~gieGlIhiSels~~~v~--~~~~~~kvGd~V~vkVi~vD   72 (275)
T 3aev_A            6 REYPEEGEFVVATVKRIHNYGAFLEL--------DEYPGKEAFMHISEVASTWVR--NIRDYLKEGQKVVAKVIRVD   72 (275)
T ss_dssp             -CCCCTTCEEEEEEEEEETTEEEEEE--------TTSTTCEEEEEGGGSCSSCCS--CGGGTCCTTCEEEEEEEEEE
T ss_pred             ccCCCCCCEEEEEEEEEECcEEEEEE--------CCCCCeEEEEEHHHcCccccc--CHHhccCCCCEEEEEEEEEE
Confidence            35689999999999999999999999        4  368999999999866666  78999999999999999874

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

Probab=98.73  E-value=1.8e-08  Score=67.89  Aligned_cols=61  Identities=16%  Similarity=0.272  Sum_probs=52.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEeeccccccc--ceeeEEecc-ccccccccccccccCCCCCCEEEEEEEEee
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE--KFSGIIRQQ-DVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~--~~~g~l~~s-di~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .|++|+++.|+|+ +++..|+|+|        ..  ..+|++|+| ++...+..  +.++.| +||.|+++|+++.
T Consensus         8 ~~~vG~~~~G~V~-v~~fG~FVel--------~~~~~~eGLvhis~el~~~~~~--~~~~~~-~Gd~V~VkV~~vd   71 (88)
T 1luz_A            8 LPNAGDVIKGRVY-EKDYALYIYL--------FDYPHFEAILAESVKMHMDRYV--EYRDKL-VGKTVKVKVIRVD   71 (88)
T ss_dssp             CCCTTCEEEEEEE-EETTEEEEEE--------TTCTTSEEEEGGGSSCCHHHHH--HHHHHH-TTCEEEEEEEEEE
T ss_pred             CCCCCCEEEEEEE-EEccEEEEEE--------CCCCCeEEEEEeeHHhCccccc--CHhHEe-CCCEEEEEEEEEE
Confidence            4899999999999 9999999999        42  589999999 99755444  667888 9999999999874

>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=98.68  E-value=4.8e-08  Score=79.67  Aligned_cols=64  Identities=19%  Similarity=0.257  Sum_probs=56.5

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccc--cceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~--~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ..|++|++|.|+|+++.+..|+|+|        .  ....|++|.|++......  ++.+.|++||.|.++|+++.
T Consensus         9 ~~~~vG~iv~G~V~~I~~fGaFV~L--------~ey~gveGLvhiSels~~~i~--~~~~~~kvGd~V~VkVl~vD   74 (308)
T 1q8k_A            9 KFPEVEDVVMVNVRSIQEMGAYVSL--------LEYNNIEGMIHLSELSRRRIR--SINKLIRIGRNECVKVIRVD   74 (308)
T ss_dssp             CCCSSCCEEEEEEEEEETTEEEEES--------CTTTSCCEEECGGGTSCSSCS--CCTTTCSSSCEEEEEEEEEE
T ss_pred             cCCCCCCEEEEEEEEEeCcEEEEEE--------CCCCCeEEEEEhHHcCccccc--CHHHhcCCCCEEEEEEEEEe
Confidence            3478999999999999999999998        4  468899999999765555  88999999999999999874

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*

Probab=98.58  E-value=5.2e-08  Score=77.91  Aligned_cols=65  Identities=14%  Similarity=0.250  Sum_probs=57.5

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccc--cceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~--~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .+.|++|+++.|+|+++.+..|+|+|        .  ....|++|.|++......  ++.+.|++||.|.++|+++.
T Consensus         6 ~~~~~vG~iv~G~V~~I~~~GaFV~l--------~e~~~~~GlihiSels~~~v~--~~~~~~~vGd~V~VkVi~vd   72 (266)
T 3cw2_C            6 SKLPSEGEILIATVKQVFDYGSYVSL--------DEYGGLQAFLPWSEVSSKWVK--NIRDVLKENRKVIVKVIRVD   72 (266)
T ss_dssp             SSSCCTTCEEEEEEEECCSSSBEEEE--------TTTTSEECBBCGGGSSCSSCC--CHHHHSCTTCEEEEEECCCC
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEE--------cCCCCeEEEEEhHHcCccccc--CHHHhCcCCCEEEEEEEEEe
Confidence            46789999999999999999999999        4  468999999999766655  78899999999999998764

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=98.54  E-value=2.5e-07  Score=69.72  Aligned_cols=65  Identities=18%  Similarity=0.263  Sum_probs=53.6

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccc--c-------cccccCCCCCCEEEEEEE
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID--K-------VDMHLSFRPGDIVRASVV  142 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d--~-------~~~~~~~~~GDiV~A~Vi  142 (146)
                      +-|++|+++.|+|+++++..++|++         .+++|++|++++...+..  .       .+..+.|++||.|+++|+
T Consensus        77 ~~~~~Gev~~G~V~~v~~~G~fV~l---------~~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~  147 (187)
T 1go3_E           77 YIPEMYELIEGEVVDVVEFGSFVRL---------GPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIV  147 (187)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEC---------SSSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEE
T ss_pred             EccCCCCEEEEEEEEEeCcEEEEEE---------cCccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEE
Confidence            4589999999999999999999998         348999999998643321  0       146788999999999999


Q ss_pred             Eee
Q 032149          143 SFM  145 (146)
Q Consensus       143 s~~  145 (146)
                      ++.
T Consensus       148 ~vd  150 (187)
T 1go3_E          148 AIS  150 (187)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            864

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=98.43  E-value=3.9e-07  Score=64.15  Aligned_cols=64  Identities=13%  Similarity=0.172  Sum_probs=48.1

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEeecccccc-cceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~-~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      -+++|+++.|+|+++.+..|+|+|        . ....|+++.++...+ ....+..+.|++||.|+|+|+++.
T Consensus        18 ~l~~G~i~~G~V~~v~~fG~fV~l--------~~~~~~~l~~~~~~~~~-~~~~~~~~~~~~Gd~V~vkV~~vd   82 (119)
T 1wi5_A           18 ALKPGMLLTGTVSSLEDHGYLVDI--------GVDGTRAFLPLLKAQEY-IRQKNKGAKLKVGQYLNCIVEKVK   82 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEEC--------CCSSCEEEEEHHHHHHH-HHHHSSSCCCCTTCEEEEEEEECC
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEE--------CCCCeEEEEEEeccccc-ccccCccCEeCCCCEEEEEEEEEe
Confidence            369999999999999999999999        3 234566665543221 111256789999999999999864

>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=98.39  E-value=1e-06  Score=65.71  Aligned_cols=65  Identities=25%  Similarity=0.216  Sum_probs=52.0

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc-ccc---------ccccCCCCCCEEEEEE
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKV---------DMHLSFRPGDIVRASV  141 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~-d~~---------~~~~~~~~GDiV~A~V  141 (146)
                      +-|.+|+++.|+|+++++..|+|++         .+++|++|++++...+. +..         .....|+.||.|++||
T Consensus        77 ~~~~~Gev~~G~V~~v~~fG~fV~l---------~~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV  147 (172)
T 2c35_B           77 FRPFKGEVVDAVVTQVNKVGLFTEI---------GPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKI  147 (172)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEE---------TTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEE
T ss_pred             eeCCCCCEEEEEEEEEeCCEEEEEE---------CCEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEE
Confidence            4489999999999999999999998         46889999998853321 110         1255799999999999


Q ss_pred             EEee
Q 032149          142 VSFM  145 (146)
Q Consensus       142 is~~  145 (146)
                      +++.
T Consensus       148 ~~vd  151 (172)
T 2c35_B          148 VGTR  151 (172)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9863

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E

Probab=98.38  E-value=1.6e-06  Score=65.05  Aligned_cols=65  Identities=22%  Similarity=0.277  Sum_probs=53.7

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccc--c-------cccccCCCCCCEEEEEEE
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID--K-------VDMHLSFRPGDIVRASVV  142 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d--~-------~~~~~~~~~GDiV~A~Vi  142 (146)
                      .-|.+|+++.|+|+++++..++|++         .++.|++|++++...+..  .       .+..+.|+.||.|++||+
T Consensus        77 ~~p~~Gev~~G~V~~v~~~G~fv~l---------~~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~  147 (180)
T 4ayb_E           77 YVPVVQEVVEGEVLQVDNYGVFVNL---------GPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVI  147 (180)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEC---------SSSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEE
T ss_pred             eeccCCCEEEEEEeeeccceEEEEE---------CCccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEE
Confidence            4499999999999999999999997         468999999999754321  0       145678999999999999


Q ss_pred             Eee
Q 032149          143 SFM  145 (146)
Q Consensus       143 s~~  145 (146)
                      ++.
T Consensus       148 ~v~  150 (180)
T 4ayb_E          148 SVA  150 (180)
T ss_dssp             EEC
T ss_pred             EEe
Confidence            863

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...

