Citrus Sinensis ID: 029155

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------20
Protein Sequence
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQRKVAKVGT
Secondary Structure (PSIPRED)
ccccccccEEEEcccEEcccccEEEcccEEEEccccEEEEEEEccEEEccccccccccccEEEEEcccccccccccccEEEEEEEEEccccEEEEEEEEccEEcccccEEEEcccccccccccHHHHHcccccccEEEEEEEEEcccccEEEEEEccccEEEEEEEccccEEEEccccEEEccccccEEEEEEccccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEccccccccccccccccEEEEEcccEEEEEEEEEEEEEcccccccccccEEEEEcccccccccccccEEEEEEEEEcccEEEEEEEEEcccccccccEEEEEEccccccccccEEHHHccccccEEEEEEEEccccccEEEEccccccEEEEEEcccccccEEccccccEccccccEEccEEEEEcc
Coil and Loop (DISEMBL)
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGllrtlspppdspdqrptvevtghkahgpvpepgSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIirqqdvrateidkvdmhlsfrpgdIVRASVLSLGDARAYFLSTAKndlgvvsaestaggtmvpiswtemqcpltgqteqrkVAKVGT
Flexible Loop (DISEMBL)
mvvkeeemvlvtpgevlgkateVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGhkahgpvpepgsvVIARVTKVMTRMASADIMCVGAKSVrekfsgiirqqdvrateidkvdmhlsfrpgDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTemqcpltgqteqrkvakvgt
Low Complexity Region (SEG)
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQRKVAKVGT
Disordered region (IsUnstruct)
********VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLR******************************SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCP***************
Disordered Region (DISOPRED)
******E***VTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSP****PDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV****IDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQRKVAKV**
Disordered Region (DISEMBL)
********VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSP*************TGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTG************
Disordered Region (DISPRO)
*******MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQRKVAKVGT
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQRKVAKVGT
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	198	2.2.26 [Sep-21-2011]
Q9DAA6	195	Exosome complex component	yes	no	0.898	0.912	0.454	9e-36
Q9Y3B2	195	Exosome complex component	yes	no	0.898	0.912	0.454	9e-36
O59821	181	Exosome complex component	yes	no	0.883	0.966	0.407	4e-29
P53859	292	Exosome complex component	yes	no	0.722	0.489	0.368	9e-24

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

 Score =  149 bits (377), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 84/185 (45%), Positives = 113/185 (61%), Gaps = 7/185 (3%)

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 PGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQR 191
           PGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G  MVPISW EMQCP T   E R
Sbjct: 124 PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGVQMVPISWCEMQCPKTHTKEFR 183

Query: 192 KVAKV 196
           KVA+V
Sbjct: 184 KVARV 188

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 =  149 bits (377), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 84/185 (45%), Positives = 113/185 (61%), Gaps = 7/185 (3%)

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 PGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQR 191
           PGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G  MVPISW EMQCP T   E R
Sbjct: 124 PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTKEFR 183

Query: 192 KVAKV 196
           KVA+V
Sbjct: 184 KVARV 188

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 =  127 bits (319), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 77/189 (40%), Positives = 110/189 (58%), Gaps = 14/189 (7%)

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 HLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAEST-AGGTMVPISWTEMQCPLTG 186
             SFRPGDIVRA V+SLGD  +YFL+TA+NDLGV+ A+S+  G  M P+ +  MQ   +G
Sbjct: 109 QNSFRPGDIVRALVISLGDGSSYFLTTARNDLGVIFAQSSETGEQMFPVDYQHMQTK-SG 167

Query: 187 QTEQRKVAK 195
            TE RK AK
Sbjct: 168 YTEMRKCAK 176

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 =  109 bits (273), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 66/179 (36%), Positives = 91/179 (50%), Gaps = 36/179 (20%)

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 ASVLSLGDARAYFLSTAKNDLGVVSAEST--AGGTMVPISWTEMQCPLTGQTEQRKVAK 195
           A VLSLGD   Y+L+TA+NDLGVV A +   AGG M    W  M  P+TG TE+RK AK
Sbjct: 232 AQVLSLGDGTNYYLTTARNDLGVVFARAANGAGGLMYATDWQMMTSPVTGATEKRKCAK 290

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)

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	198
224125764	199	predicted protein [Populus trichocarpa]	0.979	0.974	0.823	2e-88
255562013	593	conserved hypothetical protein [Ricinus	0.974	0.325	0.824	4e-88
363814479	197	uncharacterized protein LOC100796154 [Gl	0.984	0.989	0.810	5e-87
357441291	1109	Ammonium transporter [Medicago truncatul	0.969	0.173	0.796	4e-86
225430615	200	PREDICTED: exosome complex component CSL	0.994	0.985	0.802	1e-85
255634132	189	unknown [Glycine max]	0.944	0.989	0.823	4e-85
297805862	191	hypothetical protein ARALYDRAFT_494089 [	0.944	0.979	0.793	5e-82
42568189	191	exosome complex component CSL4 [Arabidop	0.944	0.979	0.788	1e-81
449453260	196	PREDICTED: exosome complex component CSL	0.964	0.974	0.766	2e-79
226531832	199	3-5 exoribonuclease CSL4 [Zea mays] gi|1	0.934	0.929	0.737	2e-73

>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 =  330 bits (847), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 163/198 (82%), Positives = 176/198 (88%), Gaps = 4/198 (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 EIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEM 180
           EIDKVDMHLSFRPGDIVRA VLSLGDARAY+LSTAKN+LGVVSAES AG TMVPISWTEM
Sbjct: 122 EIDKVDMHLSFRPGDIVRALVLSLGDARAYYLSTAKNELGVVSAESAAGATMVPISWTEM 181

Query: 181 QCPLTGQTEQRKVAKVGT 198
           QCPLTGQ EQRKVAKVG+
Sbjct: 182 QCPLTGQIEQRKVAKVGS 199

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 =  329 bits (843), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 164/199 (82%), Positives = 178/199 (89%), Gaps = 6/199 (3%)

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 TEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTE 179
           TEIDKVDMHLSFRPGDIVRA VLSLGDARAY+LSTAKN+LGVVSAESTAGGTMVPISWTE
Sbjct: 515 TEIDKVDMHLSFRPGDIVRAVVLSLGDARAYYLSTAKNELGVVSAESTAGGTMVPISWTE 574

Query: 180 MQCPLTGQTEQRKVAKVGT 198
           MQCPLTGQ EQRKVAK+G 
Sbjct: 575 MQCPLTGQIEQRKVAKLGN 593

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  325 bits (834), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 158/195 (81%), Positives = 171/195 (87%)

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 KVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCP 183
           KVDMHLSF PGDIVRA VLSLGDARAYFLSTAKN+LGVVSAES AG TMVP+SWTEMQCP
Sbjct: 123 KVDMHLSFHPGDIVRALVLSLGDARAYFLSTAKNELGVVSAESIAGATMVPVSWTEMQCP 182

Query: 184 LTGQTEQRKVAKVGT 198
           LTGQ EQRKVAK  +
Sbjct: 183 LTGQIEQRKVAKAAS 197

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  322 bits (826), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 153/192 (79%), Positives = 169/192 (88%)

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 VDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPL 184
           VDMHLSFRPGDIV+A VLSLG+ARAYFL+TAKN+LGVVSAESTAG T+VPISWTEMQCPL
Sbjct: 122 VDMHLSFRPGDIVKALVLSLGNARAYFLTTAKNELGVVSAESTAGATLVPISWTEMQCPL 181

Query: 185 TGQTEQRKVAKV 196
           +GQ EQRKVAKV
Sbjct: 182 SGQIEQRKVAKV 193

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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 =  321 bits (822), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 158/197 (80%), Positives = 169/197 (85%)

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 EIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEM 180
           EIDKVDMH SFRPGDIVRA VLSLGDARAYFLSTAKN+LGVVSAES AG TMVP+SWTEM
Sbjct: 121 EIDKVDMHSSFRPGDIVRALVLSLGDARAYFLSTAKNELGVVSAESAAGATMVPMSWTEM 180

Query: 181 QCPLTGQTEQRKVAKVG 197
           QCPLTGQ EQRKVAKVG
Sbjct: 181 QCPLTGQIEQRKVAKVG 197

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  319 bits (817), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 154/187 (82%), Positives = 166/187 (88%)

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 KVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCP 183
           KVDMHLSF PGDIVRA VLSLGDARAYFLSTAKN+LGVVSAES AG TMVP+SWTEMQCP
Sbjct: 123 KVDMHLSFHPGDIVRALVLSLGDARAYFLSTAKNELGVVSAESIAGATMVPVSWTEMQCP 182

Query: 184 LTGQTEQ 190
           LTGQ EQ
Sbjct: 183 LTGQIEQ 189

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  309 bits (791), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 150/189 (79%), Positives = 167/189 (88%), Gaps = 2/189 (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 SFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTE 189
           SFR GDIVRA VLSLGDARAY+LSTAKN+LGVVSAES  G TMVPISWTEMQCPL+GQTE
Sbjct: 123 SFRAGDIVRAMVLSLGDARAYYLSTAKNELGVVSAESAEGETMVPISWTEMQCPLSGQTE 182

Query: 190 QRKVAKVGT 198
           QRKVAKVG 
Sbjct: 183 QRKVAKVGN 191

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

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 =  308 bits (788), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 149/189 (78%), Positives = 167/189 (88%), Gaps = 2/189 (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 SFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTE 189
           SF  GDIVRA VLSLGDARAY+LSTAKN+LGVVSAES AG TMVPISWTEMQCPL+GQTE
Sbjct: 123 SFHAGDIVRAMVLSLGDARAYYLSTAKNELGVVSAESAAGETMVPISWTEMQCPLSGQTE 182

Query: 190 QRKVAKVGT 198
           QRKVAKVG 
Sbjct: 183 QRKVAKVGN 191

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 =  300 bits (769), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 148/193 (76%), Positives = 164/193 (84%), Gaps = 2/193 (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 VDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPL 184
           VDMHLSFRPGDIV+A VLSLGDARAY LSTAKN+LGVVSAESTAG  MVPISWTEMQCP+
Sbjct: 123 VDMHLSFRPGDIVKALVLSLGDARAYHLSTAKNELGVVSAESTAGAEMVPISWTEMQCPV 182

Query: 185 TGQTEQRKVAKVG 197
           TGQ +QRKVAKVG
Sbjct: 183 TGQIQQRKVAKVG 195

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226531832|ref|NP_001148354.1| 3-5 exoribonuclease CSL4 [Zea mays] gi|195618352|gb|ACG31006.1| 3-5 exoribonuclease CSL4 [Zea mays] gi|223975657|gb|ACN32016.1| unknown [Zea mays] gi|413939469|gb|AFW74020.1| 3-5 exoribonuclease CSL4 [Zea mays]

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 138/187 (73%), Positives = 159/187 (85%), Gaps = 2/187 (1%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
           +VTPGE+LG +  + AG+GAY    +  V AS+TG  R + P P S DQR TVEV GHKA
Sbjct: 14  VVTPGELLGNSLTLAAGRGAYADGRS--VRASVTGRRRIVPPAPGSDDQRSTVEVVGHKA 71

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHL 129
           HG VP+PGSVVIARVTKVM RMASADIMCV +K++REKF+G+IRQQDVRATEIDKVDM+ 
Sbjct: 72  HGAVPQPGSVVIARVTKVMARMASADIMCVDSKAIREKFTGMIRQQDVRATEIDKVDMYQ 131

Query: 130 SFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTE 189
           S+RPGDIV+A VLSLGDARAY+LSTAKN+LGVVSA+S AGGT+VPISWTEMQC LTGQ E
Sbjct: 132 SYRPGDIVKAMVLSLGDARAYYLSTAKNELGVVSAQSIAGGTLVPISWTEMQCDLTGQIE 191

Query: 190 QRKVAKV 196
           QRKVAKV
Sbjct: 192 QRKVAKV 198

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

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	198
TAIR|locus:2152297	191	AT5G38890 [Arabidopsis thalian	0.939	0.973	0.792	4.5e-75
UNIPROTKB|G4ML19	213	MGG_08628 "3'-5' exoribonuclea	0.686	0.638	0.503	2.2e-36
ZFIN|ZDB-GENE-080926-3	194	exosc1 "exosome component 1" [	0.919	0.938	0.450	1.5e-35
UNIPROTKB|Q5E9E9	195	EXOSC1 "Uncharacterized protei	0.898	0.912	0.454	3.6e-34
UNIPROTKB|Q9Y3B2	195	EXOSC1 "Exosome complex compon	0.898	0.912	0.459	3.6e-34
UNIPROTKB|E2RT56	207	EXOSC1 "Uncharacterized protei	0.898	0.859	0.454	4.6e-34
MGI|MGI:1913833	195	Exosc1 "exosome component 1" [	0.898	0.912	0.459	4.6e-34
UNIPROTKB|F1S8Y4	196	EXOSC1 "Uncharacterized protei	0.898	0.908	0.451	5.2e-33
ASPGD|ASPL0000007077	246	AN11250 [Emericella nidulans (	0.449	0.361	0.561	6e-33
UNIPROTKB|B1AMU3	170	EXOSC1 "Exosome complex compon	0.570	0.664	0.561	8.8e-32

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

 Score = 757 (271.5 bits), Expect = 4.5e-75, P = 4.5e-75
 Identities = 149/188 (79%), Positives = 167/188 (88%)

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 SFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTE 189
             SF  GDIVRA VLSLGDARAY+LSTAKN+LGVVSAES AG TMVPISWTEMQCPL+GQTE
Sbjct:   123 SFHAGDIVRAMVLSLGDARAYYLSTAKNELGVVSAESAAGETMVPISWTEMQCPLSGQTE 182

Query:   190 QRKVAKVG 197
             QRKVAKVG
Sbjct:   183 QRKVAKVG 190

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 = 323 (118.8 bits), Expect = 2.2e-36, Sum P(2) = 2.2e-36
 Identities = 69/137 (50%), Positives = 91/137 (66%)

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 ATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWT 178
             ATE D+V +  SFRPGDIVRA V+SLGD   Y+L+TA N+LGV+ A S AG  M P+SW 
Sbjct:   136 ATEKDRVKIGESFRPGDIVRAQVISLGDQANYYLTTASNELGVIMANSDAGNPMYPVSWK 195

Query:   179 EMQCPLTGQTEQRKVAK 195
             E + P TG +E RKVAK
Sbjct:   196 EYKDPETGLSEPRKVAK 212

GO:0005575 "cellular_component" evidence=ND

GO:0009405 "pathogenesis" evidence=IMP

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

 Score = 384 (140.2 bits), Expect = 1.5e-35, P = 1.5e-35
 Identities = 86/191 (45%), Positives = 120/191 (62%)

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 MHLSFRPGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLT 185
              + SFRPGDIV A V+SLGD ++ Y L+TA+N+LGVV A S AG  MVP+SW EMQCP T
Sbjct:   117 TYKSFRPGDIVLAKVISLGDVQSNYLLTTAENELGVVVAHSEAGAQMVPVSWCEMQCPRT 176

Query:   186 GQTEQRKVAKV 196
                E RKVA+V
Sbjct:   177 HSKEFRKVARV 187

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=ISS

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

 Score = 371 (135.7 bits), Expect = 3.6e-34, P = 3.6e-34
 Identities = 84/185 (45%), Positives = 114/185 (61%)

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 PGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQR 191
             PGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G  MVPISW EMQCP T   E R
Sbjct:   124 PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGVQMVPISWCEMQCPKTHTKEFR 183

Query:   192 KVAKV 196
             KVA+V
Sbjct:   184 KVARV 188

GO:0005730 "nucleolus" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

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

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

 Score = 371 (135.7 bits), Expect = 3.6e-34, P = 3.6e-34
 Identities = 85/185 (45%), Positives = 114/185 (61%)

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 PGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQR 191
             PGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G  MVPISW EMQCP T   E R
Sbjct:   124 PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTKEFR 183

Query:   192 KVAKV 196
             KVA+V
Sbjct:   184 KVARV 188

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

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

 Score = 370 (135.3 bits), Expect = 4.6e-34, P = 4.6e-34
 Identities = 84/185 (45%), Positives = 114/185 (61%)

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 PGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQR 191
             PGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G  MVPISW EMQCP T   E R
Sbjct:   136 PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGVQMVPISWCEMQCPKTHTKEFR 195

Query:   192 KVAKV 196
             KVA+V
Sbjct:   196 KVARV 200

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 = 370 (135.3 bits), Expect = 4.6e-34, P = 4.6e-34
 Identities = 85/185 (45%), Positives = 114/185 (61%)

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 PGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQR 191
             PGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G  MVPISW EMQCP T   E R
Sbjct:   124 PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGVQMVPISWCEMQCPKTHTKEFR 183

Query:   192 KVAKV 196
             KVA+V
Sbjct:   184 KVARV 188

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 = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 84/186 (45%), Positives = 114/186 (61%)

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 RPGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQ 190
             RPGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G  MVPISW EMQCP T   E 
Sbjct:   124 RPGDIVLAKVISLGDAQSHYLLTTAENELGVVVAHSESGVQMVPISWCEMQCPKTHTKEF 183

Query:   191 RKVAKV 196
             RKVA+V
Sbjct:   184 RKVARV 189

GO:0005730 "nucleolus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

ASPGD|ASPL0000007077 AN11250 [Emericella nidulans (taxid:162425)]

 Score = 259 (96.2 bits), Expect = 6.0e-33, Sum P(3) = 6.0e-33
 Identities = 50/89 (56%), Positives = 66/89 (74%)

Query:   107 KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAES 166
             +F  +IR++DVRA E D+V +   FR GDIVR +V+SLGD   Y+++TA+NDLGVV A S
Sbjct:   156 RFQALIRKEDVRAVEKDRVVLDEMFRVGDIVRGTVISLGDQSYYYITTARNDLGVVMARS 215

Query:   167 TAGGTMVPISWTEMQCPLTGQTEQRKVAK 195
              AG  M P+SW EM+ P+TG  EQRKVA+
Sbjct:   216 EAGNMMFPVSWKEMRDPVTGAAEQRKVAR 244

GO:0005829 "cytosol" evidence=IEA

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

GO:0000176 "nuclear exosome (RNase complex)" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0071035 "nuclear polyadenylation-dependent rRNA catabolic process" evidence=IEA

GO:0070481 "nuclear-transcribed mRNA catabolic process, non-stop decay" evidence=IEA

GO:0034427 "nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'" evidence=IEA

GO:0000467 "exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IEA

GO:0071038 "nuclear polyadenylation-dependent tRNA catabolic process" evidence=IEA

UNIPROTKB|B1AMU3 EXOSC1 "Exosome complex component CSL4" [Homo sapiens (taxid:9606)]

 Score = 309 (113.8 bits), Expect = 8.8e-32, Sum P(2) = 8.8e-32
 Identities = 64/114 (56%), Positives = 84/114 (73%)

Query:    84 VTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLS 143
             V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ SFRPGDIV A V+S
Sbjct:    50 VSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVIS 109

Query:   144 LGDARA-YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQRKVAKV 196
             LGDA++ Y L+TA+N+LGVV A S +G  MVPISW EMQCP T   E RKVA+V
Sbjct:   110 LGDAQSNYLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTKEFRKVARV 163

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

GO:0003723 "RNA binding" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9Y3B2	EXOS1_HUMAN	No assigned EC number	0.4540	0.8989	0.9128	yes	no
Q9DAA6	EXOS1_MOUSE	No assigned EC number	0.4540	0.8989	0.9128	yes	no
O59821	CSL4_SCHPO	No assigned EC number	0.4074	0.8838	0.9668	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	198
cd05791	92	cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-bindi	8e-44
pfam10447	72	pfam10447, EXOSC1, Exosome component EXOSC1/CSL4	1e-33
COG1096	188	COG1096, COG1096, Predicted RNA-binding protein (c	5e-31
PRK09521	189	PRK09521, PRK09521, exosome complex RNA-binding pr	2e-20
cd04454	82	cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1	8e-12
pfam14382	39	pfam14382, ECR1_N, Exosome complex exonuclease RRP	1e-08
COG1097	239	COG1097, RRP4, RNA-binding protein Rrp4 and relate	1e-06
PRK04163	235	PRK04163, PRK04163, exosome complex RNA-binding pr	2e-06

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

 Score =  140 bits (356), Expect = 8e-44
 Identities = 55/91 (60%), Positives = 75/91 (82%)

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 RPGDIVRASVLSLGDARAYFLSTAKNDLGVV 162
           RPGDIVRA V+SLGDA +Y+LSTA+N+LGVV
Sbjct: 62  RPGDIVRAKVISLGDASSYYLSTAENELGVV 92

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|192591 pfam10447, EXOSC1, Exosome component EXOSC1/CSL4

 Score =  114 bits (287), Expect = 1e-33
 Identities = 40/72 (55%), Positives = 55/72 (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 PGDIVRASVLSL 144
           PGDIVRA V+SL
Sbjct: 61  PGDIVRAKVISL 72

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

 Score =  111 bits (279), Expect = 5e-31
 Identities = 61/197 (30%), Positives = 91/197 (46%), Gaps = 21/197 (10%)

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  VTGHKAHGPVPEPGSVVIARVTKV-----MTRMASADIMCVGAKSVREKFSGIIRQQDVR 118
           V   K   P+P+ G +V  RVT V     + R+   +       +     +  I    VR
Sbjct: 52  VKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELAT---SGAADIHVSQVR 108

Query: 119 ATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWT 178
              ++K+    +FR GDIVRA V+S GD     LST  NDLGV+ A  +     +     
Sbjct: 109 DGYVEKLSD--AFRIGDIVRARVISTGDP--IQLSTKGNDLGVIYARCSRCRAPLVKKGN 164

Query: 179 EMQCPLTGQTEQRKVAK 195
            ++CP  G TE+RK+AK
Sbjct: 165 MLKCPNCGNTEKRKIAK 181

Length = 188

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

 Score = 83.9 bits (208), Expect = 2e-20
 Identities = 57/195 (29%), Positives = 84/195 (43%), Gaps = 18/195 (9%)

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-DMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGT-MVPISWTE 179
           ++ + D    F+ GDIVRA V+S  D     LST   DLGV+ A  +   T +V     E
Sbjct: 112 VESLTDA---FKIGDIVRAKVISYTDPLQ--LSTKGKDLGVIYAMCSRCRTPLVKKGENE 166

Query: 180 MQCPLTGQTEQRKVA 194
           ++CP  G  E RK++
Sbjct: 167 LKCPNCGNIETRKLS 181

Length = 189

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

 Score = 58.3 bits (141), Expect = 8e-12
 Identities = 35/90 (38%), Positives = 51/90 (56%), Gaps = 10/90 (11%)

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

Query: 133 PGDIVRASVLSLGDARAYFLSTAKNDLGVV 162
           PGD++ A V+SLGD     L+TA N+LGV+
Sbjct: 53  PGDLILAKVISLGDDMNVLLTTADNELGVI 82

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

 Score = 48.9 bits (118), Expect = 1e-08
 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|224022 COG1097, RRP4, RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 38/169 (22%), Positives = 62/169 (36%), Gaps = 27/169 (15%)

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 HLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPIS 176
                 GD+V A V+ +       L+     LG +       G +V I 
Sbjct: 110 RPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLK-----NGQIVKIP 153

Length = 239

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

 Score = 46.0 bits (110), Expect = 2e-06
 Identities = 45/184 (24%), Positives = 73/184 (39%), Gaps = 40/184 (21%)

Query: 1   MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRP 60
           M +  E+  +V PG++L +  E KAG+G Y    NG +Y+++ GL               
Sbjct: 1   MKIFVEDRKIVVPGDLLAEG-EFKAGRGTYKE--NGKIYSTVVGL--------------- 42

Query: 61  TVEVTGHKA-----HGP-VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQ 114
            V++   K       G  +P+ G +VI +VT V       DI           +   +  
Sbjct: 43  -VDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDI--------NSPYKAYLPV 93

Query: 115 QDV--RATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTM 172
            +V  R   ++  D+      GD + A V  +   R   L+     LG +      GGT+
Sbjct: 94  SEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIE-----GGTI 148

Query: 173 VPIS 176
           V I 
Sbjct: 149 VEIK 152

Length = 235

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	198
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	100.0
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	100.0
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	99.98
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	99.97
KOG3013	301	consensus Exosomal 3'-5' exoribonuclease complex,	99.95
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	99.95
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	99.88
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.79
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.68
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	99.63
KOG1004	230	consensus Exosomal 3'-5' exoribonuclease complex s	99.5
PF14382	39	ECR1_N: Exosome complex exonuclease RRP4 N-termina	99.44
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.4
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.39
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.28
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.23
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.21
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.2
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.17
PRK08582	139	hypothetical protein; Provisional	99.16
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.14
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.13
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.13
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.11
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	99.11
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.08
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.08
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.07
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.04
PRK07252	120	hypothetical protein; Provisional	99.03
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.02
PRK05807	136	hypothetical protein; Provisional	99.01
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.99
PRK08059	123	general stress protein 13; Validated	98.98
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.95
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.94
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	98.94
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	98.92
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	98.92
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	98.87
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	98.85
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.85
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.84
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.82
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.81
PHA02945	88	interferon resistance protein; Provisional	98.75
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.73
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.7
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.7
PRK07400	318	30S ribosomal protein S1; Reviewed	98.7
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.69
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.68
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.64
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.63
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.62
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.55
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	98.54
PRK07400	318	30S ribosomal protein S1; Reviewed	98.52
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	98.51
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	98.48
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.47
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.47
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	98.45
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.45
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	98.43
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	98.42
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.42
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	98.41
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	98.39
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	98.37
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	98.35
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	98.31
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	98.3
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	98.28
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.24
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	98.2
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	98.2
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	98.17
COG2183	780	Tex Transcriptional accessory protein [Transcripti	98.09
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	98.07
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	98.06
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	97.99
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.8
PRK09202	470	nusA transcription elongation factor NusA; Validat	97.74
PRK12327	362	nusA transcription elongation factor NusA; Provisi	97.58
TIGR01953	341	NusA transcription termination factor NusA. This m	97.55
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.52
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	97.4
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.22
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	97.04
PRK11642	813	exoribonuclease R; Provisional	96.81
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.7
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	96.69
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.6
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	96.52
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	96.47
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	96.41
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	96.16
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	95.94
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	95.86
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	95.69
KOG2916	304	consensus Translation initiation factor 2, alpha s	95.38
PRK11712	489	ribonuclease G; Provisional	95.13
PRK10811	1068	rne ribonuclease E; Reviewed	95.04
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	94.54
PF01016	81	Ribosomal_L27: Ribosomal L27 protein; InterPro: IP	94.39
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	94.2
COG1571	421	Predicted DNA-binding protein containing a Zn-ribb	93.44
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	93.26
PRK05435	82	rpmA 50S ribosomal protein L27; Validated	93.09
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	92.97
CHL00121	86	rpl27 ribosomal protein L27; Reviewed	92.95
smart00661	52	RPOL9 RNA polymerase subunit 9.	92.89
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	92.09
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	91.83
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	91.52
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	91.0
PRK05054	644	exoribonuclease II; Provisional	90.7
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	90.66
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	90.59
PRK00420	112	hypothetical protein; Validated	89.77
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	89.64
KOG4600	144	consensus Mitochondrial ribosomal protein MRP7 (L2	88.82
TIGR00062	83	L27 ribosomal protein L27. Eubacterial, chloroplas	88.57
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	88.12
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	87.39
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	87.36
COG0557	706	VacB Exoribonuclease R [Transcription]	87.34
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	87.3
COG1545	140	Predicted nucleic-acid-binding protein containing	87.3
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	87.22
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	87.03
PRK07218	423	replication factor A; Provisional	86.32
PRK00432	50	30S ribosomal protein S27ae; Validated	86.31
COG1656	165	Uncharacterized conserved protein [Function unknow	84.69
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	84.62
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	83.4
PF01927	147	Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 T	82.96
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	82.89
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	82.43
PF01959	354	DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); Inte	82.42
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	82.28
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	82.28
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	81.63
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	81.15
PRK02290	344	3-dehydroquinate synthase; Provisional	81.09
COG2816	279	NPY1 NTP pyrophosphohydrolases containing a Zn-fin	80.98
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	80.69
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	80.03

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

Probab=100.00  E-value=1.5e-51  Score=330.26  Aligned_cols=177  Identities=34%  Similarity=0.503  Sum_probs=167.0

Q ss_pred             cCCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 029155            6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT   85 (198)
Q Consensus         6 ~~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~   85 (198)
                      .++.+|+|||.|+++|||++|.|||+++|+  |+|+.+|.+..       |++|.+++|.|.+..+.+|+.||+|+|+|+
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 KDGTFVLPGDVLAVIEEFLPGEGTYEEGGE--IRAAATGVVRR-------DDKNRVISVKPGKKTPPLPKGGDIVYGRVT   73 (188)
T ss_pred             ccCcEEcCcceeeeeeeeecCCCeEeECCE--EEEeecccEEE-------cccceEEEeccCCCCCCCCCCCCEEEEEEe
Confidence            578899999999999999999999999988  99999999999       356889999998876889999999999999


Q ss_pred             EEecceEEEEEeeecccc--ccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCeeeE
Q 029155           86 KVMTRMASADIMCVGAKS--VREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS  163 (198)
Q Consensus        86 ~v~~~~~~V~I~~v~~~~--l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~  163 (198)
                      +++.+.|.|+|.++++..  +...+.|.||+||++..+..  +++++|+|||+|+|+|+|.+  .++.|||++++||||+
T Consensus        74 ~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~--~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~dlGVI~  149 (188)
T COG1096          74 DVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVE--KLSDAFRIGDIVRARVISTG--DPIQLSTKGNDLGVIY  149 (188)
T ss_pred             eccceEEEEEEEEEecccccCCCCceeeEEEEeccccccc--ccccccccccEEEEEEEecC--CCeEEEecCCcceEEE
Confidence            999999999999999954  78899999999999998877  88999999999999999987  5899999999999999


Q ss_pred             Eec-CCCceeEEccCCeEEeCCCCCEEeeeeCCC
Q 029155          164 AES-TAGGTMVPISWTEMQCPLTGQTEQRKVAKV  196 (198)
Q Consensus       164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~~  196 (198)
                      |+| +||++|.+ .|++|+||+||++|+||+|++
T Consensus       150 A~CsrC~~~L~~-~~~~l~Cp~Cg~tEkRKia~~  182 (188)
T COG1096         150 ARCSRCRAPLVK-KGNMLKCPNCGNTEKRKIAKD  182 (188)
T ss_pred             EEccCCCcceEE-cCcEEECCCCCCEEeeeeccc
Confidence            999 99999998 899999999999999999986