Probab=98.22  E-value=5.3e-06  Score=61.80  Aligned_cols=64  Identities=9%  Similarity=0.044  Sum_probs=50.5

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc-ccccc-------ccCCCCCCEEEEEEEEe
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKVDM-------HLSFRPGDIVRASVVSF  144 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~-d~~~~-------~~~~~~GDiV~A~Vis~  144 (146)
                      -|.+|+++.|+|+++++..++|++        .. ..|++|+|++...+. +..+.       ++.|+.||.|++||+++
T Consensus        80 ~~~~Gev~~G~V~~v~~fG~FV~l--------~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~v  150 (171)
T 1y14_B           80 KPFKGEVVDGTVVSCSQHGFEVQV--------GP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGC  150 (171)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEE--------TT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEE
T ss_pred             cCCCCCEEEEEEEEEecCEEEEEe--------cC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEE
Confidence            388999999999999999999999        44 899999999853321 11111       26799999999999986


Q ss_pred             e
Q 032149          145 M  145 (146)
Q Consensus       145 ~  145 (146)
                      .
T Consensus       151 d  151 (171)
T 1y14_B          151 I  151 (171)
T ss_dssp             E
T ss_pred             E
Confidence            3

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

Probab=98.12  E-value=5.6e-06  Score=77.76  Aligned_cols=64  Identities=13%  Similarity=0.115  Sum_probs=56.5

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccc-ccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE-IDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~-~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      --+++|++|.|+|++|++..++|+|        .....|++|+|++.... ..  +..+.|++||.|.|+|+++.
T Consensus       898 ~~l~~G~iv~G~V~~V~~fGaFV~L--------~~gveGLVHiSelsd~~~v~--~p~~v~kvGd~V~vkVl~VD  962 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWHNDIICTT--------NSEVECVVNAQRHAGAQLRR--PANEIYEIGKTYPAKVIYID  962 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEEC--------TTSCEEEECTTSSSSTTSCS--CSTTTSCTTCEEEEEEEEEE
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEe--------CCCceEEEEHHHcCCCcccC--CHHHcCCCCCEEEEEEEEEE
Confidence            4478999999999999999999998        56689999999998665 44  77899999999999999874

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

Probab=98.10  E-value=4e-07  Score=81.58  Aligned_cols=64  Identities=16%  Similarity=0.252  Sum_probs=0.0

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ..|++|+++.|+|+++.+..|||+|        .....|++|+|++...+..  ++.+.|++||.|++||+++.
T Consensus       633 ~~~~vG~v~~G~V~~I~~fGaFVel--------~~g~eGLvHiSels~~rv~--~~~d~~kvGD~V~VkVi~iD  696 (726)
T 4aid_A          633 DEAEVGKIYDGKVVKVVDFGAFVNF--------FGAKDGLVHVSQISNERVA--KPSDVLKEGQMVKVKLLGFD  696 (726)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             hhhcCCcEEEEEEEEEeccEEEEEE--------CCCcEEEEEHHHcCccccc--CccccCCCCCEEEEEEEEEC
Confidence            3489999999999999999999999        4568999999999876666  88999999999999999863

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=98.09  E-value=2.2e-06  Score=64.13  Aligned_cols=65  Identities=23%  Similarity=0.076  Sum_probs=52.4

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccc-c-------cccccCCCCCCEEEEEEEE
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-K-------VDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d-~-------~~~~~~~~~GDiV~A~Vis  143 (146)
                      ..|.+|+++.|+|+++++..++|++         .+++|++|++++...+.. .       .+..+.|++||.|++||++
T Consensus        80 f~p~~Gev~~G~V~~v~~fG~FV~l---------~~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~  150 (172)
T 3h0g_G           80 WRPFRGEVVDAIVTTVNKMGFFANI---------GPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVG  150 (172)
T ss_dssp             ECCCTTCEEECCCCEEETTEEECCB---------TTBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEE
T ss_pred             eccCCCCEEEEEEEEEEcceEEEEe---------CCeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEE
Confidence            4489999999999999999999998         468899999998533211 0       1234689999999999998


Q ss_pred             ee
Q 032149          144 FM  145 (146)
Q Consensus       144 ~~  145 (146)
                      +.
T Consensus       151 vd  152 (172)
T 3h0g_G          151 TR  152 (172)
T ss_dssp             EE
T ss_pred             EE
Confidence            63

>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=98.04  E-value=1.1e-05  Score=62.63  Aligned_cols=65  Identities=9%  Similarity=0.024  Sum_probs=51.4

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc-ccccc-------ccCCCCCCEEEEEEEE
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKVDM-------HLSFRPGDIVRASVVS  143 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~-d~~~~-------~~~~~~GDiV~A~Vis  143 (146)
                      .-|++|+++.|+|+++++..++|+|        .. ..|++|++++...+. |....       ++.|++||.|+.||++
T Consensus        79 ~~p~vGev~~G~V~~vt~fG~FVel--------g~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~  149 (215)
T 2b8k_G           79 FKPFKGEVVDGTVVSCSQHGFEVQV--------GP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEG  149 (215)
T ss_dssp             ECCCTTEEEEEEEEEEETTEEEEEC--------TT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEE
T ss_pred             eccCCCCEEEEEEEEEecceEEEEe--------cC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEE
Confidence            3489999999999999999999998        33 899999999864322 11111       2679999999999998


Q ss_pred             ee
Q 032149          144 FM  145 (146)
Q Consensus       144 ~~  145 (146)
                      +.
T Consensus       150 vd  151 (215)
T 2b8k_G          150 CI  151 (215)
T ss_dssp             EE
T ss_pred             EE
Confidence            64

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

Probab=98.01  E-value=1.5e-05  Score=64.09  Aligned_cols=54  Identities=17%  Similarity=0.112  Sum_probs=48.3

Q ss_pred             CCCCCEEEEEEEEEecceEEE-EEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASA-DIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v-~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++||+|.|+|.++++..|+| .+        ...+.|++|.||+.          +.|++||.|.|+|+++.
T Consensus       150 ~~~G~~V~g~V~~i~~~G~fV~~i--------~~g~~Glih~SEl~----------~~l~~Gd~v~~~V~~id  204 (285)
T 3go5_A          150 NMQNQNWPAIVYRLKLSGTFVYLP--------ENNMLGFIHPSERY----------AEPRLGQVLDARVIGFR  204 (285)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEET--------TTTEEEEECGGGCS----------SCCCTTCEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEEe--------CCCeEEEEEHHHcc----------ccCCCCCEEEEEEEEEE
Confidence            478999999999999999999 87        67799999998864          56899999999999874

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A

Probab=97.90  E-value=4.8e-06  Score=75.20  Aligned_cols=62  Identities=26%  Similarity=0.302  Sum_probs=55.5

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +++|+++.|+|++|++..++|+|        .....|++|+|++...+..  +..+.|++||.|.++|+++.
T Consensus       652 l~vG~iv~G~V~~V~~fGaFV~l--------~~~~eGLVhiS~Lsd~~v~--d~~~~~~vGd~V~VkVi~VD  713 (785)
T 3bzc_A          652 LKPGMVLEGVVTNVTNFGAFVDI--------GVHQDGLVHISALSEKFVK--DPYEVVKAGDIVKVKVMEVD  713 (785)
T ss_dssp             CCTTCBCCCEEEEEETTEEEEEC--------SSSSEEEEETTTSCSSCCS--CHHHHCCTTCCCCCBEEEEE
T ss_pred             cCCCCEEEEEEEEEecCCeEEEe--------CCCcEEEEEHHHcCccccC--ChhheeCCCCEEEEEEEEEE
Confidence            68999999999999999999998        4567899999999876555  78899999999999999874

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

Probab=97.83  E-value=2.4e-06  Score=76.55  Aligned_cols=64  Identities=17%  Similarity=0.214  Sum_probs=0.0

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .-+++|+++.|+|+++.+..+||+|        .....|++|+|++...+..  +..+.|++||.|++||+++.
T Consensus       623 ~~~~vG~i~~G~V~~i~~fGaFVel--------~~g~eGLvHiSel~~~~v~--~~~~~~~vGd~V~VkVi~vd  686 (723)
T 3cdi_A          623 AEIEVGRVYTGKVTRIVDFGAFVAI--------GGGKEGLVHISQIADKRVE--KVTDYLQMGQEVPVKVLEVD  686 (723)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             hhhhcCcEEEEEEEEEecceEEEEe--------CCCceEEEEHHHcCCcccc--CcccccCCCCEEEEEEEEEC
Confidence            3489999999999999999999999        4568999999999766665  78899999999999999863

>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=97.81  E-value=9.7e-05  Score=60.97  Aligned_cols=58  Identities=21%  Similarity=0.288  Sum_probs=50.0

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .|..+.|++|.|+|.++..+.++|++        . ...|+||.++..        ..+.|++||.|+|.|.++.
T Consensus       129 e~~~~~GeIV~G~V~ri~~~~v~VDl--------G-k~EgiLp~sE~i--------p~E~~~vGD~Vkv~V~~V~  186 (344)
T 1hh2_P          129 KYSELKGTVTTAEVIRVMGEWADIRI--------G-KLETRLPKKEWI--------PGEEIKAGDLVKVYIIDVV  186 (344)
T ss_dssp             CTTCCTTCEEEEEEEEECSSEEEEEE--------T-TEEEEEEGGGSC--------TTCCCCTTCEEEEEEEEEE
T ss_pred             HHhhcCCCEEEEEEEEEecCcEEEEe--------C-CeEEEEeHHHcC--------CCcCCCCCCEEEEEEEEEE
Confidence            34567999999999999999999999        4 689999998874        3578999999999999763

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=97.78  E-value=7.6e-05  Score=57.11  Aligned_cols=65  Identities=17%  Similarity=0.160  Sum_probs=51.7

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc--cc---------------cccccCCCCC
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DK---------------VDMHLSFRPG  134 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~--d~---------------~~~~~~~~~G  134 (146)
                      .-|.+|+++.|+|+++++..++|++         .++.|++|+++....+-  |.               .+-...|+.|
T Consensus        77 f~p~~GEv~~G~Vs~vt~~GifV~l---------g~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~G  147 (203)
T 3ayh_B           77 FRPFRGEVMLGKIKSCSEEGIRVTI---------SFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDID  147 (203)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEC---------SSCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTT
T ss_pred             EccCCCCEEEEEEEEEeccEEEEEE---------eCceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCC
Confidence            3489999999999999999999998         36889999998854331  00               1335679999


Q ss_pred             CEEEEEEEEee
Q 032149          135 DIVRASVVSFM  145 (146)
Q Consensus       135 DiV~A~Vis~~  145 (146)
                      |.|+.||.++.
T Consensus       148 d~VrvrV~~v~  158 (203)
T 3ayh_B          148 EEIRFQIESED  158 (203)
T ss_dssp             CEEEEEEEEEE
T ss_pred             CEEEEEEEEEE
Confidence            99999999863

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

Probab=97.78  E-value=3.3e-06  Score=78.17  Aligned_cols=63  Identities=13%  Similarity=0.120  Sum_probs=0.0

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccc-ccccccccCCCCCCEEEEEEEEee
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE-IDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~-~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      -+++|++|.|+|++|++..++|+|        .....|++|+|++.... ..  +..+.|++||.|.|+|+++.
T Consensus       902 ~l~~G~iv~G~V~~V~~fGaFV~L--------~~gveGLVHiSelsd~~~v~--~~~~v~kvGd~V~vkVl~VD  965 (1030)
T 3psf_A          902 TFFKGSIIPVRVERFWHNDIICTT--------NSEVECVVNAQRHAGAQLRR--PANEIYEIGKTYPAKVIYID  965 (1030)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             HhcCCCEEEEEEEEEccCeEEEEe--------CCCcEEEEEHHHcCCCcccC--CHHHcCCCCCEEEEEEEEEE
Confidence            468999999999999999999998        55679999999998654 44  77899999999999999864

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=97.68  E-value=0.00011  Score=57.01  Aligned_cols=66  Identities=15%  Similarity=0.167  Sum_probs=52.1

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc--c---c-------cccccCCCCCCEEEE
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--D---K-------VDMHLSFRPGDIVRA  139 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~--d---~-------~~~~~~~~~GDiV~A  139 (146)
                      ..|.+|+++.|+|++++...++|++        ..++.|++|+++....+-  |   .       ..-...|+.||.|+.
T Consensus        77 f~p~vGEv~~G~Is~Vt~fGifVeL--------~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~Vrv  148 (218)
T 2ckz_B           77 FKPFLGEIVTGWISKCTAEGIKVSL--------LGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRF  148 (218)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEC--------TTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEE
T ss_pred             ecCCCCCEEEEEEEEEccCcEEEEc--------cCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEE
Confidence            4489999999999999999999998        567899999998854331  0   0       123566999999999


Q ss_pred             EEEEee
Q 032149          140 SVVSFM  145 (146)
Q Consensus       140 ~Vis~~  145 (146)
                      ||.++.
T Consensus       149 rV~~v~  154 (218)
T 2ckz_B          149 RIEREV  154 (218)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            999863

>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=97.65  E-value=0.00012  Score=57.96  Aligned_cols=58  Identities=17%  Similarity=0.228  Sum_probs=48.8

Q ss_pred             CCCCCCCEEEEEEEE----EecceEEEEEEeeccccccc---ceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           72 PVPEPGSVVIARVTK----VMTRMASADIMCVGAKSVRE---KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        72 ~~P~~GdiViG~V~~----v~~~~~~v~I~~v~~~~l~~---~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      |..+.|++|.|+|.+    +..+.++|+|        ..   ...|+|+.++..        ..+.|++||-|+|.|.++
T Consensus         3 ~~~r~GeIVtG~V~r~~~~v~~~~ViVdl--------G~~~~k~EgiLP~~Eqi--------p~E~~~~GDrIkayV~~V   66 (251)
T 2asb_A            3 FSTREGEIVAGVIQRDSRANARGLVVVRI--------GTETKASEGVIPAAEQV--------PGESYEHGNRLRCYVVGV   66 (251)
T ss_dssp             -CCCTTCEEEEEEECCHHHHHTTCEEEEE--------CSSSSCEEEEECGGGSC--------TTCCCCTTCEEEEEEEEE
T ss_pred             hhhcCCCEEEEEEEEccccccCCeEEEEe--------CCCCcceEEEEcHHHcC--------CCccCCCCCEEEEEEEEE
Confidence            567899999999999    8999999999        33   489999987753        367899999999999976


Q ss_pred             e
Q 032149          145 M  145 (146)
Q Consensus       145 ~  145 (146)
                      -
T Consensus        67 ~   67 (251)
T 2asb_A           67 T   67 (251)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=97.63  E-value=3e-06  Score=76.33  Aligned_cols=64  Identities=16%  Similarity=0.257  Sum_probs=32.6

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccc----ccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV----RATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi----~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ..|++|+++.|+|+++.+..+||++        .....|++|+|++    ...+..  +..+.|++||.|+++|+++.
T Consensus       663 ~~~~vG~i~~G~V~~i~~fGaFV~l--------~~g~eGLvHiSel~~~~s~~rv~--~~~~~~~vGd~V~VkVi~vd  730 (757)
T 1e3p_A          663 TSPEVGERILGSVVKTTTFGAFVSL--------LPGKDGLLHISQIRKLAGGKRVE--NVEDVLGVGQKVQVEIAEID  730 (757)
T ss_dssp             ----------CBEEECC-CSCEECC--------C---CCCCC---------------------CCSSCBCCCCCCCCC
T ss_pred             hhcccccEEEEEEEEccccEEEEEE--------cCCcEEEEEhHHhccccCCCccc--CcccccCCCCEEEEEEEEEC
Confidence            3579999999999999999999998        4568999999999    555555  78899999999999998764

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

Probab=97.53  E-value=0.00019  Score=59.62  Aligned_cols=59  Identities=17%  Similarity=0.235  Sum_probs=49.3

Q ss_pred             CCCCCCCCEEEEEEEE----EecceEEEEEEeeccccccc---ceeeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 032149           71 GPVPEPGSVVIARVTK----VMTRMASADIMCVGAKSVRE---KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~----v~~~~~~v~I~~v~~~~l~~---~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis  143 (146)
                      .|..++|++|.|+|.+    +....++|+|        ..   ...|+|+.++..+        .+.|++||-|+|.|.+
T Consensus       125 ef~~r~GeIVtG~V~r~~~~v~~~~v~VdL--------G~~~~k~EgiLP~~EqiP--------~E~~~~GDrVkvyV~~  188 (366)
T 1k0r_A          125 EFSTREGEIVAGVIQRDSRANARGLVVVRI--------GTETKASEGVIPAAEQVP--------GESYEHGNRLRCYVVG  188 (366)
T ss_dssp             --CCCTTCEEEEEEECCHHHHHTTCEEEEE--------CCSSSCEEEEECGGGSCT--------TCCCCTTCEEEEEEEE
T ss_pred             HHHhcCCCEEEEEEEEccccccCCeEEEEe--------CCCccceEEEEcHHHcCC--------CccCCCCCEEEEEEEE
Confidence            3557899999999999    9999999999        33   4899999887643        5799999999999998


Q ss_pred             ee
Q 032149          144 FM  145 (146)
Q Consensus       144 ~~  145 (146)
                      +.
T Consensus       189 V~  190 (366)
T 1k0r_A          189 VT  190 (366)
T ss_dssp             EE
T ss_pred             Ee
Confidence            63

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A

Probab=97.42  E-value=0.00051  Score=59.46  Aligned_cols=63  Identities=11%  Similarity=0.189  Sum_probs=52.5

Q ss_pred             CCCCCEEEEEEEEEecc--eEEEEEEeecccccccceeeEEecccccccccc-------ccccccCCCCCCEEEEEEEEe
Q 032149           74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATEID-------KVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~--~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d-------~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      +.+|++..|+|+++.+.  .|||+|        ...-.|+||.+|+...+..       ..++.+.+++||.|..+|++.
T Consensus        43 ~~vGnIY~GkV~rv~p~~~aAFVdi--------G~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke  114 (517)
T 2bx2_L           43 QKKANIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE  114 (517)
T ss_dssp             CCTTCEEEEEEEEEETTTTEEEEES--------SSSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEEC
T ss_pred             CCCCCEEEEEEEEeccCCceEEEEe--------CCCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEee
Confidence            67899999999999998  899999        6677899999998543311       225778999999999999873

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

Probab=96.15  E-value=0.0048  Score=42.00  Aligned_cols=40  Identities=13%  Similarity=0.244  Sum_probs=35.7

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccc
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT  120 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~  120 (146)
                      .|++|+.|.+.|+++.+..++|+|        ....+|++|+|++...
T Consensus        58 ~l~~Ge~V~g~V~~i~~fG~fv~l--------~~~~eGlvhis~i~~~   97 (101)
T 2bh8_A           58 NPQQGDRVEGKIKSITDFGIFIGL--------DGGIDGLVHLSDISWA   97 (101)
T ss_dssp             CCCTTCEEEEEEEECCSEEEEECT--------TSCEEEEEEEEEEEEC
T ss_pred             CCCCCCEEEEEEEEeCCcEEEEEc--------CCCceEEEEHHHCccC
Confidence            689999999999999999999998        5568999999998643

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

Probab=95.89  E-value=0.027  Score=45.10  Aligned_cols=35  Identities=6%  Similarity=0.041  Sum_probs=30.3