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

Probab=100.00  E-value=1.7e-50  Score=319.08  Aligned_cols=185  Identities=45%  Similarity=0.702  Sum_probs=167.0

Q ss_pred             CCcEEecCCccCCCC-CeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 029155            7 EMVLVTPGEVLGKAT-EVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT   85 (198)
Q Consensus         7 ~~~iV~PGd~l~~~~-e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~   85 (198)
                      ...+++|||+++..+ +|..|.|||+.+++  |+||.+|......    ..+++++.++........+|.+||||+++|+
T Consensus         4 a~~~~lpG~~~c~~e~~~~~g~Gtye~~~y--I~aS~ag~~~~~~----~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~   77 (193)
T KOG3409|consen    4 AETLVLPGEVVCRAEGEYRMGEGTYERNGY--IFASVAGVNFRDN----LVQKIEVVSVEKQLFNELLPFVGAIVTARVS   77 (193)
T ss_pred             ceEEEcccceeeecccccccccceeecCCe--EEeccccceeecC----CccceeeeeecccchhhcCCccCcEEEEEEE
Confidence            357899999999876 49999999999988  9999999554421    2234445555544456789999999999999


Q ss_pred             EEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCeeeEEe
Q 029155           86 KVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAE  165 (198)
Q Consensus        86 ~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a~  165 (198)
                      +++.++|.|+|+++++++|...|+|+||.+|+|++++|++++.++|+|||+|+|+|+|.+++.+|.|||+++|||||+|+
T Consensus        78 ~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAeneLGVV~a~  157 (193)
T KOG3409|consen   78 RINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAENELGVVFAR  157 (193)
T ss_pred             eeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEecccceEEEEe
Confidence            99999999999999999999999999999999999999999999999999999999999989999999999999999999


Q ss_pred             c-CCCceeEEccCCeEEeCCCCCEEeeeeCCCC
Q 029155          166 S-TAGGTMVPISWTEMQCPLTGQTEQRKVAKVG  197 (198)
Q Consensus       166 ~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~~~  197 (198)
                      . +.|.+|+|++|++|+||.+|.+|+||+||+.
T Consensus       158 as~~g~~M~pvdw~~mqsp~Tg~tE~RK~AKv~  190 (193)
T KOG3409|consen  158 ASETGEPMVPVDWQEMQSPKTGKTEPRKCAKVP  190 (193)
T ss_pred             ccccCCceeeccceeEEcCccCcccchhhccCC
Confidence            9 9999999999999999999999999999963

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=100.00  E-value=1.5e-49  Score=324.72  Aligned_cols=177  Identities=29%  Similarity=0.414  Sum_probs=164.7

Q ss_pred             CCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 029155            7 EMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK   86 (198)
Q Consensus         7 ~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~   86 (198)
                      ++++|+|||.|+..++|++|+|||+++|.  |||+++|.+++.       ..++.|+|.|.....+.|++||+|+|+|++
T Consensus         4 ~~~~V~PGe~l~~~~e~~~G~Gty~~~~~--i~as~~G~~~id-------~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~   74 (189)
T PRK09521          4 QGDLVLPGDYLAVIEEYLPGEGTYEDNGE--VYASVVGKVFID-------DINRKISVIPFKKTPPLLKKGDIVYGRVVD   74 (189)
T ss_pred             cCCEECCCCccccccceEcCCCEEeeCCE--EEEEeeEEEEEc-------CCCCEEEEecCcCCCCCCCCCCEEEEEEEE
Confidence            67899999999998999999999999988  999999999983       346789999987668999999999999999


Q ss_pred             EecceEEEEEeeec--cccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCeeeEE
Q 029155           87 VMTRMASADIMCVG--AKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSA  164 (198)
Q Consensus        87 v~~~~~~V~I~~v~--~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a  164 (198)
                      +.+++|+|+|.+++  +.++..++.|+||.+|++..+.+  +|.+.|++||+|+|+|++++  +.+.||+++++||||+|
T Consensus        75 i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~--~~~~~~~~GD~V~akV~~i~--~~i~LS~k~~~lGvv~a  150 (189)
T PRK09521         75 VKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVE--SLTDAFKIGDIVRAKVISYT--DPLQLSTKGKDLGVIYA  150 (189)
T ss_pred             EcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhh--hHHhccCCCCEEEEEEEecC--CcEEEEEecCCceEEEE
Confidence            99999999999887  67788899999999999876655  89999999999999999997  68999999999999999


Q ss_pred             ec-CCCceeEEccCCeEEeCCCCCEEeeeeCCC
Q 029155          165 ES-TAGGTMVPISWTEMQCPLTGQTEQRKVAKV  196 (198)
Q Consensus       165 ~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~~  196 (198)
                      +| +||.+|+|.+|++|+||+||++|+||+|++
T Consensus       151 ~~~~~g~~~~~~~~~~~~c~~~~~~e~rkva~~  183 (189)
T PRK09521        151 MCSRCRTPLVKKGENELKCPNCGNIETRKLSSY  183 (189)
T ss_pred             EccccCCceEECCCCEEECCCCCCEEeeccchh
Confidence            99 799999999999999999999999999975

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=99.98  E-value=1.5e-31  Score=225.23  Aligned_cols=137  Identities=26%  Similarity=0.439  Sum_probs=123.7

Q ss_pred             cCCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 029155            6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT   85 (198)
Q Consensus         6 ~~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~   85 (198)
                      .++++|+|||.|+ +++|.+|+|||+++|+  |+||++|.+...         ++.++|.|... +|+|++||+|+|+|+
T Consensus         6 ~~~~~V~PGd~l~-~~~~~~G~Gty~~~g~--i~As~~G~~~~~---------~~~i~V~p~~~-~y~P~vGDiViG~V~   72 (235)
T PRK04163          6 EDRKIVVPGDLLA-EGEFKAGRGTYKENGK--IYSTVVGLVDIK---------DDKVRVIPLEG-KYIPKVGDLVIGKVT   72 (235)
T ss_pred             eCCcEECCCCCcC-cCCeecCCceEEeCCE--EEEEEeEEEEEE---------CCEEEEEECCC-cccCCCCCEEEEEEE
Confidence            3458999999997 5889999999999988  999999999984         25899999875 599999999999999


Q ss_pred             EEecceEEEEEeeeccccccCcceeEEeccccccccc--cccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCeeeE
Q 029155           86 KVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS  163 (198)
Q Consensus        86 ~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~--d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~  163 (198)
                      ++.+++|+|+|        ..++.|+||.++++..+.  |..+|+++|++||+|+|||+++++.+.+.||+++++||+|.
T Consensus        73 ~i~~~~~~vdI--------~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~~lG~L~  144 (235)
T PRK04163         73 DVTFSGWEVDI--------NSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIE  144 (235)
T ss_pred             EEeCceEEEEe--------CCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCCCCCccC
Confidence            99999999999        678999999999986543  56699999999999999999998767799999999999995

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

Probab=99.97  E-value=3.2e-30  Score=214.62  Aligned_cols=140  Identities=24%  Similarity=0.350  Sum_probs=127.0

Q ss_pred             eccCCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEE
Q 029155            4 KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIAR   83 (198)
Q Consensus         4 ~~~~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~   83 (198)
                      ...++++|+|||.|...+.|..|+|||.++++  |||+++|++++.         ++.+.|+|+.+ +|+|++||+|||+
T Consensus         4 ~~~~~~iV~PGd~vl~~~~~~~G~Gty~~~~~--iyssv~G~~~~~---------~~~v~VIpl~g-~YiP~~gD~VIG~   71 (239)
T COG1097           4 SVSMRKIVLPGDLVLAEGSYKLGHGTYFEGGK--IYSSVVGLLDVK---------GKLVRVIPLEG-RYIPEVGDVVIGK   71 (239)
T ss_pred             eccccceecCCCccCCCCCEecCCCcEecCCE--EEEEEEeEEEEe---------CCEEEEEeCCC-cccCCCCCEEEEE
Confidence            45678999999987777899999999999988  999999999995         46899999976 9999999999999


Q ss_pred             EEEEecceEEEEEeeeccccccCcceeEEeccccc--cccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCee
Q 029155           84 VTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVR--ATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGV  161 (198)
Q Consensus        84 V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~--~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGv  161 (198)
                      |+++.+++|.|||        +++|.++||.|+..  ..+.++.+|+++|++||+|+|||.+++..+.+.|++++..||.
T Consensus        72 I~~v~~~~W~VDI--------~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~Gk  143 (239)
T COG1097          72 IIEVGPSGWKVDI--------GSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGK  143 (239)
T ss_pred             EEEEcccceEEEc--------CCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCcc
Confidence            9999999999999        78999999999983  3334467999999999999999999998889999999999999


Q ss_pred             eE
Q 029155          162 VS  163 (198)
Q Consensus       162 v~  163 (198)
                      +.
T Consensus       144 L~  145 (239)
T COG1097         144 LK  145 (239)
T ss_pred             cc
Confidence            84

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

Probab=99.95  E-value=3.1e-29  Score=209.29  Aligned_cols=145  Identities=25%  Similarity=0.393  Sum_probs=126.7

Q ss_pred             ccCCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 029155            5 EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV   84 (198)
Q Consensus         5 ~~~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V   84 (198)
                      +....+|+||+.+...+.|+.|||||..++.  |+||++|.++..         |++|+|+|++ .+|.|++||+|+|||
T Consensus        26 ~~~~~ivtPG~~V~~d~~fmRGHGTy~~d~~--i~ssvaG~v~rv---------NkLi~V~plk-~rY~pEvGDvVVgRV   93 (301)
T KOG3013|consen   26 SDHSTIVTPGELVTDDPGFMRGHGTYVRDGE--IYSSVAGVVQRV---------NKLISVKPLK-SRYAPEVGDVVVGRV   93 (301)
T ss_pred             ccCceeecCCccccCchhhhhcccceecCCe--EEEeecchhhhh---------cceEEEeehh-hhcCCccCCEEEEEe
Confidence            4556799999999998899999999999999  999999999984         6899999997 689999999999999


Q ss_pred             EEEecceEEEEEeeeccccccC---cceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCee
Q 029155           85 TKVMTRMASADIMCVGAKSVRE---KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGV  161 (198)
Q Consensus        85 ~~v~~~~~~V~I~~v~~~~l~~---~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGv  161 (198)
                      +.|.++.|+||+++-.+..|..   ++.|-+   +.|.+..|+..|+++|+.||+|.|+|+++...++..|+||+..||+
T Consensus        94 ~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~---~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sLhTRS~KYGK  170 (301)
T KOG3013|consen   94 IEVQQKRWKVDLNSKQDAVLMLSSVNLPGGI---QRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSLHTRSLKYGK  170 (301)
T ss_pred             eeeecceeEEecccccceEEEeecccCCchh---hhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEEEecchhccc
Confidence            9999999999998877655432   344432   3456778899999999999999999999987789999999999999


Q ss_pred             eEE
Q 029155          162 VSA  164 (198)
Q Consensus       162 v~a  164 (198)
                      +..
T Consensus       171 L~~  173 (301)
T KOG3013|consen  171 LGQ  173 (301)
T ss_pred             ccC
Confidence            843

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

Probab=99.95  E-value=2.8e-28  Score=177.88  Aligned_cols=91  Identities=60%  Similarity=1.022  Sum_probs=88.4

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYF  151 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~  151 (198)
                      |+|++||+|+|+|++++.++|.|+|++++++++..+|.|+||+||+++++.++.+|+++|++||+|+|||+++++.++++
T Consensus         2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~   81 (92)
T cd05791           2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYY   81 (92)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcE
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999878899


Q ss_pred             EEEecCCCeee
Q 029155          152 LSTAKNDLGVV  162 (198)
Q Consensus       152 LSt~~~~lGvv  162 (198)
                      |||++++||||
T Consensus        82 Lst~~~~lGVv   92 (92)
T cd05791          82 LSTAENELGVV   92 (92)
T ss_pred             EEecCCCCccC
Confidence            99999999996

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".

>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=99.88  E-value=9.9e-23  Score=145.31  Aligned_cols=72  Identities=61%  Similarity=0.963  Sum_probs=52.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeee----------ccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCV----------GAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVL  142 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v----------~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~  142 (198)
                      +|++||+|+|+|+++++++|.|+|+++          ++.++..+|.|+||.+|+|+++.|+++|.++|+|||+|+|+|+
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            589999999999999999999999999          7778899999999999999999999999999999999999999


Q ss_pred             Ee
Q 029155          143 SL  144 (198)
Q Consensus       143 s~  144 (198)
                      |+
T Consensus        81 Sl   82 (82)
T PF10447_consen   81 SL   82 (82)
T ss_dssp             EE
T ss_pred             eC
Confidence            85

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.

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

Probab=99.79  E-value=7.1e-19  Score=124.93  Aligned_cols=82  Identities=33%  Similarity=0.552  Sum_probs=74.6

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccE
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAY  150 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~  150 (198)
                      +|.|++||+|+|+|+++.+++|+|+|        ...++|+||.+++...+..  ++.+.|++||+|.|+|+++++.+.+
T Consensus         1 ~y~p~~GdiV~G~V~~v~~~~~~V~i--------~~~~~g~l~~~~~~~~~~~--~~~~~~~~GD~i~~~V~~~~~~~~i   70 (82)
T cd04454           1 RYLPDVGDIVIGIVTEVNSRFWKVDI--------LSRGTARLEDSSATEKDKK--EIRKSLQPGDLILAKVISLGDDMNV   70 (82)
T ss_pred             CCCCCCCCEEEEEEEEEcCCEEEEEe--------CCCceEEeechhccCcchH--HHHhcCCCCCEEEEEEEEeCCCCCE
Confidence            48999999999999999999999999        6679999999999754433  8899999999999999999866789


Q ss_pred             EEEEecCCCeee
Q 029155          151 FLSTAKNDLGVV  162 (198)
Q Consensus       151 ~LSt~~~~lGvv  162 (198)
                      .||+++++||+|
T Consensus        71 ~LS~~~~~~Gvi   82 (82)
T cd04454          71 LLTTADNELGVI   82 (82)
T ss_pred             EEEECCCCCccC
Confidence            999999999986

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".

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

Probab=99.68  E-value=2.3e-16  Score=112.80  Aligned_cols=84  Identities=27%  Similarity=0.396  Sum_probs=73.3

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccc--cccccccccCCCCCCEEEEEEEEeCCCc
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT--EIDKVDMHLSFRPGDIVRASVLSLGDAR  148 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~--~~d~~~~~~~~~~GDiV~AkV~s~~~~~  148 (198)
                      +|.|++||+|.|+|+++.+++|+|+|        ...+.|+||.+++...  .....++.+.|++||.|.|+|+++++.+
T Consensus         1 ~y~p~~GdiV~g~V~~i~~~g~~v~i--------~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~   72 (86)
T cd05789           1 RYIPEVGDVVIGRVTEVGFKRWKVDI--------NSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDG   72 (86)
T ss_pred             CCcCCCCCEEEEEEEEECCCEEEEEC--------CCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCC
Confidence            48899999999999999999999999        6789999999998631  1122377889999999999999997657


Q ss_pred             cEEEEEecCCCeee
Q 029155          149 AYFLSTAKNDLGVV  162 (198)
Q Consensus       149 ~~~LSt~~~~lGvv  162 (198)
                      .+.||++.++||++
T Consensus        73 ~i~LS~~~~~~g~~   86 (86)
T cd05789          73 SVSLHTRSLKYGKL   86 (86)
T ss_pred             CEEEEeCcccccCC
Confidence            89999999999985

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".