Q ss_pred             CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccc
Q 032149           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVR  118 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~  118 (146)
                      .+|+++.|+|+++++..++|++        . ...|+||.+++.
T Consensus         5 ~~G~~v~g~V~~~~~~G~fv~~--------~-g~egllp~se~~   39 (285)
T 3go5_A            5 NLASFIVGLIIDENDRFYFVQK--------D-GQTYALAKEEGQ   39 (285)
T ss_dssp             TTTEEEEEEEEEECSSEEEEEE--------T-TEEEEEEGGGCC
T ss_pred             cCCCEEEEEEEEEECCEEEEEc--------C-CeEEEEEHHHCc
Confidence            5799999999999999999998        3 567888888773

>3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, STR genomics, PSI-2, protein structure initiative; 1.64A {Nitrosomonas europaea atcc 19718}

Probab=95.72  E-value=0.059  Score=36.52  Aligned_cols=60  Identities=15%  Similarity=0.184  Sum_probs=44.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc---cccc-cccCCCCCCEEEEE
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI---DKVD-MHLSFRPGDIVRAS  140 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~---d~~~-~~~~~~~GDiV~A~  140 (146)
                      .|..|+...|.|+++.++.+.+.+        .....+.|..++++--..   .... ..+.|++||+|+.+
T Consensus        30 ~~~~~~~~~AvV~~v~~~~~~v~~--------~~g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           30 IGNSDDILAAVVLSATPGAVEAFR--------KNGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             SCTTTTCEEEEEEEEETTEEEEEE--------TTSCEEEECGGGGSTTGGGTTTCTTTGGGSCCTTEEEEEE
T ss_pred             cCccCCeEEEEEEEeCCCeEEEEE--------cCCCeEEEcHHHChhhhhcccccccchhccCCCCCEEEEE
Confidence            477799999999999999988876        444556677777652211   1124 67889999999987

>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A

Probab=95.25  E-value=0.043  Score=48.42  Aligned_cols=65  Identities=8%  Similarity=0.109  Sum_probs=50.1

Q ss_pred             CCCCC--EEEEEEEEEecceEEEEEEeecccccccceeeEEecccccc---cc-cc--cc----ccccCCCCCCEEEEEE
Q 032149           74 PEPGS--VVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRA---TE-ID--KV----DMHLSFRPGDIVRASV  141 (146)
Q Consensus        74 P~~Gd--iViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~---~~-~d--~~----~~~~~~~~GDiV~A~V  141 (146)
                      .++|+  ...|+|+++++..++|.|.       .....|++|.+++..   .+ .+  ..    +....|++||.|+.+|
T Consensus       556 ~~vGe~~~f~g~V~~V~~~G~fV~L~-------~~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV  628 (644)
T 2id0_A          556 DKAGTDTRFAAEIVDISRGGMRVRLV-------DNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTI  628 (644)
T ss_dssp             GGTTSCCCEEEEEEEEETTEEEEEET-------TTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEE
T ss_pred             hccCCCceEEEEEEEEeCCceEEEEc-------CCcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEE
Confidence            57898  9999999999999999981       245899999998852   11 11  11    2356799999999999


Q ss_pred             EEee
Q 032149          142 VSFM  145 (146)
Q Consensus       142 is~~  145 (146)
                      .++.
T Consensus       629 ~~vd  632 (644)
T 2id0_A          629 AEVR  632 (644)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            9874

>3v2d_0 50S ribosomal protein L27; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgj_Z 2hgq_Z 2hgu_Z 2j01_0 2j03_0 2jl6_0 2jl8_0 2wdi_0 2wdj_0 2wdl_0 2wdn_0 2wh2_0 2wh4_0 2wrj_0 2wrl_0 2wro_0 2wrr_0 2x9s_0 2x9u_0 2xg0_0 ...

Probab=93.65  E-value=0.1  Score=34.49  Aligned_cols=60  Identities=23%  Similarity=0.266  Sum_probs=46.0

Q ss_pred             ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecC
Q 032149            3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (146)
Q Consensus         3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~   67 (146)
                      +|.-..+.|.||..|..  -..|-||.++-.-. |..|||..-|.+.....    ...++.|+|.|.
T Consensus        23 vK~~~Gq~V~aG~IivRQRGtk~hPG~NVg~Gk-D~TLfAl~~G~V~f~~~----~~~r~~VsV~p~   84 (85)
T 3v2d_0           23 VKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGR-DFTLFALVDGVVEFQDR----GRLGRYVHVRPL   84 (85)
T ss_dssp             ESSCTTCEECTTCEEEECSSCSEEECTTEEECT-TCCEEESSSEEEEEEEC----GGGCEEEEEEEC
T ss_pred             eEecCCeEEcCCeEEEecCCccCcCCCCEeEcC-CCeEEEecCEEEEEEEc----CCCCEEEEEEEC
Confidence            45566889999998864  34699999998854 99999999999988531    123567888874

>3r8s_W 50S ribosomal protein L27; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 3j19_W 2qam_W* 1p85_U 1p86_U 2awb_W 2gya_U 2gyc_U 2aw4_W 2i2v_W 2j28_W 2i2t_W* 2qao_W* 2qba_W* 2qbc_W* 2qbe_W 2qbg_W 2qbi_W* 2qbk_W* 2qov_W 2qox_W ...

Probab=92.48  E-value=0.14  Score=33.26  Aligned_cols=60  Identities=18%  Similarity=0.282  Sum_probs=45.2

Q ss_pred             ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEec
Q 032149            3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTG   66 (146)
Q Consensus         3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p   66 (146)
                      +|.-..+.|.||..|..  -..|-||.++-.-. |..|||..-|.++....   ....++.|+|.|
T Consensus        14 vK~~~Gq~V~aG~IivRQRGtk~hPG~NVG~Gk-D~TLfAl~~G~V~f~~~---~~~~r~~VsV~p   75 (76)
T 3r8s_W           14 VKRFGGESVLAGSIIVRQRGTKFHAGANVGCGR-DHTLFAKADGKVKFEVK---GPKNRKFISIEA   75 (76)
T ss_dssp             ESSCTTCEECTTCEEEECSSCSSEECTTEEECT-TSCEEESSSEEEEEEEE---TTTTEEEEEEEC
T ss_pred             EEecCCeEEecCcEEEeccCccCcCCCCeeecC-CCeEEEccCEEEEEEEe---CCCCCEEEEEEe
Confidence            45667889999998864  34699999998854 99999999999988520   012346788876

>2zjr_T 50S ribosomal protein L27; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.84.4.1 PDB: 1nwx_U* 1nwy_U* 1sm1_U* 1xbp_U* 1y69_U 1yl3_3 2b66_0 2b9n_0 2b9p_0 2zjp_T* 2zjq_T 1nkw_U 3cf5_T* 3dll_T* 3pio_T* 3pip_T* 1pnu_U 1pny_U 1vor_X 1vou_X ...

Probab=91.57  E-value=0.17  Score=33.91  Aligned_cols=60  Identities=20%  Similarity=0.295  Sum_probs=45.9

Q ss_pred             ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecC
Q 032149            3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (146)
Q Consensus         3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~   67 (146)
                      +|.-..+.|.||..|..  -..|-||.++-.-. |..|||...|.+++...    ..+++.|+|.|.
T Consensus        23 vK~~gGq~V~aG~IivRQRGtk~hPG~NVg~Gk-D~TLfAl~~G~V~f~~~----~~~r~~V~V~p~   84 (91)
T 2zjr_T           23 VKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGR-DHTLFALSDGKVVFINK----GKGARFISIEAA   84 (91)
T ss_dssp             CSSCTTCEECSSCEEECCSSSSSEECTTEECCT-TSCEEESSCEEEEEEEE----TTTEEEEEECCC
T ss_pred             EEecCCeEEcCCeEEEecCCCEEcCCCCEEEcC-CCcEEeccceEEEEEEc----CCCcEEEEEEeC
Confidence            45566889999998864  24699999998753 89999999999988520    133568999874

>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=91.29  E-value=0.31  Score=43.72  Aligned_cols=60  Identities=22%  Similarity=0.188  Sum_probs=44.4

Q ss_pred             CEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccc--c-cc-cc--cc-----c----cccCCCCCCEEEEEE
Q 032149           78 SVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVR--A-TE-ID--KV-----D----MHLSFRPGDIVRASV  141 (146)
Q Consensus        78 diViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~--~-~~-~d--~~-----~----~~~~~~~GDiV~A~V  141 (146)
                      ....|.|++++...++|.|        .. ...|++|.+++.  . .+ -+  ..     +    ....|++||.|+++|
T Consensus       671 ~~~~g~V~~V~~~G~fV~l--------~~~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV  742 (760)
T 2vnu_D          671 STETGYVIKVFNNGIVVLV--------PKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQV  742 (760)
T ss_dssp             SEEEEEEEEEETTEEEEEE--------TTTTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEE
T ss_pred             eEEEEEEEEEECCeEEEEE--------eCCCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCCEEEEEE
Confidence            6899999999999999999        43 689999999884  1 11 01  00     1    247899999999999


Q ss_pred             EEee
Q 032149          142 VSFM  145 (146)
Q Consensus       142 is~~  145 (146)
                      .++.
T Consensus       743 ~~vd  746 (760)
T 2vnu_D          743 RSVM  746 (760)
T ss_dssp             C---
T ss_pred             EEEE
Confidence            8763

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=90.05  E-value=0.47  Score=43.88  Aligned_cols=60  Identities=20%  Similarity=0.162  Sum_probs=46.7