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

Probab=99.63  E-value=2e-15  Score=108.62  Aligned_cols=76  Identities=20%  Similarity=0.152  Sum_probs=64.6

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccE
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAY  150 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~  150 (198)
                      +|+|++||+|+|+|+++..+.|+|||        ++++.|+||.++....   ...++..|++||+|+|||.+++.....
T Consensus         1 rY~P~~gD~VIG~V~~~~~~~~~VdI--------~s~~~a~L~~~~f~ga---tk~~rp~L~~GDlV~ArV~~~~~~~~~   69 (86)
T cd05790           1 RYVPAKGDHVIGIVVAKAGDFFKVDI--------GGSEPASLSYLAFEGA---TKRNRPNLNVGDLVYARVVKANRDMEP   69 (86)
T ss_pred             CCcCCCCCEEEEEEEEEcCCeEEEEc--------CCCcceEechHHcccc---cccccccCCCCCEEEEEEEecCCCCCe
Confidence            59999999999999999999999999        6778899998776322   125789999999999999999876678


Q ss_pred             EEEEecC
Q 029155          151 FLSTAKN  157 (198)
Q Consensus       151 ~LSt~~~  157 (198)
                      .||..++
T Consensus        70 eLtc~~~   76 (86)
T cd05790          70 ELSCVDS   76 (86)
T ss_pred             EEEEeCC
Confidence            8888653

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".

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

Probab=99.50  E-value=5.2e-13  Score=109.38  Aligned_cols=145  Identities=22%  Similarity=0.286  Sum_probs=105.5

Q ss_pred             cEEecCCccCC--CCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 029155            9 VLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK   86 (198)
Q Consensus         9 ~iV~PGd~l~~--~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~   86 (198)
                      ++.+|||.+..  ..+..+|+|.|..++.  +..+.+|.+....+   ....-.+.+|.. .+.+|+|.+||.|||+|+.
T Consensus         2 ~~~~pg~~~~~~~~~sv~~G~g~~~~g~~--~~~~~~G~~~~~~~---gk~~~~v~~vds-~~kRYiP~~~D~VIGiV~~   75 (230)
T KOG1004|consen    2 TFYFPGDSIPRPRLCSVVLGPGLRRRGQE--RLVTKCGRLRHKEP---GKGGGGVYWVDS-QQKRYIPVKGDHVIGIVTS   75 (230)
T ss_pred             ceecCCcccccCccCceeecCCccccCce--EEeccccceeeccC---CcccceeEEEec-ccceecCCCCCEEEEEEEe
Confidence            46789998764  2357899999998877  99999998877531   000112557765 4679999999999999999


Q ss_pred             EecceEEEEEeeeccccccC-cceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecC-----CCe
Q 029155           87 VMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKN-----DLG  160 (198)
Q Consensus        87 v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~-----~lG  160 (198)
                      -..+++.|||...+-+.|+. +|+|        +++.+    ++.|+.||+|+|||...+......|+--+.     .+|
T Consensus        76 ~~gd~ykVDigg~~~a~L~~laFe~--------AtkrN----rPnl~vGdliyakv~~a~~~~Epel~Cids~graaGfG  143 (230)
T KOG1004|consen   76 KSGDIYKVDIGGSEPASLSYLAFEG--------ATKRN----RPNLQVGDLIYAKVVDANKDMEPELTCIDSTGRAAGFG  143 (230)
T ss_pred             ccCceEEEecCCCCeeeeeeccccC--------ccccC----CCccccccEEEEEEEecCCCcCcceEEEcccCcccCcc
Confidence            99999999996544444443 4555        35544    688999999999999987544455554444     666


Q ss_pred             eeEEecCCCceeEEcc
Q 029155          161 VVSAESTAGGTMVPIS  176 (198)
Q Consensus       161 vv~a~~~~g~~m~~~~  176 (198)
                      ++     .++.|.+++
T Consensus       144 ~L-----kdG~if~vs  154 (230)
T KOG1004|consen  144 VL-----KDGMIFKVS  154 (230)
T ss_pred             cc-----cCceEEEec
Confidence            66     367777776

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

Probab=99.44  E-value=8.8e-14  Score=85.78  Aligned_cols=37  Identities=41%  Similarity=0.803  Sum_probs=33.8

Q ss_pred             EEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEE
Q 029155           10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRT   48 (198)
Q Consensus        10 iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~   48 (198)
                      ||+|||+|+.+++|++|+|||+++|+  ||||++|.+++
T Consensus         1 iV~PG~~l~~~~e~~~G~GTY~~~g~--I~asv~G~v~~   37 (39)
T PF14382_consen    1 IVVPGDRLGSSEEYMPGHGTYVRDGN--IYASVAGTVKI   37 (39)
T ss_dssp             EE-TT-EEEETTTSEESTTEEEETTE--EEESSSEEEEE
T ss_pred             CCCCCCEeecCCCEecCCCEEEeCCE--EEEEeeEEEEE
Confidence            69999999999999999999999999  99999999987

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

Probab=99.40  E-value=4.1e-13  Score=101.72  Aligned_cols=75  Identities=19%  Similarity=0.290  Sum_probs=70.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS  153 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS  153 (198)
                      +++|+++.|+||.|++.+|+|++        ...-+|++|+|++...++.  ++.|.+++||.|.|+|+++++.+.+.||
T Consensus         3 ~kvG~~l~GkItgI~~yGAFV~l--------~~g~tGLVHISEIa~~fVk--dI~d~L~vG~eV~vKVl~ide~GKisLS   72 (129)
T COG1098           3 MKVGSKLKGKITGITPYGAFVEL--------EGGKTGLVHISEIADGFVK--DIHDHLKVGQEVKVKVLDIDENGKISLS   72 (129)
T ss_pred             ccccceEEEEEEeeEecceEEEe--------cCCCcceEEehHhhhhhHH--hHHHHhcCCCEEEEEEEeeccCCCccee
Confidence            68999999999999999999999        6667899999999999988  9999999999999999999988899999


Q ss_pred             EecCC
Q 029155          154 TAKND  158 (198)
Q Consensus       154 t~~~~  158 (198)
                      +|..+
T Consensus        73 Ir~~~   77 (129)
T COG1098          73 IRKLE   77 (129)
T ss_pred             hHHhh
Confidence            98754

>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=99.39  E-value=2.2e-12  Score=89.67  Aligned_cols=70  Identities=29%  Similarity=0.408  Sum_probs=62.2

Q ss_pred             CCCCEEEEEEEEEec-ceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155           75 EPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS  153 (198)
Q Consensus        75 ~vGDiViG~V~~v~~-~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS  153 (198)
                      ++||+|.|+|+++.+ ..+++++        ..+..|++|+++++..+..  ++.+.|++||.|+|+|+++++ +.+.||
T Consensus         2 ~~G~iv~G~V~~i~~~~g~~v~l--------~~~~~Glvhis~~s~~~~~--~~~~~~~~Gd~v~~kV~~~~~-~~i~LS   70 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQL--------PFGKTGLVSIFHLSDSYTE--NPLEGFKPGKIVRCCILSKKD-GKYQLS   70 (72)
T ss_pred             CCCCEEEEEEEEeeCCcEEEEEC--------CCCCEEEEEHHHhcCcccC--CHHHhCCCCCEEEEEEEEecC-CEEEEE
Confidence            689999999999986 7899998        7789999999999876655  677999999999999999975 689999


Q ss_pred             Ee
Q 029155          154 TA  155 (198)
Q Consensus       154 t~  155 (198)
                      ++
T Consensus        71 l~   72 (72)
T cd05704          71 LR   72 (72)
T ss_pred             eC
Confidence            85

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.

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

Probab=99.28  E-value=2.8e-11  Score=82.93  Aligned_cols=69  Identities=26%  Similarity=0.286  Sum_probs=60.6

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC-CCccEEEEEe
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG-DARAYFLSTA  155 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~-~~~~~~LSt~  155 (198)
                      ||+|.|+|+++.+++|+|++        ...+.|+||.+++...+.+  ++.+.|++||.|.|+|++++ +.+.+.||.+
T Consensus         1 G~iv~g~V~~i~~~~~~v~l--------~~~~~g~l~~~e~~~~~~~--~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDI--------GYKSEGIIPISEFSDDPIE--NGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEe--------CCCceEEEEHHHhCccccC--CHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            89999999999999999999        5578999999999866655  78899999999999999997 4466888864

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.

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

Probab=99.23  E-value=1.1e-10  Score=80.48  Aligned_cols=71  Identities=30%  Similarity=0.354  Sum_probs=61.8

Q ss_pred             CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS  153 (198)
Q Consensus        75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS  153 (198)
                      ++|++|.|+|+++.+++++|++        ....+|++|.++++..+..  ++.+.|++||.|.|+|++++. .+.+.||
T Consensus         2 ~~G~iv~g~V~~v~~~gi~v~l--------~~~~~g~v~~s~l~~~~~~--~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls   71 (73)
T cd05706           2 KVGDILPGRVTKVNDRYVLVQL--------GNKVTGPSFITDALDDYSE--ALPYKFKKNDIVRACVLSVDVPNKKIALS   71 (73)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEe--------CCCcEEEEEhhhccCcccc--ccccccCCCCEEEEEEEEEeCCCCEEEEE
Confidence            6899999999999999999999        6679999999999765433  567899999999999999974 4679998


Q ss_pred             Ee
Q 029155          154 TA  155 (198)
Q Consensus       154 t~  155 (198)
                      ++
T Consensus        72 ~~   73 (73)
T cd05706          72 LR   73 (73)
T ss_pred             EC
Confidence            74

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.

>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=99.21  E-value=7.7e-11  Score=82.42  Aligned_cols=71  Identities=18%  Similarity=0.176  Sum_probs=59.6

Q ss_pred             CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccc-ccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-KVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d-~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      ++||+|.|+|+++++++++|++        .....|+||.++++..... ..++.+.|++||.|.|+|+++++ .+.+.|
T Consensus         2 k~G~~V~g~V~~i~~~G~fV~l--------~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~L   73 (74)
T cd05705           2 KEGQLLRGYVSSVTKQGVFFRL--------SSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVEL   73 (74)
T ss_pred             CCCCEEEEEEEEEeCCcEEEEe--------CCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEec
Confidence            7899999999999999999999        6789999999999865533 12367999999999999999975 355666


Q ss_pred             E
Q 029155          153 S  153 (198)
Q Consensus       153 S  153 (198)
                      |
T Consensus        74 S   74 (74)
T cd05705          74 S   74 (74)
T ss_pred             C
Confidence            4

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.

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

Probab=99.20  E-value=1.6e-10  Score=79.29  Aligned_cols=72  Identities=25%  Similarity=0.439  Sum_probs=63.1

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-ccEEEEEe
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFLSTA  155 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~~~LSt~  155 (198)
                      |++|.|+|+++.+++|+|+|        .....|++|.+++...+..  ++.+.|++||.|.|+|++++.. +.+.||++
T Consensus         1 G~~v~g~V~~v~~~g~~v~l--------~~~~~g~i~~~~~~~~~~~--~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k   70 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKL--------GDGVEGFLRAAELSRDRVE--DATERFKVGDEVEAKITNVDRKNRKISLSIK   70 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEe--------CCCCEEEEEHHHCCCcccc--CHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence            89999999999999999999        5678999999999866554  7789999999999999999854 67999998


Q ss_pred             cCC
Q 029155          156 KND  158 (198)
Q Consensus       156 ~~~  158 (198)
                      ..+
T Consensus        71 ~~~   73 (73)
T cd05691          71 AKE   73 (73)
T ss_pred             EcC
Confidence            653

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

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

Probab=99.17  E-value=2.4e-10  Score=79.24  Aligned_cols=74  Identities=18%  Similarity=0.244  Sum_probs=62.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      |++|+++.|+|+++.+.+++|++...      .+.+|+||.++++..+..  ++.+.|++||.|.|+|++++. .+.+.|
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~------~~~~gll~~s~l~~~~~~--~~~~~~~~Gd~v~vkv~~~d~~~~~i~l   72 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEY------GNIEGMILLSELSRRRIR--SIRKLVKVGRKEVVKVIRVDKEKGYIDL   72 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCC------CCeEEEEEhHHcCCcccC--CHHHeeCCCCEEEEEEEEEECCCCEEEE
Confidence            67899999999999999999999321      148999999999865544  778999999999999999975 356899


Q ss_pred             EEe
Q 029155          153 STA  155 (198)
Q Consensus       153 St~  155 (198)
                      |++
T Consensus        73 s~k   75 (76)
T cd04452          73 SKK   75 (76)
T ss_pred             EEc
Confidence            876

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

>PRK08582 hypothetical protein; Provisional

Probab=99.16  E-value=4e-10  Score=88.04  Aligned_cols=75  Identities=25%  Similarity=0.305  Sum_probs=66.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS  153 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS  153 (198)
                      +++|++|.|+|+.|++.+++|+|        .....|++|++++...+..  ++.+.|++||.|.|+|++++..+.+.||
T Consensus         3 ~kvG~iv~G~V~~I~~fG~fV~L--------~~~~~GlVhiSels~~~v~--~~~~~l~vGD~VkvkV~~id~~gkI~LS   72 (139)
T PRK08582          3 IEVGSKLQGKVTGITNFGAFVEL--------PEGKTGLVHISEVADNYVK--DINDHLKVGDEVEVKVLNVEDDGKIGLS   72 (139)
T ss_pred             CcCCCEEEEEEEEEECCeEEEEE--------CCCCEEEEEeeccCccccc--ccccccCCCCEEEEEEEEECCCCcEEEE
Confidence            57899999999999999999999        5678999999999866654  6789999999999999999865789999


Q ss_pred             EecCC
Q 029155          154 TAKND  158 (198)
Q Consensus       154 t~~~~  158 (198)
                      ++...
T Consensus        73 lk~~~   77 (139)
T PRK08582         73 IKKAK   77 (139)
T ss_pred             EEecc
Confidence            98653

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

Probab=99.14  E-value=3.8e-10  Score=78.61  Aligned_cols=71  Identities=20%  Similarity=0.181  Sum_probs=61.2

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEEEe
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLSTA  155 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LSt~  155 (198)
                      ||+|.|+|+++.+++++|++        ....+|+||.++++.......+..+.|++||.|.|+|++++. .+.+.||.+
T Consensus         1 G~~V~g~V~~i~~~g~~V~l--------~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k   72 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTI--------SPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEe--------CCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            89999999999999999999        678999999999975432223778999999999999999984 467999976

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.

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

Probab=99.13  E-value=1.9e-10  Score=85.05  Aligned_cols=76  Identities=18%  Similarity=0.291  Sum_probs=63.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc-----------------cccccccCCCCCCE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-----------------DKVDMHLSFRPGDI  136 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~-----------------d~~~~~~~~~~GDi  136 (198)
                      +++|++|.|+|+++.+..+++++        .....|++|.+|+...+.                 +..++.+.|++||+
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L--------~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~   72 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISL--------PNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQL   72 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEEC--------CCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCE
Confidence            37899999999999999999988        667999999999975331                 12357899999999


Q ss_pred             EEEEEEEeCCC----ccEEEEEecC
Q 029155          137 VRASVLSLGDA----RAYFLSTAKN  157 (198)
Q Consensus       137 V~AkV~s~~~~----~~~~LSt~~~  157 (198)
                      |+|+|+++++.    +.+.||++..
T Consensus        73 V~~kVi~~d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          73 VRCKVVSLDKSKSGKKRIELSLEPE   97 (100)
T ss_pred             EEEEEEEccCCcCCCcEEEEEecHH
Confidence            99999999863    5799998754

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.