Q ss_pred             CCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccc--ccc--cc--ccc---------cccCCCCCCEEEEE
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVR--ATE--ID--KVD---------MHLSFRPGDIVRAS  140 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~--~~~--~d--~~~---------~~~~~~~GDiV~A~  140 (146)
                      |...-|.|++++...++|.|        .. ...|++|.+++.  ..+  -|  ...         ....|+.||.|+.+
T Consensus       887 ge~~~g~V~~V~~~G~fV~L--------~~~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~Vk  958 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLV--------PKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQ  958 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEEC--------TTTCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEE
T ss_pred             ceEEEEEEEEEcCCeEEEEE--------cCCCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEE
Confidence            88999999999999999998        43 689999999985  111  01  011         24789999999999


Q ss_pred             EEEe
Q 032149          141 VVSF  144 (146)
Q Consensus       141 Vis~  144 (146)
                      |.++
T Consensus       959 V~~v  962 (977)
T 2wp8_J          959 VRSV  962 (977)
T ss_dssp             ECCC
T ss_pred             EEEE
Confidence            9865

>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae}

Probab=89.71  E-value=1.1  Score=34.04  Aligned_cols=65  Identities=12%  Similarity=0.087  Sum_probs=44.0

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc---c------ccccc-cCCCCCCEEEEEEE
Q 032149           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI---D------KVDMH-LSFRPGDIVRASVV  142 (146)
Q Consensus        73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~---d------~~~~~-~~~~~GDiV~A~Vi  142 (146)
                      -|.+|+++.|+|+.++.....+-+        ...|+..|+...++..-.   +      ..+.. +--++|+.|+-||.
T Consensus       126 rPf~GevL~G~V~~~s~~~Ig~~~--------~G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~  197 (214)
T 2rf4_A          126 QPQVGDVLEGYIFIQSASHIGLLI--------HDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVR  197 (214)
T ss_dssp             CCCTTCEEEEEECCCCSSCEEEEE--------TTTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEE
T ss_pred             ecCCCCEEEEEEEEECCCcEEEEE--------eCCEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEE
Confidence            399999999999999998887765        356777777776642110   0      00110 11136999999999


Q ss_pred             Eee
Q 032149          143 SFM  145 (146)
Q Consensus       143 s~~  145 (146)
                      ++.
T Consensus       198 ~~~  200 (214)
T 2rf4_A          198 NVH  200 (214)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            864

>1y71_A Kinase-associated protein B; structural genomics, midwest CE structural genomics, MCSG, protein structure initiative, PS unknown function; 1.95A {Bacillus cereus} SCOP: b.34.16.1

Probab=87.67  E-value=2.4  Score=30.06  Aligned_cols=27  Identities=26%  Similarity=0.247  Sum_probs=24.2

Q ss_pred             CCCCCEE---------EEEEEEEecceEEEEEEeec
Q 032149           74 PEPGSVV---------IARVTKVMTRMASADIMCVG  100 (146)
Q Consensus        74 P~~GdiV---------iG~V~~v~~~~~~v~I~~v~  100 (146)
                      .++||+|         +|.|+..+++.+.|.|++|-
T Consensus         8 ~~~g~~v~~~yKTG~YigeI~e~~~~~~lVkVlaVl   43 (130)
T 1y71_A            8 FEIGEIVTGIYKTGKYIGEVTNSRPGSYVVKVLAVL   43 (130)
T ss_dssp             CCTTCEEEEEETTEEEEEEEEEEETTEEEEEEEEEE
T ss_pred             CCccceeEEEEecceeEEEEEeecCCeEEEEEEEEe
Confidence            4788988         89999999999999999884

>2ftc_O L27MT, MRP-L27, mitochondrial 39S ribosomal protein L27; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_O

Probab=86.74  E-value=0.66  Score=29.48  Aligned_cols=44  Identities=27%  Similarity=0.371  Sum_probs=35.4

Q ss_pred             ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEE
Q 032149            3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLR   47 (146)
Q Consensus         3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~   47 (146)
                      +|.-..+.|.||..|..  -..|-||.++-.-. |..|||...|.++
T Consensus        23 vK~~~Gq~V~aG~IivrQRgtk~hPG~nVg~Gk-D~TLfAl~~G~V~   68 (69)
T 2ftc_O           23 IKKMEGHYVHAGNIIATQRHFRWHPGAHVGVGK-NKCLYALEEGIVR   68 (69)
T ss_pred             EEecCCeEecCCeEEEecCCCeEcCCCCeeecC-CCcEEEccceEEe
Confidence            45556789999998864  24699999998753 8999999999886

---

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	146
d2nn6i1	125	b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H	3e-23
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	1e-05
d2nn6i2	55	b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Hum	3e-05

>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 = 86.1 bits (213), Expect = 3e-23
 Identities = 33/72 (45%), Positives = 51/72 (70%)

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
           +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ SFR
Sbjct: 4   LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFR 63

Query: 133 PGDIVRASVVSF 144
           PGDIV A V+S 
Sbjct: 64  PGDIVLAKVISL 75

>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 = 39.5 bits (92), Expect = 1e-05
 Identities = 13/72 (18%), Positives = 30/72 (41%)

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
           + E G +V+ R+T+V  +    +        +      +   +  R +  D++ M    +
Sbjct: 5   IGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQ 64

Query: 133 PGDIVRASVVSF 144
            GD++ A V + 
Sbjct: 65  EGDLISAEVQAV 76

>d2nn6i2 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 55

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (87), Expect = 3e-05
 Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 2/35 (5%)

Query: 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTG 44
             PGE L    E   G G Y    +G +++SL G
Sbjct: 2  YCIPGERLCNLEEGSPGSGTYT--RHGYIFSSLAG 34

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	146
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	99.89
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	99.65
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	99.64
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.6
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.53
d2ba0a2	51	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.51
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.51
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.5
d2nn6i2	55	Exosome component 1, EXOSC1 {Human (Homo sapiens)	99.5
d2nn6h2	48	Ribosomal RNA-processing protein 4, RRP4 {Human (H	99.44
d2je6i2	59	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.37
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.19
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.13
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.04
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	98.9
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	98.77
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	98.57
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.39
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.33
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	98.24
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.22
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.52
d2nn6g2	91	Ribosomal RNA-processing protein 40, RRP40 {Human	97.29
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.07
d1v8qa_	66	Ribosomal protein L27 {Thermus thermophilus [TaxId	96.66
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	96.49
d2zjrt1	84	Ribosomal protein L27 {Deinococcus radiodurans [Ta	95.94
d1e1oa1	143	Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g	90.16
d2gycu1	84	Ribosomal protein L27 {Escherichia coli [TaxId: 56	81.74
d1y71a1	124	Kinase-associated protein B {Bacillus cereus [TaxI	80.83

>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=99.89  E-value=1.3e-23  Score=150.17  Aligned_cols=75  Identities=44%  Similarity=0.739  Sum_probs=73.0

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +|+|++||+|+|+|+++++++|+|+|++++++++..+|.|++|.+|+|+++.|+.+|+++|++||+|+|||+|++
T Consensus         2 ~~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~   76 (125)
T d2nn6i1           2 QLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLG   76 (125)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEE
T ss_pred             CcCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEcc
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.65  E-value=1.3e-16  Score=106.92  Aligned_cols=64  Identities=17%  Similarity=0.145  Sum_probs=57.8

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      +|+|++||+|+|+|++++.+.|+|+|        ++++.|+||.+++. ....  ++++.|++||+|+|||+++.
T Consensus         1 rY~P~~GD~ViG~V~~~~~~~~~VdI--------~s~~~a~L~~~~f~-g~~k--~~r~~l~~GD~V~arV~~v~   64 (88)
T d2nn6g1           1 RYVPVKGDHVIGIVTAKSGDIFKVDV--------GGSEPASLSYLSFE-GATK--RNRPNVQVGDLIYGQFVVAN   64 (88)
T ss_dssp             SCCCCSSEEEEEEEEEEETTEEEEEC--------SSSSCCCEESCSSS-CCSS--CSSSSSCTTCEEEEEEEECC
T ss_pred             CCcCCCCCEEEEEEEEEeCCeEEEEc--------CCCeeEEEeHHHcC-cccc--ccCcccCCCCEEEEEEEEeC
Confidence            59999999999999999999999999        78899999999984 3344  78999999999999999864

>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=99.64  E-value=2.9e-16  Score=105.70  Aligned_cols=66  Identities=14%  Similarity=0.127  Sum_probs=58.9

Q ss_pred             CCCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        70 ~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ++|+|++||+|+|+|+++.++.|+|+|        ++++.|+|+.+........  ++++.|++||+|+|||+++.
T Consensus         1 krY~P~~gD~ViG~V~~~~~~~~~vdI--------~~~~~~~L~~~~~f~g~~k--~~r~~l~~GDlV~arV~~v~   66 (90)
T d2ja9a1           1 KRYIPSVNDFVIGVIIGTFSDSYKVSL--------QNFSSSVSLSYMAFPNASK--KNRPTLQVGDLVYARVCTAE   66 (90)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEES--------STTSCCEEEETTSSTTCCS--SSCCCCCTTCEEEEEEEECC
T ss_pred             CCccCCCCCEEEEEEEEEeCCcEEEEc--------CCcchhhhhhhhccCcccc--ccCCccCCCCEEEEEEEEEC
Confidence            379999999999999999999999999        7889999998776655445  89999999999999999874

>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=99.60  E-value=2.3e-16  Score=106.87  Aligned_cols=68  Identities=18%  Similarity=0.350  Sum_probs=57.8