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

Probab=99.13  E-value=5.7e-10  Score=75.05  Aligned_cols=69  Identities=26%  Similarity=0.352  Sum_probs=59.8

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEe
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTA  155 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~  155 (198)
                      ||++.|+|+++.+.+|+|+|        ...+.|+||.++++..+..  ++.+.|++||.|.++|++++..+.+.||++
T Consensus         1 G~~~~g~V~~i~~~g~~v~i--------~~~~~g~l~~~~l~~~~~~--~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~k   69 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVEL--------GGGISGLVHISQIAHKRVK--DVKDVLKEGDKVKVKVLSIDARGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEE--------CCCCEEEEEhHHcCCcccC--CHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence            79999999999999999999        5678999999999765543  667889999999999999976567888874

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.

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

Probab=99.11  E-value=7.2e-10  Score=76.48  Aligned_cols=72  Identities=24%  Similarity=0.308  Sum_probs=63.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      +++||++.|+|+++.+++++|+|        ..+..|+||.+++.....+  +..+.|++||.|.|+|++++. .+.+.|
T Consensus         2 ~~~G~iv~g~V~~v~~~g~~V~l--------~~~~~g~ip~~~l~~~~~~--~~~~~~~~G~~v~v~v~~vd~~~~~i~l   71 (74)
T PF00575_consen    2 LKEGDIVEGKVTSVEDFGVFVDL--------GNGIEGFIPISELSDDRID--DPSEVYKIGQTVRVKVIKVDKEKGRIRL   71 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEE--------STSSEEEEEGGGSSSSEES--SSHGTCETTCEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEEECCEEEEEE--------CCcEEEEEEeehhcCcccc--ccccccCCCCEEEEEEEEEECCCCeEEE
Confidence            68999999999999999999999        6689999999999866544  778999999999999999985 456899


Q ss_pred             EEe
Q 029155          153 STA  155 (198)
Q Consensus       153 St~  155 (198)
                      |+|
T Consensus        72 S~k   74 (74)
T PF00575_consen   72 SLK   74 (74)
T ss_dssp             EST
T ss_pred             EEC
Confidence            875

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

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

Probab=99.11  E-value=4.3e-10  Score=77.34  Aligned_cols=65  Identities=23%  Similarity=0.303  Sum_probs=55.9

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCcc
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARA  149 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~  149 (198)
                      |++|.|+|+++.+++++|++        ...++|.||.++++..+.+..++.+.|++||.|.|+|+++++.+.
T Consensus         1 G~iV~g~V~~i~~~gi~v~l--------~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~   65 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQL--------ADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT   65 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEe--------CCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence            89999999999999999999        678999999999976532233778999999999999999986543

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.

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

Probab=99.08  E-value=1.1e-09  Score=75.98  Aligned_cols=72  Identities=18%  Similarity=0.160  Sum_probs=61.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS  153 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS  153 (198)
                      |+.|+++.|+|+++.+.+++|++.       ....+|++|.++++..+.+  +..+.|++||.|.++|++++..+.+.||
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~-------~~~~eGlvh~sel~~~~~~--~~~~~~~~Gd~v~vkv~~vd~~~ki~ls   71 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIP-------GCRKQGLVHKSHMSSCRVD--DPSEVVDVGEKVWVKVIGREMKDKMKLS   71 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEEC-------CCCeEEEEEchhhCCCccc--CHhhEECCCCEEEEEEEEECCCCcEEEE
Confidence            578999999999999999999992       1135899999999876655  7788999999999999999865578887


Q ss_pred             E
Q 029155          154 T  154 (198)
Q Consensus       154 t  154 (198)
                      +
T Consensus        72 ~   72 (73)
T cd05686          72 L   72 (73)
T ss_pred             e
Confidence            5

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.

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

Probab=99.08  E-value=5.9e-10  Score=75.99  Aligned_cols=67  Identities=15%  Similarity=0.283  Sum_probs=57.7

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS  153 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS  153 (198)
                      |++|.|+|+++.+++++|++        ...+.|++|.++++..+..  ++.+.|++||.|.|+|++++. .+.+.||
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l--------~~~~~G~v~~s~l~~~~~~--~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls   68 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTL--------GRGVDARVRVSELSDSYLK--DWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEe--------CCCCEEEEEHHHCCchhhc--CHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            79999999999999999999        5569999999999765544  678999999999999999985 4556654

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.

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

Probab=99.07  E-value=1.2e-09  Score=75.50  Aligned_cols=74  Identities=24%  Similarity=0.320  Sum_probs=62.7

Q ss_pred             CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS  153 (198)
Q Consensus        75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS  153 (198)
                      ++|++|.|+|+++.+.+|+|++.       .....|++|.++++..+..  ++.+.|++||.|.|+|.+++. .+.+.||
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~-------~~~~~g~i~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   71 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDID-------GTNVSGLCHKSEISDNRVA--DASKLFRVGDKVRAKVLKIDAEKKRISLG   71 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEEC-------CCCeEEEEEHHHCCCCccC--CHhHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence            46999999999999999999993       1368999999999765533  677899999999999999985 5789999


Q ss_pred             EecC
Q 029155          154 TAKN  157 (198)
Q Consensus       154 t~~~  157 (198)
                      ++..
T Consensus        72 ~k~~   75 (77)
T cd05708          72 LKAS   75 (77)
T ss_pred             EEee
Confidence            8764

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.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.04  E-value=9.9e-10  Score=96.23  Aligned_cols=77  Identities=18%  Similarity=0.280  Sum_probs=67.7

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeecccccc-CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-Ccc
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARA  149 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~-~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~  149 (198)
                      -.|++||+|.|+|++|.+.+++|+|.       . .+..|+||.|++++....  ++++.|++||.|.++|++++. .+.
T Consensus        13 ~~P~~GdvV~g~V~~I~d~GafV~L~-------EY~gvEGlIhiSElS~~ri~--~i~d~vkvGd~v~vkVl~VD~ekg~   83 (319)
T PTZ00248         13 KFPEEDDLVMVKVVRITEMGAYVSLL-------EYDDIEGMILMSELSKRRIR--SINKLIRVGRHEVVVVLRVDKEKGY   83 (319)
T ss_pred             hCCCCCCEEEEEEEEEeCCeEEEEec-------CCCCcEEEEEHHHhcccccC--CHHHhcCCCCEEEEEEEEEeCCCCE
Confidence            46899999999999999999999993       2 268999999999877665  999999999999999999973 467


Q ss_pred             EEEEEecC
Q 029155          150 YFLSTAKN  157 (198)
Q Consensus       150 ~~LSt~~~  157 (198)
                      +.||.+.-
T Consensus        84 IdLS~K~v   91 (319)
T PTZ00248         84 IDLSKKRV   91 (319)
T ss_pred             EEEEeeec
Confidence            99999864

>PRK07252 hypothetical protein; Provisional

Probab=99.03  E-value=2.3e-09  Score=81.85  Aligned_cols=73  Identities=18%  Similarity=0.257  Sum_probs=63.5

Q ss_pred             CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS  153 (198)
Q Consensus        75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS  153 (198)
                      ++|+++.|+|++|.+.+|+|+|        .....|+||.++++..+..  +..+.|++||.|.|+|++++. .+.+.||
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei--------~~~~~GllhiseLs~~~~~--~~~~~~~vGD~V~VkI~~iD~~~~ri~lS   71 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVAL--------ENGTTGLIHISEIKTGFID--NIHQLLKVGEEVLVQVVDFDEYTGKASLS   71 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEE--------CCCCEEEEEHHHcCCcccc--ChhhccCCCCEEEEEEEEEeCCCCEEEEE
Confidence            5799999999999999999999        5568999999999865544  567889999999999999985 5678888


Q ss_pred             EecC
Q 029155          154 TAKN  157 (198)
Q Consensus       154 t~~~  157 (198)
                      ++..
T Consensus        72 lk~~   75 (120)
T PRK07252         72 LRTL   75 (120)
T ss_pred             Eeec
Confidence            8765

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

Probab=99.02  E-value=2.2e-09  Score=73.30  Aligned_cols=69  Identities=22%  Similarity=0.316  Sum_probs=59.8

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEEEe
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLSTA  155 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LSt~  155 (198)
                      |+++.|+|+++.+.+++|++        .....|++|.+++...+..  +..+.|++||.|.++|++++. .+.+.||.+
T Consensus         1 g~~~~g~V~~v~~~G~~V~l--------~~~~~gli~~s~l~~~~~~--~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k   70 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSF--------YNNVKGFLPKSELSEAFIK--DPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEE--------CCCCEEEEEHHHcChhhcC--CHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            89999999999999999999        4568999999999765544  677899999999999999985 467888864

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.

>PRK05807 hypothetical protein; Provisional

Probab=99.01  E-value=3.6e-09  Score=82.37  Aligned_cols=73  Identities=21%  Similarity=0.312  Sum_probs=64.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS  153 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS  153 (198)
                      .++|++|.|+|+.+.+.+|+|+|        . ...|+||+++++..+..  ++.+.|++||.|.++|++++..+.+.||
T Consensus         3 ~~vG~vv~G~Vt~i~~~GafV~L--------~-~~~Glvhiseis~~~v~--~~~~~~kvGd~V~VkV~~id~~gkI~LS   71 (136)
T PRK05807          3 LKAGSILEGTVVNITNFGAFVEV--------E-GKTGLVHISEVADTYVK--DIREHLKEQDKVKVKVISIDDNGKISLS   71 (136)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEhhhccccccc--CccccCCCCCEEEEEEEEECCCCcEEEE
Confidence            46899999999999999999999        2 34899999999876665  7789999999999999999866789999


Q ss_pred             EecC
Q 029155          154 TAKN  157 (198)
Q Consensus       154 t~~~  157 (198)
                      ++..
T Consensus        72 lk~~   75 (136)
T PRK05807         72 IKQA   75 (136)
T ss_pred             EEec
Confidence            9874

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

Probab=98.99  E-value=3.5e-09  Score=71.02  Aligned_cols=71  Identities=27%  Similarity=0.356  Sum_probs=60.2

Q ss_pred             CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-ccEEEE
Q 029155           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFLS  153 (198)
Q Consensus        75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~~~LS  153 (198)
                      ++|++|.|+|+++.+.++++++        ...+.|++|.+++...+..  ++.+.|++||.|.|+|.+++.. +.+.||
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i--------~~~~~g~l~~~~~~~~~~~--~~~~~~~~G~~v~~~V~~~~~~~~~i~ls   70 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDL--------GNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLSVDEEKGRIILS   70 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEe--------CCCCEEEEEHHHCCccccC--CHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence            4699999999999999999999        5578999999998765433  5678899999999999999753 678887


Q ss_pred             Ee
Q 029155          154 TA  155 (198)
Q Consensus       154 t~  155 (198)
                      ++
T Consensus        71 ~~   72 (72)
T smart00316       71 LK   72 (72)
T ss_pred             eC
Confidence            64

>PRK08059 general stress protein 13; Validated

Probab=98.98  E-value=4.7e-09  Score=80.25  Aligned_cols=76  Identities=26%  Similarity=0.323  Sum_probs=65.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      +++|++|.|+|+++.+.+|+|+|        ...+.|+||.++++..+..  ++.+.|++||.|.|+|++++. .+.+.|
T Consensus         5 ~k~G~iv~G~V~~i~~~G~fV~i--------~~~~~Gli~~sel~~~~~~--~~~~~~~vGD~I~vkI~~id~~~~~i~l   74 (123)
T PRK08059          5 YEVGSVVTGKVTGIQPYGAFVAL--------DEETQGLVHISEITHGFVK--DIHDFLSVGDEVKVKVLSVDEEKGKISL   74 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEE--------CCCCEEEEEHHHCCccccc--CHHHcCCCCCEEEEEEEEEECCCCeEEE
Confidence            57899999999999999999999        5678999999999765544  667899999999999999964 578999


Q ss_pred             EEecCCC
Q 029155          153 STAKNDL  159 (198)
Q Consensus       153 St~~~~l  159 (198)
                      |++..+.
T Consensus        75 slk~~~~   81 (123)
T PRK08059         75 SIRATEE   81 (123)
T ss_pred             EEEEccc
Confidence            9987654

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

Probab=98.95  E-value=4.5e-09  Score=90.12  Aligned_cols=78  Identities=19%  Similarity=0.192  Sum_probs=66.3

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY  150 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~  150 (198)
                      -.|++||+|.|+|+++.+.+|+|++...      .+..|+||.++++.....  ++++.|++||.|.|+|++++. .+.+
T Consensus         4 ~~P~~GdiV~G~V~~I~~~G~fV~L~e~------~gieGlI~iSEls~~~i~--~i~~~~kvGd~V~vkVi~VD~~k~~I   75 (262)
T PRK03987          4 EWPEEGELVVGTVKEVKDFGAFVTLDEY------PGKEGFIHISEVASGWVK--NIRDHVKEGQKVVCKVIRVDPRKGHI   75 (262)
T ss_pred             CCCCCCCEEEEEEEEEECCEEEEEECCC------CCcEEEEEHHHcCccccc--CHHHhCCCCCEEEEEEEEEecccCeE
Confidence            4689999999999999999999999311      157999999999765554  788999999999999999985 3679


Q ss_pred             EEEEecC
Q 029155          151 FLSTAKN  157 (198)
Q Consensus       151 ~LSt~~~  157 (198)
                      .||++.-
T Consensus        76 ~LSlK~v   82 (262)
T PRK03987         76 DLSLKRV   82 (262)
T ss_pred             EEEEEec
Confidence            9999853

>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=98.94  E-value=6.1e-09  Score=71.13  Aligned_cols=68  Identities=19%  Similarity=0.345  Sum_probs=58.5

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEEE
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLST  154 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LSt  154 (198)
                      |+++.|+|+++.+.+++|++        .....|++|.++++.....  ++.+.|++||.|.++|++++. .+.+.||.
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l--------~~~v~g~i~~~~l~~~~~~--~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~   69 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKL--------SDHIKGLVPPMHLADVRLK--HPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEe--------cCCcEEEEEHHHCCCcccc--CHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            79999999999999999999        5679999999999765443  567889999999999999985 46788873

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=98.94  E-value=6.8e-09  Score=71.79  Aligned_cols=68  Identities=21%  Similarity=0.293  Sum_probs=58.2

Q ss_pred             CCEEE-EEEEEE-ecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155           77 GSVVI-ARVTKV-MTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS  153 (198)
Q Consensus        77 GDiVi-G~V~~v-~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS  153 (198)
                      |+++- |+|+++ .+++++|++        ..+.+|++|.+++...+.+  ++.+.|++||.+.|+|++++. .+.+.||
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l--------~~gv~G~i~~s~l~~~~~~--~~~~~~~vG~~v~~kV~~id~~~~~i~lS   70 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFEL--------KDGLLGFVHISHLSDDKVP--SDTGPFKAGTTHKARIIGYSPMDGLLQLS   70 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEe--------CCCCEEEEEHHHCCcchhc--CcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence            78888 999999 699999999        5679999999999765555  677889999999999999985 4578887


Q ss_pred             E
Q 029155          154 T  154 (198)
Q Consensus       154 t  154 (198)
                      +
T Consensus        71 ~   71 (71)
T cd05696          71 L   71 (71)
T ss_pred             C
Confidence            4

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.