Q ss_pred             CCCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccc--------cccccccccccCCCCCCEEEEEE
Q 032149           70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVR--------ATEIDKVDMHLSFRPGDIVRASV  141 (146)
Q Consensus        70 ~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~--------~~~~d~~~~~~~~~~GDiV~A~V  141 (146)
                      .+|.|++||+|+|+|+++.++.|+|+|        ...+.|+||.+++.        .+..+..+|+++|++||.|.|+|
T Consensus         2 ~~Y~P~vGdiV~G~V~~v~~~g~~V~I--------~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV   73 (95)
T d2nn6h1           2 TRYIGEVGDIVVGRITEVQQKRWKVET--------NSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEV   73 (95)
T ss_dssp             CCCCCCSSBCCCEEEEEEETTEEEEEC--------SSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEE
T ss_pred             CcccCCCCCEEEEEEEEEecCcEEEEe--------CCCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEE
Confidence            479999999999999999999999999        67789999999873        34556668999999999999999


Q ss_pred             EEee
Q 032149          142 VSFM  145 (146)
Q Consensus       142 is~~  145 (146)
                      +++.
T Consensus        74 ~~v~   77 (95)
T d2nn6h1          74 QAVF   77 (95)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9874

>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=99.53  E-value=1.5e-14  Score=96.08  Aligned_cols=67  Identities=21%  Similarity=0.217  Sum_probs=59.2

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc-cccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~-d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .|+|++||+|+|+|++++++.|+|+|        ...+.|+||.+++..... +..++++.|++||.|.|+|+++.
T Consensus         2 ~Y~Pk~Gdiv~G~V~~i~~~g~fV~i--------~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd   69 (87)
T d2je6i1           2 FYYPKINDIVIGLVEDVEIYGWVVDI--------KAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFD   69 (87)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEEC--------SSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEE
T ss_pred             cccCCCCCEEEEEEEEEECCEEEEEe--------CCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEEC
Confidence            59999999999999999999999999        778999999999975433 33478999999999999999864

>d2ba0a2 b.84.4.2 (A:2-52) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.51  E-value=6.4e-15  Score=89.16  Aligned_cols=50  Identities=36%  Similarity=0.577  Sum_probs=45.1

Q ss_pred             CcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCC
Q 032149            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA   69 (146)
Q Consensus         8 ~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~   69 (146)
                      +++|+|||.|++ ++|++|+|||++  +++|+||++|.++..         ++.|+|.|+++
T Consensus         1 r~iV~PGe~i~~-~~~~~G~Gty~~--~~~i~ss~~G~v~~~---------n~~i~V~PL~g   50 (51)
T d2ba0a2           1 RKIVLPGDLLST-NPRAAGYGTYVE--GGKVYAKIIGLFDQT---------ETHVRVIPLKG   50 (51)
T ss_dssp             CCEECTTCEEES-CTTSBCTTEEEE--TTEEEECSSEEEEEC---------SSCEEEEECSS
T ss_pred             CCEEcCCcEeec-CCeeCCCCcEEE--CCEEEEEEEEEEEEE---------CCEEEEEeCcc
Confidence            479999999987 579999999999  999999999999884         57999999863

>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=99.51  E-value=3.5e-14  Score=93.25  Aligned_cols=64  Identities=19%  Similarity=0.227  Sum_probs=57.4

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccc-cccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT-EIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~-~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |.|++||+|.|+|++++++.|+|+|        ...+.|+||.+++... ...  ++++.|++||.|.|+|+++.
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i--------~~~~~g~l~~se~s~~~~~~--~~~~~~~vGd~V~~kV~~vd   65 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDI--------YSPYQAFLPVSENPEMKPNK--KPNEVLDIGDAIIAKVLNID   65 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEC--------SSSSCEEEEGGGCTTCCTTS--CGGGTCCTTCEEEEEEEEEC
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEec--------CCCeeEEEeccccccccccc--ChhhhcccccEEEEEEEEEC
Confidence            7899999999999999999999999        7789999999998643 234  88999999999999999873

>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=99.50  E-value=2.6e-14  Score=94.97  Aligned_cols=67  Identities=28%  Similarity=0.343  Sum_probs=59.0

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccc--ccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE--IDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~--~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .|.|++||+|.|+|++++++.|+|+|        ...+.|+||.+++....  .+..++++.|++||.|.|+|+++.
T Consensus         2 ~Y~Pk~GdvV~G~V~~v~~~g~fV~i--------~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd   70 (88)
T d2z0sa1           2 IYVPQAGDVVIGLIQSVGIMNWFVDI--------NSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFD   70 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEEC--------SSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEEC
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEe--------CCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEEC
Confidence            59999999999999999999999999        77899999999996443  233488999999999999999874

>d2nn6i2 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=4.5e-16  Score=95.47  Aligned_cols=39  Identities=33%  Similarity=0.563  Sum_probs=37.0

Q ss_pred             cEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEc
Q 032149            9 VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTL   49 (146)
Q Consensus         9 ~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~   49 (146)
                      ++++|||+||.+++|.+|+|||++  +|.||||++|.+.+.
T Consensus         1 k~~lPGe~L~~~eey~~G~gTy~~--~g~I~as~~G~v~id   39 (55)
T d2nn6i2           1 RYCIPGERLCNLEEGSPGSGTYTR--HGYIFSSLAGCLMKS   39 (55)
T ss_dssp             CCCCTTCEEEETTTCCCSSSCEEE--TTEEECCSCSCBCCC
T ss_pred             CcccCCcEEeehheecCCCCeEEc--CCEEEEEeeEEEEEe
Confidence            478999999999999999999999  999999999999883

>d2nn6h2 b.84.4.2 (H:25-72) Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=3.7e-14  Score=84.15  Aligned_cols=48  Identities=25%  Similarity=0.438  Sum_probs=44.3

Q ss_pred             cEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecC
Q 032149            9 VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (146)
Q Consensus         9 ~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~   67 (146)
                      .+|+|||.|...+.|+.|+|||.+  +++|+||++|.++..         |+.++|+|+
T Consensus         1 ~iv~PGe~It~~~~~mrGHGTy~~--~~~i~aSv~G~verv---------NKLvsV~pL   48 (48)
T d2nn6h2           1 HLVVPGDTITTDTGFMRGHGTYMG--EEKLIASVAGSVERV---------NKLICVKAL   48 (48)
T ss_dssp             CBCCTTCBCCCCTTCCBCTTEEEC--SSSEEECSSEEEEEE---------TTEEEEEES
T ss_pred             CEecCCcEeecCCCeEcccccEec--CCEEEEEEeeeEEEe---------ccEEEEEcC
Confidence            379999999998899999999999  999999999999885         689999984

>d2je6i2 b.84.4.2 (I:7-65) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.37  E-value=2.1e-13  Score=84.58  Aligned_cols=51  Identities=22%  Similarity=0.272  Sum_probs=45.9

Q ss_pred             CCcEEecCCccCCCCCeee-CCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCC
Q 032149            7 EMVLVTPGEVLGKATEVKA-GKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK   68 (146)
Q Consensus         7 ~~~iV~PGd~l~~~~~~~~-G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~   68 (146)
                      ++++|+|||+|++...|.+ |+|||.+  +++|+||++|.+++.         ++.|+|+|++
T Consensus         7 ~r~iV~PGdvi~~~~~~~~~g~~ty~~--~~ki~asv~G~v~~~---------nkli~ViPL~   58 (59)
T d2je6i2           7 PRSIVVPGELLAEGEFQIPWSPYILKI--NSKYYSTVVGLFDVK---------DTQFEVIPLE   58 (59)
T ss_dssp             SSCEECTTCEEEEECCCCCCCTTEEEE--TTEEEECSSEEEEEE---------TTEEEEEESC
T ss_pred             CCeEECCCcEeeeCCccccCCCEEEec--CCEEEEEEEEEEEEE---------CCEEEEEECC
Confidence            4689999999998777885 9999999  999999999999995         5799999985

>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=99.19  E-value=5.3e-11  Score=78.25  Aligned_cols=66  Identities=18%  Similarity=0.238  Sum_probs=47.4

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      ..|++||+|.|+|+++++..++|++.      ......|++|.+++......  ++.+.|++||.|.|+|+++.
T Consensus         9 ~~p~~G~iv~G~V~~i~~~G~fV~l~------~~~~i~G~i~~sels~~~~~--~~~~~~~~Gd~v~~kV~~vd   74 (86)
T d1kl9a2           9 KFPEVEDVVMVNVRSIAEMGAYVSLL------EYNNIEGMILLSELSRRRIR--SINKLIRIGRNECVVVIRVD   74 (86)
T ss_dssp             SSCCTTCEEEEEEEEECSSEEEEEET------TTTTEEEEEEGGGC--------------CTTCEEEEEEEEEE
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEEe------cCCCEEEEEEeeeccccccc--cceEEeecccEEEEEEEEEE
Confidence            46899999999999999999999991      01258999999999876666  89999999999999999874

>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=99.13  E-value=5.2e-11  Score=77.84  Aligned_cols=65  Identities=14%  Similarity=0.250  Sum_probs=54.5

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEEeecccccc--cceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~--~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .-+|++|++|.|+|+++++..++|++        .  ....|++|.+++.....+  ++.+.|++||.|.|+|+++.
T Consensus         6 ~~~p~~G~iv~G~V~~v~~~G~fV~l--------~~~~gi~Gli~~sels~~~~~--~~~~~~~~G~~v~~kV~~vd   72 (84)
T d2ahob2           6 SKLPSEGEILIATVKQVFDYGSYVSL--------DEYGGLQAFLPWSEVSSKWVK--NIRDVLKENRKVIVKVIRVD   72 (84)
T ss_dssp             SSSCCTTCCCEEEEEEEETTEEEEEE--------TTTTTEEEEECGGGCC-------CHHHHTCSSCEEECEEEEEE
T ss_pred             ccCCCCCCEEEEEEEEEECCEEEEEE--------CCcCCEEEEEEcccccccccc--ccceEeecccEEEEEEEEEE
Confidence            45799999999999999999999999        4  257999999999877666  88999999999999999874