>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=98.92  E-value=7.6e-09  Score=73.32  Aligned_cols=72  Identities=21%  Similarity=0.319  Sum_probs=62.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF  151 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~  151 (198)
                      -+++|+++.|+|.++.+++++|++        .....|++|.++++..+..  ++.+.|++||.|.++|++++. .+.+.
T Consensus        11 ~~~~G~i~~g~V~~v~~~G~fv~l--------~~~~~g~v~~~el~~~~~~--~~~~~~~~Gd~v~vkV~~id~~~~~i~   80 (83)
T cd04461          11 DLKPGMVVHGYVRNITPYGVFVEF--------LGGLTGLAPKSYISDEFVT--DPSFGFKKGQSVTAKVTSVDEEKQRFL   80 (83)
T ss_pred             hCCCCCEEEEEEEEEeeceEEEEc--------CCCCEEEEEHHHCCccccc--CHHHhcCCCCEEEEEEEEEcCCCCEEE
Confidence            478999999999999999999999        4568999999999765544  778999999999999999975 46788


Q ss_pred             EEE
Q 029155          152 LST  154 (198)
Q Consensus       152 LSt  154 (198)
                      ||+
T Consensus        81 lsl   83 (83)
T cd04461          81 LSL   83 (83)
T ss_pred             EeC
Confidence            874

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.

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

Probab=98.92  E-value=3.7e-09  Score=98.13  Aligned_cols=75  Identities=24%  Similarity=0.276  Sum_probs=68.8

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC-CCccEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG-DARAYF  151 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~-~~~~~~  151 (198)
                      ..++||+|.|+|++|++.+++|+|        . ++.|++|++++++.+.+  .+++.|++||.|.++|++++ +.+.+.
T Consensus       189 ~l~~G~vV~G~V~~It~~GafVdi--------g-GvdGLlHiseiS~~rv~--~P~~vvkvGd~VkvkVi~~D~e~~RVs  257 (541)
T COG0539         189 KLEVGEVVEGVVKNITDYGAFVDI--------G-GVDGLLHISEISWKRVD--HPSEVVKVGDEVKVKVISLDEERGRVS  257 (541)
T ss_pred             cCCCCceEEEEEEEeecCcEEEEe--------c-CeeeEEehhhccccccC--CHHHhcccCCEEEEEEEEEccCCCeEE
Confidence            478999999999999999999999        3 59999999999998888  99999999999999999998 457899


Q ss_pred             EEEecCC
Q 029155          152 LSTAKND  158 (198)
Q Consensus       152 LSt~~~~  158 (198)
                      ||++...
T Consensus       258 LSlK~l~  264 (541)
T COG0539         258 LSLKQLE  264 (541)
T ss_pred             EEehhcc
Confidence            9998753

>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=98.87  E-value=2.7e-08  Score=69.54  Aligned_cols=68  Identities=21%  Similarity=0.219  Sum_probs=58.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeecccccc-CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF  151 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~-~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~  151 (198)
                      .+.|++|.|.|.+|.+.++++++        . ..+.|+||.+++...        +.|++||.+.|+|++++. .+.+.
T Consensus         2 l~~G~~v~g~V~si~d~G~~v~~--------g~~gv~Gfl~~~~~~~~--------~~~~~Gq~v~~~V~~vd~~~~~v~   65 (74)
T cd05694           2 LVEGMVLSGCVSSVEDHGYILDI--------GIPGTTGFLPKKDAGNF--------SKLKVGQLLLCVVEKVKDDGRVVS   65 (74)
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEe--------CCCCcEEEEEHHHCCcc--------cccCCCCEEEEEEEEEECCCCEEE
Confidence            46899999999999999999999        4 468999999997532        789999999999999974 46789


Q ss_pred             EEEecC
Q 029155          152 LSTAKN  157 (198)
Q Consensus       152 LSt~~~  157 (198)
                      ||++..
T Consensus        66 ls~k~~   71 (74)
T cd05694          66 LSADPS   71 (74)
T ss_pred             EEEeec
Confidence            998754

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.

>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=98.85  E-value=1.8e-08  Score=68.74  Aligned_cols=65  Identities=26%  Similarity=0.377  Sum_probs=54.5

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS  153 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS  153 (198)
                      ||+|.|+|+++.+++++|++        ...+.|++|.+++.....   . .+.|++||.|.|+|++++. .+.+.||
T Consensus         1 G~~V~g~V~~i~~~G~~v~l--------~~~v~g~v~~~~l~~~~~---~-~~~~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDF--------LSSFTGTVDFLHLDPEKS---S-KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEE--------cCCceEEEEHHHcCCccC---c-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            89999999999999999999        456999999999864332   2 7889999999999999984 4556665

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=98.85  E-value=1.4e-08  Score=68.30  Aligned_cols=67  Identities=21%  Similarity=0.256  Sum_probs=55.3

Q ss_pred             CCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155           76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS  153 (198)
Q Consensus        76 vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS  153 (198)
                      +|+++.|+|+++.+.+|+|++        . ...|+||.++++..+..  .+.+.|++||.|+|+|.+++. .+.+.||
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l--------~-~~~g~l~~~e~~~~~~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDL--------G-GVDGLLHISDMSWGRVK--HPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEE--------C-CeEEEEEhHHCCCcccc--CHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            499999999999999999999        3 47899999998754443  567889999999999999974 3455554

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

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

Probab=98.84  E-value=2.7e-08  Score=66.95  Aligned_cols=68  Identities=19%  Similarity=0.299  Sum_probs=57.3

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEE
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLST  154 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt  154 (198)
                      |+++.|+|+++.+++|+|+|        .....|++|.++++..+..  ...+.|++||.|.++|.+++..+.+.||+
T Consensus         1 g~~~~g~V~~v~~~G~~v~l--------~~~~~g~l~~~~l~~~~~~--~~~~~~~~Gd~v~v~v~~~d~~~~i~ls~   68 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEI--------LPGKDGLVHISELSDERVE--KVEDVLKVGDEVKVKVIEVDDRGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEe--------CCCCEEEEEhHHcCCcccc--CHHHccCCCCEEEEEEEEECCCCcEEeeC
Confidence            78999999999999999999        5568999999999755443  55688999999999999997655677763

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

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

Probab=98.82  E-value=1.8e-08  Score=67.54  Aligned_cols=67  Identities=28%  Similarity=0.267  Sum_probs=56.3

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS  153 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS  153 (198)
                      |+++.|+|+++.+.+|+|++        .....|++|.++++.....  ++.+.|++||.|.|+|.+++. .+.+.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l--------~~~~~g~~~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDI--------GVKQDGLIHISKMADRFVS--HPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEc--------CCCCEEEEEHHHCCCcccc--CHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            78999999999999999999        5568999999999765444  667889999999999999974 3556554

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.

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

Probab=98.81  E-value=4e-08  Score=70.92  Aligned_cols=74  Identities=19%  Similarity=0.239  Sum_probs=58.0

Q ss_pred             CCCCCEEEEEEEEEecc--eEEEEEeeeccccccCcceeEEecccccccc-ccccccccCCCCCCEEEEEEEEeCC-Ccc
Q 029155           74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE-IDKVDMHLSFRPGDIVRASVLSLGD-ARA  149 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~--~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~-~d~~~~~~~~~~GDiV~AkV~s~~~-~~~  149 (198)
                      +++|+++.|+|+++.+.  .|+|+|        ....+|+||.++++... ....++.+.|++||.|.++|+...- ...
T Consensus         5 ~~~G~iy~g~V~~i~~~~~GaFV~l--------~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~   76 (88)
T cd04453           5 PIVGNIYLGRVKKIVPGLQAAFVDI--------GLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKG   76 (88)
T ss_pred             CCCCCEEEEEEEEeccCCcEEEEEe--------CCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCC
Confidence            57999999999999996  999999        55689999999986511 1122567899999999999999752 344


Q ss_pred             EEEEEe
Q 029155          150 YFLSTA  155 (198)
Q Consensus       150 ~~LSt~  155 (198)
                      ..||+.
T Consensus        77 ~~lt~~   82 (88)
T cd04453          77 PRLTTN   82 (88)
T ss_pred             ceEEEE
Confidence            556554

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

>PHA02945 interferon resistance protein; Provisional

Probab=98.75  E-value=8.6e-08  Score=68.74  Aligned_cols=73  Identities=12%  Similarity=0.128  Sum_probs=61.1

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEecccc--ccccccccccccCCCCCCEEEEEEEEeCCC-
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDV--RATEIDKVDMHLSFRPGDIVRASVLSLGDA-  147 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v--~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-  147 (198)
                      -.|++||+|+|+|.. .+..++|++.       .+ ..+|+||.|++  ...-..  + ++.+ .|..|.|||+.++.. 
T Consensus         7 ~~P~~GelvigtV~~-~d~ga~v~L~-------EY~g~eg~i~~seveva~~wvK--~-rd~l-~GqkvV~KVirVd~~k   74 (88)
T PHA02945          7 SLPNVGDVLKGKVYE-NGYALYIDLF-------DYPHSEAILAESVQMHMNRYFK--Y-RDKL-VGKTVKVKVIRVDYTK   74 (88)
T ss_pred             cCCCCCcEEEEEEEe-cCceEEEEec-------ccCCcEEEEEeehhhhccceEe--e-eeEe-cCCEEEEEEEEECCCC
Confidence            469999999999999 9999999994       23 67999999955  554444  5 8999 999999999999864 


Q ss_pred             ccEEEEEec
Q 029155          148 RAYFLSTAK  156 (198)
Q Consensus       148 ~~~~LSt~~  156 (198)
                      +.+-||++.
T Consensus        75 g~IDlSlK~   83 (88)
T PHA02945         75 GYIDVNYKR   83 (88)
T ss_pred             CEEEeEeeE
Confidence            678999874

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.73  E-value=1.4e-08  Score=97.54  Aligned_cols=100  Identities=17%  Similarity=0.218  Sum_probs=79.3

Q ss_pred             CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEE
Q 029155           33 KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGII  112 (198)
Q Consensus        33 ~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l  112 (198)
                      +|.  ++++..+.....       ..+..|...+.     .+++|+++.|+|+++.+++++|+|        ....+|++
T Consensus       592 ~G~--v~i~~~~~~~~~-------~a~~~I~~~~~-----~~~vG~v~~G~V~~I~~fGafVei--------~~~~~Gll  649 (693)
T PRK11824        592 DGT--VKIAATDGEAAE-------AAKERIEGITA-----EPEVGEIYEGKVVRIVDFGAFVEI--------LPGKDGLV  649 (693)
T ss_pred             Cce--EEEEcccHHHHH-------HHHHHHHHhcc-----cCcCCeEEEEEEEEEECCeEEEEE--------CCCCEEEE
Confidence            445  777777766652       12234444332     378999999999999999999999        45689999


Q ss_pred             eccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEec
Q 029155          113 RQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAK  156 (198)
Q Consensus       113 ~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~  156 (198)
                      |+++++..+..  +..+.|++||.|.++|++++..+.+.||++.
T Consensus       650 hiSels~~~v~--~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~  691 (693)
T PRK11824        650 HISEIADERVE--KVEDVLKEGDEVKVKVLEIDKRGRIRLSRKA  691 (693)
T ss_pred             EeeeccCcccc--CccceeCCCCEEEEEEEEECCCCcEEEEEEe
Confidence            99999876655  7789999999999999999865789999875

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

Probab=98.70  E-value=2.9e-08  Score=84.19  Aligned_cols=78  Identities=22%  Similarity=0.241  Sum_probs=68.0

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-cc
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RA  149 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~  149 (198)
                      +-.|.+||+|+|+|.+|.+.+|+|.+.-.      .+.+|++|+|++...-..  ++++.++.|..+.|+|++++.. +.
T Consensus         6 ~~~PeeGEiVv~tV~~V~~~GAyv~L~EY------~g~Eg~ihiSEvas~wVk--nIrd~vkegqkvV~kVlrVd~~rg~   77 (269)
T COG1093           6 REYPEEGEIVVGTVKQVADYGAYVELDEY------PGKEGFIHISEVASGWVK--NIRDYVKEGQKVVAKVLRVDPKRGH   77 (269)
T ss_pred             cCCCCCCcEEEEEEEEeeccccEEEeecc------CCeeeeEEHHHHHHHHHH--HHHHHhhcCCeEEEEEEEEcCCCCe
Confidence            45799999999999999999999999421      247899999999877766  9999999999999999999864 66


Q ss_pred             EEEEEec
Q 029155          150 YFLSTAK  156 (198)
Q Consensus       150 ~~LSt~~  156 (198)
                      +.||++.
T Consensus        78 IDLSlkr   84 (269)
T COG1093          78 IDLSLKR   84 (269)
T ss_pred             Eeeehhh
Confidence            8999875

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

Probab=98.70  E-value=1.8e-07  Score=76.16  Aligned_cols=83  Identities=22%  Similarity=0.262  Sum_probs=66.8

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccc--c-------cccccCCCCCCEEEEEEE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID--K-------VDMHLSFRPGDIVRASVL  142 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d--~-------~~~~~~~~~GDiV~AkV~  142 (198)
                      +.|.+|++|.|+|+++...++++++        . +++|++|.+++...+..  .       .+....|+.||.|++||.
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--------G-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIV  147 (187)
T ss_pred             EeccCCCEEEEEEEEEEccEEEEEE--------e-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEE
Confidence            4588999999999999999999999        3 58999999988643211  0       124567899999999999


Q ss_pred             EeCCC------ccEEEEEecCCCeeeE
Q 029155          143 SLGDA------RAYFLSTAKNDLGVVS  163 (198)
Q Consensus       143 s~~~~------~~~~LSt~~~~lGvv~  163 (198)
                      +++-.      ..+.||++++.||.+.
T Consensus       148 ~v~~~~~~~~~~~I~ls~~~~~LG~~~  174 (187)
T PRK08563        148 AVSLKERRPRGSKIGLTMRQPGLGKLE  174 (187)
T ss_pred             EEEcccCCCCCCEEEEEecCCCCCcHH
Confidence            98632      3689999999999874

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=98.70  E-value=9.3e-08  Score=84.14  Aligned_cols=76  Identities=24%  Similarity=0.290  Sum_probs=65.8

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY  150 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~  150 (198)
                      .-+++|++|.|+|+++.+.+++|++.         +..|++|+++++..+..  ++.+.|++||.|.|+|++++. .+.+
T Consensus       192 ~~~k~G~vv~G~V~~I~~~G~fV~i~---------gv~Gllhisels~~~~~--~~~~~~~vGd~VkvkVl~iD~e~~rI  260 (318)
T PRK07400        192 NRLEVGEVVVGTVRGIKPYGAFIDIG---------GVSGLLHISEISHEHIE--TPHSVFNVNDEMKVMIIDLDAERGRI  260 (318)
T ss_pred             ccCCCCCEEEEEEEEEECCeEEEEEC---------CEEEEEEHHHccccccc--ChhhccCCCCEEEEEEEEEeCCCCEE
Confidence            34789999999999999999999982         46799999999876655  788999999999999999974 5789


Q ss_pred             EEEEecCC
Q 029155          151 FLSTAKND  158 (198)
Q Consensus       151 ~LSt~~~~  158 (198)
                      .||++..+
T Consensus       261 ~LS~K~l~  268 (318)
T PRK07400        261 SLSTKQLE  268 (318)
T ss_pred             EEEEeccc
Confidence            99998644

>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=98.69  E-value=1.8e-07  Score=65.47  Aligned_cols=72  Identities=15%  Similarity=0.206  Sum_probs=59.5

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc-cccccccCCCCCCEEEEEEEEeCCCccEEEEEe
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKVDMHLSFRPGDIVRASVLSLGDARAYFLSTA  155 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~-d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~  155 (198)
                      |+++.|+|+++.+.+++|+|...     ..+..|++|.++++.... +  ++.+.|++||.|.++|++++ .+.+.||++
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~-----~~~~~gll~~s~l~~~~~~~--~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k   72 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGL-----KGRKEGLVHISQLSFEGRVA--NPSDVVKRGQKVKVKVISIQ-NGKISLSMK   72 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCC-----CCCcEEEEEhHhccCCCCcC--ChhheeCCCCEEEEEEEEEe-CCEEEEEEE
Confidence            78999999999999999999310     035799999999975543 4  67789999999999999998 678888886


Q ss_pred             c
Q 029155          156 K  156 (198)
Q Consensus       156 ~  156 (198)
                      .
T Consensus        73 ~   73 (79)
T cd05684          73 D   73 (79)
T ss_pred             e
Confidence            5

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

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

Probab=98.68  E-value=9.1e-08  Score=64.90  Aligned_cols=66  Identities=17%  Similarity=0.260  Sum_probs=54.2

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccc-ccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRA-TEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~-~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      |+++.|+|+++.+.+++|++        ....+|++|.++++. ....  +..+.|++||.|.|+|++++. .+.+.|
T Consensus         1 G~~~~g~V~~i~~~G~fv~l--------~~~~~Glv~~~~l~~~~~~~--~~~~~~~~G~~v~v~v~~id~~~~~i~l   68 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGL--------DGGIDGLVHISDISWTQRVR--HPSEIYKKGQEVEAVVLNIDVERERISL   68 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEe--------CCCCEEEEEHHHCCCccccC--ChhhEECCCCEEEEEEEEEECCcCEEeC
Confidence            78999999999999999999        556899999999973 2222  557889999999999999974 344554

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.

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

Probab=98.64  E-value=1.5e-07  Score=69.02  Aligned_cols=77  Identities=21%  Similarity=0.264  Sum_probs=61.4

Q ss_pred             CEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccccc---------ccccCCCCCCEEEEEEEEeCCC-
Q 029155           78 SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKV---------DMHLSFRPGDIVRASVLSLGDA-  147 (198)
Q Consensus        78 DiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~---------~~~~~~~~GDiV~AkV~s~~~~-  147 (198)
                      +++.|+|+++.+.+++|++        . +..|++|.++++..+....         ...+.|++||.|.++|.+++.. 
T Consensus         1 ~vv~g~V~~i~~~GifV~l--------~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~   71 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRI--------G-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKE   71 (99)
T ss_pred             CEEEEEEEEEEeccEEEEE--------c-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHH
Confidence            4789999999999999999        3 3789999999864432210         1236789999999999999732 


Q ss_pred             -----ccEEEEEecCCCeeeE
Q 029155          148 -----RAYFLSTAKNDLGVVS  163 (198)
Q Consensus       148 -----~~~~LSt~~~~lGvv~  163 (198)
                           ..+.||++++.||.+.
T Consensus        72 ~~~~~~~i~ls~k~~~~g~~~   92 (99)
T cd04460          72 RRPRESKIGLTMRQPGLGKLE   92 (99)
T ss_pred             CcCCCceEEEEEecCCCCcHH
Confidence                 4799999999999864

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.

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

Probab=98.63  E-value=1.8e-07  Score=75.74  Aligned_cols=84  Identities=23%  Similarity=0.294  Sum_probs=67.4

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc--ccc-------ccccCCCCCCEEEEEE
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DKV-------DMHLSFRPGDIVRASV  141 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~--d~~-------~~~~~~~~GDiV~AkV  141 (198)
                      .+.|.+|+++.|+|++++..++++++        . +++|++|.+++...+.  |..       +....|+.||.|++||
T Consensus        76 ~f~p~~gEvv~G~V~~v~~~GifV~l--------g-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV  146 (179)
T TIGR00448        76 VFKPELGEIVEGEVIEIVEFGAFVSL--------G-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARI  146 (179)
T ss_pred             EEeccCCCEEEEEEEEEEeeEEEEEe--------C-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEE
Confidence            34588999999999999999999999        3 5899999998763321  110       2346799999999999


Q ss_pred             EEeC------CCccEEEEEecCCCeeeE
Q 029155          142 LSLG------DARAYFLSTAKNDLGVVS  163 (198)
Q Consensus       142 ~s~~------~~~~~~LSt~~~~lGvv~  163 (198)
                      .+++      +...+.||++++.||.+.
T Consensus       147 ~~v~~~~~~~~~~~I~lt~k~~~LG~~~  174 (179)
T TIGR00448       147 VALSLKDRRPEGSKIGLTMRQPLLGKLE  174 (179)
T ss_pred             EEEEccCCCCCcceEEEEeccCcCCccc
Confidence            9985      235699999999999874

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

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.62  E-value=1.4e-07  Score=90.36  Aligned_cols=71  Identities=15%  Similarity=0.281  Sum_probs=61.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccc---c-ccccccccccCCCCCCEEEEEEEEeCCCc
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVR---A-TEIDKVDMHLSFRPGDIVRASVLSLGDAR  148 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~---~-~~~d~~~~~~~~~~GDiV~AkV~s~~~~~  148 (198)
                      .|++|+++.|+|++|.+++++|+|        ..+.+|++|+|+++   + .+..  ++.+.|++||.|.++|+++++.+
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel--------~~G~eGLvHISeisdls~~~rv~--~~~dv~kvGd~V~VKVl~ID~~g  713 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSL--------LPGKDGLLHISQIRKLAGGKRVE--NVEDVLSVGQKIQVEIADIDDRG  713 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEe--------cCCceEEEEhhhccccccccCcC--CHHHcCCCCCEEEEEEEEECCCC
Confidence            489999999999999999999999        56789999999885   2 2333  88999999999999999998666


Q ss_pred             cEEEE
Q 029155          149 AYFLS  153 (198)
Q Consensus       149 ~~~LS  153 (198)
                      .+.|+
T Consensus       714 KI~L~  718 (719)
T TIGR02696       714 KLSLV  718 (719)
T ss_pred             Ceeec
Confidence            77775

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.

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

Probab=98.55  E-value=2.7e-07  Score=60.53  Aligned_cols=64  Identities=19%  Similarity=0.283  Sum_probs=51.8

Q ss_pred             EEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155           80 VIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS  153 (198)
Q Consensus        80 ViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS  153 (198)
                      +.|+|+++.+.+++|++        .....|++|.++++.....  ++.+.|++||.|+|+|++++. .+.+.||
T Consensus         1 v~g~V~~v~~~g~~v~l--------~~~~~g~~~~~~~~~~~~~--~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           1 VTGKVVSITKFGVFVEL--------EDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             CEEEEEEEEeeeEEEEe--------cCCCEEEEEHHHCCCcccc--CHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            47999999999999999        5568999999998754432  567889999999999999974 3445543

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.

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

Probab=98.54  E-value=6.3e-07  Score=61.42  Aligned_cols=69  Identities=19%  Similarity=0.300  Sum_probs=55.3

Q ss_pred             CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-ccEEE
Q 029155           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFL  152 (198)
Q Consensus        75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~~~L  152 (198)
                      .+|+++.|+|+++.+.+++|++        ....+|++|.+++...+ ...+..+.|++||.|.++|++++.. +.+.|
T Consensus         2 ~~g~~~~g~V~~i~~~G~fv~l--------~~~~~Gl~~~~~l~~~~-~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~   71 (72)
T cd05689           2 PEGTRLFGKVTNLTDYGCFVEL--------EEGVEGLVHVSEMDWTN-KNIHPSKVVSLGDEVEVMVLDIDEERRRISL   71 (72)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEc--------CCCCEEEEEEEeccCcc-cccCcccEeCCCCEEEEEEEEeeCCcCEEeC
Confidence            4799999999999999999999        45689999999996421 1225568899999999999999743 34443

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.

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=98.52  E-value=4.3e-07  Score=79.93  Aligned_cols=76  Identities=20%  Similarity=0.202  Sum_probs=66.2

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY  150 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~  150 (198)
                      +..++||+|.|+|+++.+++++|+|        .....|+||.++++..+..  ++.+.|++||.|.++|++.++ .+.+
T Consensus        27 ~~~~~G~iv~G~V~~i~~~g~~Vdi--------g~k~~g~lp~sEis~~~~~--~~~~~~~~G~~v~~~Vi~~~~~~~~i   96 (318)
T PRK07400         27 YHFKPGDIVNGTVFSLEPRGALIDI--------GAKTAAFMPIQEMSINRVE--GPEEVLQPNETREFFILSDENEDGQL   96 (318)
T ss_pred             hhcCCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcccccc--CHHHccCCCCEEEEEEEEEeCCCCeE
Confidence            3479999999999999999999999        5667999999999876655  778999999999999999864 4679


Q ss_pred             EEEEecC
Q 029155          151 FLSTAKN  157 (198)
Q Consensus       151 ~LSt~~~  157 (198)
                      .||.+..
T Consensus        97 ~lS~k~~  103 (318)
T PRK07400         97 TLSIRRI  103 (318)
T ss_pred             EEehhhh
Confidence            9999864

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=98.51  E-value=4.3e-07  Score=84.19  Aligned_cols=74  Identities=19%  Similarity=0.215  Sum_probs=64.9

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC-CCccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG-DARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~-~~~~~~L  152 (198)
                      .++|++|.|+|+++.+++++|++        ..++.|++|.+++...+..  +..+.|++||.|.|+|++++ +.+.+.|
T Consensus       377 ~~vG~~v~G~V~~i~~~G~FV~l--------~~gv~Gli~~se~s~~~~~--~~~~~~~~Gd~v~~~V~~id~e~~ri~L  446 (491)
T PRK13806        377 FAPGTTVTGTVEKRAQFGLFVNL--------APGVTGLLPASVISRAGKP--ATYEKLKPGDSVTLVVEEIDTAKRKISL  446 (491)
T ss_pred             CCCCCEEEEEEEEEecCceEEEc--------CCCcEEEEEHHHcCccccc--chhhcCCCCCEEEEEEEEEeCCCCEEEE
Confidence            46899999999999999999999        5689999999999865554  67889999999999999997 3567999


Q ss_pred             EEecC
Q 029155          153 STAKN  157 (198)
Q Consensus       153 St~~~  157 (198)
                      |++..
T Consensus       447 s~~~~  451 (491)
T PRK13806        447 APAGA  451 (491)
T ss_pred             Eeehh
Confidence            99854

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

Probab=98.48  E-value=1.3e-06  Score=59.29  Aligned_cols=66  Identities=17%  Similarity=0.273  Sum_probs=53.8

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEEEe
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLSTA  155 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LSt~  155 (198)
                      |++|.|+|+++.+.+++|++        . .+.|+||.+++...+..  ++.+  .+||.+.|+|++++. .+.+.||.+
T Consensus         1 G~iv~g~V~~v~~~G~~v~l--------~-g~~gfip~s~~~~~~~~--~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k   67 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI--------E-GVRAFLPASQVDLRPVE--DLDE--YVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHCCCcccC--ChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            78999999999999999999        3 58999999998754433  3333  389999999999985 567888853

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.

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

Probab=98.47  E-value=1.4e-06  Score=59.43  Aligned_cols=62  Identities=26%  Similarity=0.401  Sum_probs=51.3

Q ss_pred             CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC---ccEE
Q 029155           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA---RAYF  151 (198)
Q Consensus        75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~---~~~~  151 (198)
                      +.|++|.|+|.++.++.++|+|        .. .+|+||.+++..        .+.|++||.|.+.|.++++.   .++.
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdi--------g~-~eg~lp~~e~~~--------~~~~~~Gd~v~v~v~~v~~~~~~~~i~   64 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDL--------GK-VEAILPKKEQIP--------GESYRPGDRIKAYVLEVRKTSKGPQII   64 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEc--------CC-eEEEeeHHHCCC--------CCcCCCCCEEEEEEEEEecCCCCCEEE
Confidence            5799999999999999999999        44 799999988752        35689999999999999742   3455


Q ss_pred             EE
Q 029155          152 LS  153 (198)
Q Consensus       152 LS  153 (198)
                      ||
T Consensus        65 lS   66 (67)
T cd04455          65 LS   66 (67)
T ss_pred             Ee
Confidence            55

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=98.47  E-value=3.6e-06  Score=58.89  Aligned_cols=63  Identities=19%  Similarity=0.258  Sum_probs=54.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS  153 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS  153 (198)
                      +++|+.+.|+|+++++.++++++        .....|++|.+++          .+.|+.||.+.++|.++.+.+.+.||
T Consensus        14 ~~~G~~~~g~V~~i~~~G~fV~l--------~~~~~Glv~~se~----------~~~~~iGd~v~v~I~~i~e~~~i~l~   75 (77)
T cd04473          14 LEVGKLYKGKVNGVAKYGVFVDL--------NDHVRGLIHRSNL----------LRDYEVGDEVIVQVTDIPENGNIDLI   75 (77)
T ss_pred             CCCCCEEEEEEEeEecceEEEEE--------CCCcEEEEEchhc----------cCcCCCCCEEEEEEEEECCCCcEEEE
Confidence            78999999999999999999999        5569999999874          35699999999999999545677777


Q ss_pred             E
Q 029155          154 T  154 (198)
Q Consensus       154 t  154 (198)
                      .
T Consensus        76 ~   76 (77)
T cd04473          76 P   76 (77)
T ss_pred             E
Confidence            4

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.