>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=99.04  E-value=1.7e-10  Score=74.28  Aligned_cols=61  Identities=18%  Similarity=0.249  Sum_probs=56.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      .++|+++.|+|+++.+..|+|++        .....|++|.+++.....+  ++++.|++||.|.|+|+++
T Consensus         3 ~kvG~iv~G~V~~v~~~G~fV~l--------~~~~~Glv~~sels~~~~~--~~~~~~~~G~~v~v~Vi~i   63 (76)
T d1sroa_           3 IEVGRVYTGKVTRIVDFGAFVAI--------GGGKEGLVHISQIADKRVE--KVTDYLQMGQEVPVKVLEV   63 (76)
T ss_dssp             CCTTSEEEEEEEEEETTEEEEEC--------SSSCCCBCCTTSSCSSCCS--CHHHHCCTTCEEEEEEEEC
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEe--------CCCCEEEEEhHHhCccccC--CHHHccCCCCEEEEEEEEE
Confidence            58999999999999999999998        5678999999999887777  8999999999999999986

>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=98.90  E-value=2.2e-09  Score=71.44  Aligned_cols=62  Identities=26%  Similarity=0.302  Sum_probs=56.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|++|.|+|+++..+.++|++        .....|++|.+++.....+  ++++.|++||.|.|+|+++.
T Consensus        16 ~k~G~iv~g~V~~v~~~G~~V~l--------~~~i~G~i~~~~ls~~~~~--~~~~~~~vGq~v~~~V~~id   77 (94)
T d3bzka4          16 LKPGMVLEGVVTNVTNFGAFVDI--------GVHQDGLVHISALSEKFVK--DPYEVVKAGDIVKVKVMEVD   77 (94)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEC--------SSSSCEEEEGGGGCSSCCS--CHHHHCCTTCEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEECcEEEEEe--------CCCceEEeehhhhhccccc--ChhhhhccCcEEEEEEEEEE
Confidence            47899999999999999999999        6788999999999877666  89999999999999999874

>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=98.77  E-value=1.4e-08  Score=69.01  Aligned_cols=63  Identities=19%  Similarity=0.270  Sum_probs=53.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccc--c-------cccccCCCCCCEEEEEEEEe
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID--K-------VDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d--~-------~~~~~~~~~GDiV~A~Vis~  144 (146)
                      |++|+++-|+|++|++..++|+|        . +.+|++|.+++......  .       .+..+.|++||.|+++|+++
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel--------~-~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~v   71 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRL--------G-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAI   71 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEC--------S-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEe--------e-CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEE
Confidence            89999999999999999999998        3 58999999999754321  0       14568999999999999987


Q ss_pred             e
Q 032149          145 M  145 (146)
Q Consensus       145 ~  145 (146)
                      .
T Consensus        72 d   72 (106)
T d1go3e1          72 S   72 (106)
T ss_dssp             E
T ss_pred             c
Confidence            4

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.57  E-value=5.2e-08  Score=67.32  Aligned_cols=62  Identities=11%  Similarity=0.137  Sum_probs=53.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccc-cceeeEEecccccccc-ccccccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATE-IDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~-~~~~g~l~~sdi~~~~-~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      .++|++|.|+|+++.++.++|++        . ..+.|++|.+++.... ..  +..+.|++||.|.|+|+++.
T Consensus        19 l~~G~iv~G~V~~i~~~G~~V~l--------g~~~~~G~l~~~els~~~~~~--~~~~~~~vGq~v~~~V~~vd   82 (119)
T d1wi5a_          19 LKPGMLLTGTVSSLEDHGYLVDI--------GVDGTRAFLPLLKAQEYIRQK--NKGAKLKVGQYLNCIVEKVK   82 (119)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEC--------CCSSCEEEEEHHHHHHHHHHH--SSSCCCCTTCEEEEEEEECC
T ss_pred             cCCCCEEEEEEEEEeccEEEEEE--------eccccceEEeHHHhccccccC--CHHHhcccceEEEEEEEEEe
Confidence            58899999999999999999998        4 4689999999987543 22  56789999999999999863

>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=98.39  E-value=8.4e-07  Score=58.03  Aligned_cols=63  Identities=10%  Similarity=0.033  Sum_probs=51.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccc-c-------cccccCCCCCCEEEEEEEEee
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-K-------VDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d-~-------~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |-+|+++-|+|+++++..++|++         .+++|++|.+++...+.- .       .+-...|+.||.|++||+++.
T Consensus         1 Pf~Gev~~g~I~~v~~~G~fv~l---------g~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~   71 (91)
T d1y14b1           1 PFKGEVVDGTVVSCSQHGFEVQV---------GPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCI   71 (91)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE---------TTEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEE---------cCeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEe
Confidence            67899999999999999999999         467999999988644321 0       123557999999999999863

>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=98.33  E-value=2.4e-06  Score=54.01  Aligned_cols=56  Identities=21%  Similarity=0.288  Sum_probs=48.8

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      |.-+.|++|.|.|.++..+.+.|++         ....|+|+.++.        -..+.|++||-|+|-|.++
T Consensus         4 f~~~~geiv~G~V~r~~~~~~~Vdl---------g~~eaiLp~~eq--------ip~E~~~~Gdrik~~i~~V   59 (72)
T d1hh2p1           4 YSELKGTVTTAEVIRVMGEWADIRI---------GKLETRLPKKEW--------IPGEEIKAGDLVKVYIIDV   59 (72)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEEE---------TTEEEEEEGGGS--------CTTCCCCTTCEEEEEEEEE
T ss_pred             HhhccCcEEEEEEEEEcCCCEEEEE---------CCcEEECCHHHc--------CCCCCCCCCCEEEEEEEEE
Confidence            5678999999999999999999998         468999997764        3478899999999999876

>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=98.24  E-value=1.7e-08  Score=62.42  Aligned_cols=56  Identities=14%  Similarity=0.127  Sum_probs=32.5

Q ss_pred             EEEEEEecceEEEEEEeecccccccceeeEEecccccccc--ccccccccCCCCCCEEEEEEEEee
Q 032149           82 ARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE--IDKVDMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        82 G~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~--~d~~~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |+|+++.+..++|+|        ....+|++|+|++....  ....++++.|++||.|.|+|+++.
T Consensus         1 G~V~~i~~fG~FV~l--------~~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD   58 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSL--------LPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEID   58 (62)
T ss_dssp             CBEEECC-CSCEECC--------C---CCCCC-------------------CCSSCBCCCCCCCCC
T ss_pred             CEEEEEEeceEEEEe--------cCCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEc
Confidence            789999999999998        56789999999997532  122288999999999999999874

>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=98.22  E-value=2.9e-06  Score=55.76  Aligned_cols=62  Identities=24%  Similarity=0.277  Sum_probs=50.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc---cc-------cccccCCCCCCEEEEEEEE
Q 032149           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI---DK-------VDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~---d~-------~~~~~~~~~GDiV~A~Vis  143 (146)
                      |-+|+++.|+|+++++..++|++         .+++|++|.+++.....   ++       .+-...|+.||.|++||++
T Consensus         2 Pf~Gev~~g~V~~v~~~G~fv~l---------g~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~   72 (94)
T d2c35b1           2 PFKGEVVDAVVTQVNKVGLFTEI---------GPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVG   72 (94)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE---------TTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEe---------cCceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEE
Confidence            77899999999999999999998         46899999999875431   11       1234578999999999997


Q ss_pred             e
Q 032149          144 F  144 (146)
Q Consensus       144 ~  144 (146)
                      +
T Consensus        73 v   73 (94)
T d2c35b1          73 T   73 (94)
T ss_dssp             E
T ss_pred             E
Confidence            6

>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=97.52  E-value=0.00013  Score=46.19  Aligned_cols=57  Identities=18%  Similarity=0.229  Sum_probs=44.1

Q ss_pred             CCCCEEEEEEEEEecc----eEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149           75 EPGSVVIARVTKVMTR----MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF  144 (146)
Q Consensus        75 ~~GdiViG~V~~v~~~----~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~  144 (146)
                      +.|++|.|.|.++..+    .+.|++..     -....+|+|+.++-        -..+.|++||-|+|-|..+
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~-----~~~~~EaiLp~~eq--------ip~E~y~~Gdrik~~i~~V   63 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGT-----ETKASEGVIPAAEQ--------VPGESYEHGNRLRCYVVGV   63 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECS-----SSSCEEEEECGGGS--------CTTCCCCTTCEEEEEEEEE
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCC-----CCCCEEEECCHHHc--------CCCcccCCCCEEEEEEEEE
Confidence            7899999999999654    47899820     00247899997654        4478899999999999876

>d2nn6g2 b.84.4.2 (G:16-106) Ribosomal RNA-processing protein 40, RRP40 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Ribosomal RNA-processing protein 40, RRP40
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.29  E-value=7.2e-05  Score=48.61  Aligned_cols=56  Identities=25%  Similarity=0.194  Sum_probs=31.7

Q ss_pred             CCcEEecCCccCCCC-------------------------CeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCe
Q 032149            7 EMVLVTPGEVLGKAT-------------------------EVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPT   61 (146)
Q Consensus         7 ~~~iV~PGd~l~~~~-------------------------~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~   61 (146)
                      -.++|+|||.|...+                         ..+.|+|.+.+  ++.|.|+.+|.++..++.  .-.....
T Consensus         8 ~~qvVlPGD~l~lp~~~~~~g~~~~~~~~l~L~~~~~~~~~v~lGPGLRq~--~d~v~atKaG~LR~k~P~--~~~~~~~   83 (91)
T d2nn6g2           8 LGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRC--GDRLLVTKCGRLRHKEPG--SGSGGGV   83 (91)
T ss_dssp             GSSBCCSSEEECCSCSCCEECSSEEECC-------------------------CCCEEECSCCEEEEECCT--TTSSCCE
T ss_pred             cCCEEeCCcEEEecccccccccCcCcccccccccccCCCceEEeCCcccee--CCEEEEeecceeeecCCC--CCCCcce
Confidence            468999999994211                         47889999999  999999999999986531  0011336


Q ss_pred             EEEec
Q 032149           62 VEVTG   66 (146)
Q Consensus        62 i~V~p   66 (146)
                      .||..
T Consensus        84 yWVDs   88 (91)
T d2nn6g2          84 YWVDS   88 (91)
T ss_dssp             EEEEC
T ss_pred             EEeec
Confidence            88875

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=97.07  E-value=0.0012  Score=42.56  Aligned_cols=58  Identities=12%  Similarity=0.231  Sum_probs=46.9

Q ss_pred             CEEEEEEEEEec--ceEEEEEEeecccccccceeeEEeccccccccc-------cccccccCCCCCCEEEEEEEE
Q 032149           78 SVVIARVTKVMT--RMASADIMCVGAKSVREKFSGIIRQQDVRATEI-------DKVDMHLSFRPGDIVRASVVS  143 (146)
Q Consensus        78 diViG~V~~v~~--~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~-------d~~~~~~~~~~GDiV~A~Vis  143 (146)
                      +|-.|+|++|.+  +.|||||        ...-.|.||.+|+...+.       .+..+.+.+++||.|..+|.+
T Consensus         2 NIY~G~V~~V~pgl~AAFVDi--------G~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~K   68 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDK   68 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEES--------SSSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEE
T ss_pred             CcEEEEEEEecCCceEEEEEe--------CCCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEee
Confidence            577899999987  5599999        777889999998764331       234678899999999999975

>d1v8qa_ b.84.4.1 (A:) Ribosomal protein L27 {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: Ribosomal L27 protein
domain: Ribosomal protein L27
species: Thermus thermophilus [TaxId: 274]

Probab=96.66  E-value=0.001  Score=40.83  Aligned_cols=60  Identities=23%  Similarity=0.266  Sum_probs=46.7

Q ss_pred             ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecC
Q 032149            3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (146)
Q Consensus         3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~   67 (146)
                      +|.-..++|.||..|..  -..|.||.++..-. |..|||...|.++....    ..+++.|+|.|.
T Consensus         4 vK~~~Gq~V~~G~IivRQRGtk~~pG~nVg~Gk-D~TLfAl~~G~V~F~~~----~~~~~~VsV~P~   65 (66)
T d1v8qa_           4 VKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGR-DFTLFALVDGVVEFQDR----GRLGRYVHVRPL   65 (66)
T ss_dssp             ECSCTTCEECTTCEEEECSSCSSEECTTEEECT-TCCEEESSSEEEEEEEC----GGGCEEEEEEEC
T ss_pred             cEEeCCEEEeCCeEEEEeccCeEeCCCCeeecC-CCcEEEeeeeEEEEEEe----CCCCeEEEEEEC
Confidence            35556789999998863  35799999999864 99999999999988531    123568999985

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=96.49  E-value=0.0058  Score=39.04  Aligned_cols=62  Identities=6%  Similarity=0.071  Sum_probs=46.8

Q ss_pred             CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc--c--cc------ccccCCCCCCEEEEEEEEee
Q 032149           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--D--KV------DMHLSFRPGDIVRASVVSFM  145 (146)
Q Consensus        77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~--d--~~------~~~~~~~~GDiV~A~Vis~~  145 (146)
                      |..--|.|+++++...+|+|.       .....|++|.+++...+-  +  ..      +-...|+.||.|+++|+++.
T Consensus         4 ~~~F~g~Is~v~~~GifV~L~-------e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd   75 (87)
T d2ix0a3           4 DTRFAAEIVDISRGGMRVRLV-------DNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVR   75 (87)
T ss_dssp             CCCEEEEEEEEETTEEEEEET-------TTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEE
T ss_pred             CCEEEEEEEEEEcCeEEEEEe-------cCCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEe
Confidence            455679999999999999991       246899999999964321  1  01      12357999999999999874

>d2zjrt1 b.84.4.1 (T:2-85) Ribosomal protein L27 {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: Ribosomal L27 protein
domain: Ribosomal protein L27
species: Deinococcus radiodurans [TaxId: 1299]

Probab=95.94  E-value=0.0029  Score=40.47  Aligned_cols=59  Identities=19%  Similarity=0.281  Sum_probs=45.3

Q ss_pred             cccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecC
Q 032149            4 KEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (146)
Q Consensus         4 ~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~   67 (146)
                      |.-..++|.||+.|..  ...|.||.++..-. |..|||..-|.+.....    ...++.|+|.|.
T Consensus        23 K~~~Gq~V~~G~IivRQRGtk~hpG~nVg~Gk-D~TLfA~~~G~V~F~k~----~~~rk~V~V~p~   83 (84)
T d2zjrt1          23 KKFGGEVVKAGNILVRQRGTKFKAGQGVGMGR-DHTLFALSDGKVVFINK----GKGARFISIEAA   83 (84)
T ss_dssp             SSCTTCEECSSCEEECCSSSSSEECTTEECCT-TSCEEESSCEEEEEEEE----TTTEEEEEECCC
T ss_pred             EECCCEEEeCCcEEEEecCceEcCCCCccccC-CCcEEEeeceEEEEEEc----CCCCEEEEEEeC
Confidence            4446789999998864  34699999999854 89999999999988531    123457888874

>d1e1oa1 b.40.4.1 (A:11-153) Lysyl-tRNA synthetase (LysRS) {Escherichia coli, gene lysU [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Lysyl-tRNA synthetase (LysRS)
species: Escherichia coli, gene lysU [TaxId: 562]

Probab=90.16  E-value=0.46  Score=32.32  Aligned_cols=55  Identities=15%  Similarity=0.181  Sum_probs=37.7

Q ss_pred             EEEEEEEEEe--cceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEE
Q 032149           79 VVIARVTKVM--TRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRAS  140 (146)
Q Consensus        79 iViG~V~~v~--~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~  140 (146)
                      .|-|||+.++  ++.+|++|-.     -....|-+++...+....-+  .....++.||+|-++
T Consensus        58 ~vaGRI~~~R~~Gk~~F~~i~D-----~~g~iQi~~~~~~~~~~~~~--~~~k~ld~GDiIgv~  114 (143)
T d1e1oa1          58 SVAGRMMTRRIMGKASFVTLQD-----VGGRIQLYVARDSLPEGVYN--DQFKKWDLGDIIGAR  114 (143)
T ss_dssp             EEEEEEEEEEEETTEEEEEEEE-----TTEEEEEEEETTTSSTTHHH--HTGGGCCTTCEEEEE
T ss_pred             EEEEEEEEEcccCCeeEEEEEe-----CCceEEEEEccccchhhhHH--HHHhcCCcccEEEee
Confidence            4789999886  6779999832     23457788876655432222  355789999999764

>d2gycu1 b.84.4.1 (U:1-84) Ribosomal protein L27 {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: Ribosomal L27 protein
domain: Ribosomal protein L27
species: Escherichia coli [TaxId: 562]

Probab=81.74  E-value=0.023  Score=36.08  Aligned_cols=46  Identities=20%  Similarity=0.250  Sum_probs=37.1

Q ss_pred             ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEc
Q 032149            3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTL   49 (146)
Q Consensus         3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~   49 (146)
                      +|.-..++|.||+.|..  -..|.||.++..-. |..|||...|.++..
T Consensus        22 vK~~~Gq~V~~G~IivRQRGtk~hPG~nVg~Gk-D~TLfAl~~G~V~F~   69 (84)
T d2gycu1          22 VKRFGGESVLAGSIIVRQRGTKFHAGANVGCGR-DHTLFAKADGKVKFE   69 (84)
T ss_dssp             CSSSCCCSSCCSBSSCCCCCCSSCCCCCSSSCC-CCCCCCCSCCCCSSS
T ss_pred             eEEcCCEEEcCCcEEEEeccceEcCCCCeeecC-CCeEEEeccEEEEEE
Confidence            35556788999998864  24699999998743 999999999999874

>d1y71a1 b.34.16.1 (A:4-127) Kinase-associated protein B {Bacillus cereus [TaxId: 1396]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Kinase-associated protein B-like
family: Kinase-associated protein B-like
domain: Kinase-associated protein B
species: Bacillus cereus [TaxId: 1396]

Probab=80.83  E-value=3.5  Score=27.24  Aligned_cols=20  Identities=20%  Similarity=0.159  Sum_probs=18.2

Q ss_pred             EEEEEEEecceEEEEEEeec
Q 032149           81 IARVTKVMTRMASADIMCVG  100 (146)
Q Consensus        81 iG~V~~v~~~~~~v~I~~v~  100 (146)
                      +|.|+..+++.+.|.+.+|-
T Consensus        18 igei~e~~~~~~lVkVlaVl   37 (124)
T d1y71a1          18 IGEVTNSRPGSYVVKVLAVL   37 (124)
T ss_dssp             EEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEeecCCeEEEEEEEEe
Confidence            68999999999999999884