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

Probab=98.45  E-value=5.3e-07  Score=83.96  Aligned_cols=74  Identities=20%  Similarity=0.207  Sum_probs=67.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      ..+|+.+.|+|+.+++++++|+|        ..+.+|++|+|++++++..  ..++.++.||.|.++|++++. .+.+.|
T Consensus       275 ~~~g~~v~G~Vt~i~~~GafVei--------~~GvEGlvhvSEisw~~~~--~P~evv~~Gq~V~V~Vl~id~e~rRIsL  344 (541)
T COG0539         275 YPVGDKVEGKVTNLTDYGAFVEI--------EEGVEGLVHVSEISWTKKN--VPSEVVKVGQEVEVKVLDIDPERRRISL  344 (541)
T ss_pred             cCCCCEEEEEEEEeecCcEEEEe--------cCCccceeechhhcccccC--CHHHhcccCCEEEEEEEeeCchhceEEe
Confidence            57899999999999999999999        7899999999999988876  499999999999999999984 578999


Q ss_pred             EEecC
Q 029155          153 STAKN  157 (198)
Q Consensus       153 St~~~  157 (198)
                      |++..
T Consensus       345 ~iKq~  349 (541)
T COG0539         345 GLKQL  349 (541)
T ss_pred             eehhh
Confidence            99863

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.45  E-value=5.2e-07  Score=86.75  Aligned_cols=91  Identities=16%  Similarity=0.224  Sum_probs=70.0

Q ss_pred             EEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccc
Q 029155           38 VYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV  117 (198)
Q Consensus        38 i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v  117 (198)
                      ++++..+.....       ..+..|....     ..|++|+++.|+|+++.+++++|+|        ..+.+|+||+|++
T Consensus       592 V~i~~~~~~~~~-------~a~~~I~~~~-----~~~~~G~i~~G~V~~I~~~GafVei--------~~g~~GllHiSei  651 (684)
T TIGR03591       592 VKIAASDGEAAE-------AAIKMIEGIT-----AEPEVGKIYEGKVVRIMDFGAFVEI--------LPGKDGLVHISEI  651 (684)
T ss_pred             EEEEECcHHHHH-------HHHHHHHhhh-----cccccCcEEEEEEEEEeCCEEEEEE--------CCCcEEEEEHHHc
Confidence            777666655442       1122344332     2479999999999999999999999        4568999999999


Q ss_pred             ccccccccccccCCCCCCEEEEEEEEeCCCccE
Q 029155          118 RATEIDKVDMHLSFRPGDIVRASVLSLGDARAY  150 (198)
Q Consensus       118 ~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~  150 (198)
                      +..+.+  ++.+.|++||.|+++|++++..+.+
T Consensus       652 ~~~~v~--~~~~~~kvGD~V~VkVi~id~~gki  682 (684)
T TIGR03591       652 ANERVE--KVEDVLKEGDEVKVKVLEIDKQGRI  682 (684)
T ss_pred             CCCccc--ChhhccCCCCEEEEEEEEECCCCCc
Confidence            876655  7889999999999999999754444

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).

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=98.43  E-value=8.2e-07  Score=86.86  Aligned_cols=74  Identities=16%  Similarity=0.258  Sum_probs=65.2

Q ss_pred             CCCCCCEEE-EEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEE
Q 029155           73 VPEPGSVVI-ARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYF  151 (198)
Q Consensus        73 ~p~vGDiVi-G~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~  151 (198)
                      .|++|+++. |+|++|.+++++|+|        ....+|++|+|++.+.+..  +..+.|++||.|.++|++++..+.+.
T Consensus       750 ~~~vG~iy~~g~V~~I~~FGaFVeL--------~~g~EGLVHISeLs~~rv~--~~~dv~kvGD~V~VkVi~ID~~grI~  819 (891)
T PLN00207        750 VPTVGDIYRNCEIKSIAPYGAFVEI--------APGREGLCHISELSSNWLA--KPEDAFKVGDRIDVKLIEVNDKGQLR  819 (891)
T ss_pred             CcCCCcEEECcEEEEEeccEEEEEe--------CCCCEEEEEhhhcCCcccc--CHHHhcCCCCEEEEEEEEECCCCcEE
Confidence            479999995 699999999999999        4568999999999876655  67899999999999999998767899


Q ss_pred             EEEec
Q 029155          152 LSTAK  156 (198)
Q Consensus       152 LSt~~  156 (198)
                      ||++.
T Consensus       820 LSlK~  824 (891)
T PLN00207        820 LSRRA  824 (891)
T ss_pred             EEEec
Confidence            99975

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=98.42  E-value=9.2e-07  Score=82.03  Aligned_cols=75  Identities=21%  Similarity=0.278  Sum_probs=64.7

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-----
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-----  147 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-----  147 (198)
                      .+++|++|.|+|+++.+.+++|+|        .....|+||.++++..+..  ++.+.|++||.|.|+|++++..     
T Consensus       199 ~l~~G~iv~G~V~~v~~~G~fV~l--------~~gv~g~v~~sels~~~~~--~~~~~~~vGd~i~vkVl~id~~~~~~~  268 (491)
T PRK13806        199 TVKEGDVVEGTVTRLAPFGAFVEL--------APGVEGMVHISELSWSRVQ--KADEAVSVGDTVRVKVLGIERAKKGKG  268 (491)
T ss_pred             hCCCCCEEEEEEEEEeCCeEEEEc--------CCCcEEEEEHHHCCCcccc--ChhHhcCCCCEEEEEEEEEecccCCcc
Confidence            378999999999999999999999        5568999999999876655  7789999999999999999753     


Q ss_pred             ccEEEEEecC
Q 029155          148 RAYFLSTAKN  157 (198)
Q Consensus       148 ~~~~LSt~~~  157 (198)
                      ..+.||++..
T Consensus       269 ~ri~lS~K~~  278 (491)
T PRK13806        269 LRISLSIKQA  278 (491)
T ss_pred             eEEEEEehhh
Confidence            2588998664

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

Probab=98.42  E-value=7.7e-07  Score=72.13  Aligned_cols=83  Identities=25%  Similarity=0.303  Sum_probs=66.4

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccc-----cccc----ccCCCCCCEEEEEEE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-----KVDM----HLSFRPGDIVRASVL  142 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d-----~~~~----~~~~~~GDiV~AkV~  142 (198)
                      +.|..|++|.|.|+++...+++|.|         .++.|++|.+|+...+.+     ..-.    ...|+.||.|+|||+
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            4588899999999999999999999         388999999998644221     1111    238999999999999


Q ss_pred             EeCC-C-----ccEEEEEecCCCeeeE
Q 029155          143 SLGD-A-----RAYFLSTAKNDLGVVS  163 (198)
Q Consensus       143 s~~~-~-----~~~~LSt~~~~lGvv~  163 (198)
                      +..- .     ..+.||++++.||++.
T Consensus       148 ~~s~~~~~~~~~~I~lTmrq~~LGkle  174 (183)
T COG1095         148 GVSLKSRRPRESKIGLTMRQPGLGKLE  174 (183)
T ss_pred             EEecccCccccceEEEEeccccCCcch
Confidence            9752 2     4589999999999874

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=98.41  E-value=1.1e-06  Score=81.33  Aligned_cols=73  Identities=19%  Similarity=0.194  Sum_probs=64.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      .++|++|.|+|+++.+.+++|+|        . ...|+||.++++..+.+  ++.+.|++||.|.++|++++. .+.+.|
T Consensus       206 lk~G~iv~G~V~~i~~~G~FVdl--------g-gv~Glv~~Sels~~~v~--~~~~~~kvGd~V~vkVl~iD~e~~rI~L  274 (486)
T PRK07899        206 LQKGQVRKGVVSSIVNFGAFVDL--------G-GVDGLVHVSELSWKHID--HPSEVVEVGQEVTVEVLDVDMDRERVSL  274 (486)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHCCCcccC--CHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence            57999999999999999999999        3 47899999999876655  778899999999999999974 477999


Q ss_pred             EEecC
Q 029155          153 STAKN  157 (198)
Q Consensus       153 St~~~  157 (198)
                      |++..
T Consensus       275 SlK~~  279 (486)
T PRK07899        275 SLKAT  279 (486)
T ss_pred             EEeec
Confidence            98753

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=98.39  E-value=1.1e-06  Score=86.35  Aligned_cols=74  Identities=20%  Similarity=0.151  Sum_probs=63.5

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      +++||+|.|+|+++.+++++|++        ..++.|++|++++++.. ...++.+.|++||.|.|+|++++. .+.+.|
T Consensus       576 ~~vG~iV~G~V~~I~~fG~fVeL--------~~gveGLvhiSEls~~~-~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsL  646 (863)
T PRK12269        576 FGVNDVVKGRVTKIADFGAFIEL--------AEGIEGLAHISEFSWVK-KTSKPSDMVKIGDEVECMILGYDIQAGRVSL  646 (863)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEe--------cCCceeeeEHHHhcCcc-ccCCHHHcCCCCCEEEEEEEEEecccCceEE
Confidence            67999999999999999999999        56789999999997522 122678899999999999999974 467999


Q ss_pred             EEec
Q 029155          153 STAK  156 (198)
Q Consensus       153 St~~  156 (198)
                      |++.
T Consensus       647 S~K~  650 (863)
T PRK12269        647 GLKQ  650 (863)
T ss_pred             Eehh
Confidence            9975

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=98.37  E-value=1.7e-06  Score=80.10  Aligned_cols=74  Identities=27%  Similarity=0.250  Sum_probs=64.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      .+.||+|.|+|+++.++.++|+|        .....|+||.++++.....  ++.+.|++||.|.|+|+++++ .+.+.|
T Consensus        33 ~~~GdiV~G~V~~v~~~gv~VdI--------g~k~eG~Ip~~Els~~~~~--~~~~~~~vGd~Ie~~V~~~~~~~g~liL  102 (486)
T PRK07899         33 FNDGDIVEGTVVKVDRDEVLLDI--------GYKTEGVIPSRELSIKHDV--DPNEVVEVGDEVEALVLQKEDKEGRLIL  102 (486)
T ss_pred             CCCCCEEEEEEEEEECCcEEEEE--------CCCcEEEEEHHHhcccccC--ChhhcCCCCCEEEEEEEEEECCCCeEEE
Confidence            68999999999999999999999        6678999999999764433  677889999999999999875 467999


Q ss_pred             EEecC
Q 029155          153 STAKN  157 (198)
Q Consensus       153 St~~~  157 (198)
                      |.+..
T Consensus       103 S~k~~  107 (486)
T PRK07899        103 SKKRA  107 (486)
T ss_pred             Eehhh
Confidence            99854

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=98.35  E-value=1.7e-06  Score=81.16  Aligned_cols=74  Identities=26%  Similarity=0.397  Sum_probs=65.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      .++||+|.|+|+++.+.+++|.+        ..++.|++|.++++..+..  ++.+.|++||.|.|+|++++. .+.+.|
T Consensus       458 ~~~G~vV~G~V~~v~~~G~fV~l--------~~gi~g~i~~se~s~~~~~--~~~~~~~~Gd~v~~~V~~vd~~~~~i~L  527 (565)
T PRK06299        458 HKKGSIVTGTVTEVKDKGAFVEL--------EDGVEGLIRASELSRDRVE--DATEVLKVGDEVEAKVINIDRKNRRISL  527 (565)
T ss_pred             cCCCCEEEEEEEEEecCceEEec--------CCCcEEEEEHHHhcchhcc--CccccCCCCCEEEEEEEEEccccCEEEE
Confidence            47899999999999999999999        4578999999999876665  788999999999999999974 578999


Q ss_pred             EEecC
Q 029155          153 STAKN  157 (198)
Q Consensus       153 St~~~  157 (198)
                      |++..
T Consensus       528 S~k~~  532 (565)
T PRK06299        528 SIKAL  532 (565)
T ss_pred             Eeeeh
Confidence            99864

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=98.31  E-value=3.2e-06  Score=75.93  Aligned_cols=73  Identities=21%  Similarity=0.229  Sum_probs=63.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      +++|++|.|+|+++.+.+++|++        . ...|++|.++++..+.+  ++.+.|++||.|.|+|++++. .+.+.|
T Consensus       190 ~~~G~~v~g~V~~v~~~G~fV~l--------~-~v~g~v~~sels~~~~~--~~~~~~~vGd~i~~~Vl~vd~~~~~i~l  258 (390)
T PRK06676        190 LKEGDVVEGTVARLTDFGAFVDI--------G-GVDGLVHISELSHERVE--KPSEVVSVGQEVEVKVLSIDWETERISL  258 (390)
T ss_pred             CCCCCEEEEEEEEEecceEEEEe--------C-CeEEEEEHHHcCccccC--CHHHhcCCCCEEEEEEEEEeCCCCEEEE
Confidence            58999999999999999999999        2 47899999999865544  778899999999999999974 467999


Q ss_pred             EEecC
Q 029155          153 STAKN  157 (198)
Q Consensus       153 St~~~  157 (198)
                      |++..
T Consensus       259 S~k~~  263 (390)
T PRK06676        259 SLKDT  263 (390)
T ss_pred             EEeec
Confidence            98753

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=98.30  E-value=4.1e-06  Score=75.23  Aligned_cols=75  Identities=16%  Similarity=0.230  Sum_probs=64.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      .++|+++.|+|+++.+.+++|++        ..++.|++|.+++...+..  +..+.|++||.|.|+|++++. .+.+.|
T Consensus       275 ~~~G~~v~g~V~~i~~~G~fV~l--------~~gi~Glv~~se~~~~~~~--~~~~~~~~Gd~v~v~V~~id~e~~~i~l  344 (390)
T PRK06676        275 LPEGDVIEGTVKRLTDFGAFVEV--------LPGVEGLVHISQISHKHIA--TPSEVLEEGQEVKVKVLEVNEEEKRISL  344 (390)
T ss_pred             hcCCcEEEEEEEEEeCceEEEEE--------CCCCeEEEEhHHcCccccC--ChhhccCCCCEEEEEEEEEECCCCEEEE
Confidence            57899999999999999999999        5578999999999765544  667889999999999999973 578999


Q ss_pred             EEecCC
Q 029155          153 STAKND  158 (198)
Q Consensus       153 St~~~~  158 (198)
                      |++...
T Consensus       345 s~k~~~  350 (390)
T PRK06676        345 SIKALE  350 (390)
T ss_pred             EEEecc
Confidence            988543

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=98.28  E-value=3.9e-06  Score=78.81  Aligned_cols=73  Identities=21%  Similarity=0.255  Sum_probs=64.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF  151 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~  151 (198)
                      -+++|++|.|+|+++.+.+++|+|        . ++.|++|.++++..+..  ++.+.|++||.|.|+|++++. .+.+.
T Consensus       198 ~l~~G~iv~g~V~~v~~~G~~V~i--------~-g~~glv~~se~s~~~~~--~~~~~~kvG~~v~v~V~~~d~~~~~i~  266 (565)
T PRK06299        198 NLEEGQVVEGVVKNITDYGAFVDL--------G-GVDGLLHITDISWKRVN--HPSEVVNVGDEVKVKVLKFDKEKKRVS  266 (565)
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEE--------C-CEEEEEEHHHhcccccC--CHhhcCCCCCEEEEEEEEEeCCCCeEE
Confidence            368999999999999999999999        5 78999999999866554  778999999999999999974 46799


Q ss_pred             EEEec
Q 029155          152 LSTAK  156 (198)
Q Consensus       152 LSt~~  156 (198)
                      ||++.
T Consensus       267 lS~k~  271 (565)
T PRK06299        267 LGLKQ  271 (565)
T ss_pred             EEEEe
Confidence            99874

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

Probab=98.24  E-value=1.1e-05  Score=56.27  Aligned_cols=71  Identities=15%  Similarity=0.171  Sum_probs=54.8

Q ss_pred             CCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEeccccccccc--cc-------cccccCCCCCCEEEEEEEEeC
Q 029155           76 PGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEI--DK-------VDMHLSFRPGDIVRASVLSLG  145 (198)
Q Consensus        76 vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~~--d~-------~~~~~~~~~GDiV~AkV~s~~  145 (198)
                      +|+++.|+|+++++.+++|++        .. ...|++|.++++....  +.       ....+.|++||.|+++|.+++
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            489999999999999999999        33 5899999999863221  00       023478999999999999997


Q ss_pred             C-CccEEEEE
Q 029155          146 D-ARAYFLST  154 (198)
Q Consensus       146 ~-~~~~~LSt  154 (198)
                      . .+.+.|++
T Consensus        73 ~~~~~i~~~l   82 (83)
T cd04471          73 LDRRKIDFEL   82 (83)
T ss_pred             cccCEEEEEE
Confidence            4 35666664

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.

>TIGR00717 rpsA ribosomal protein S1

Probab=98.20  E-value=6.2e-06  Score=76.50  Aligned_cols=72  Identities=26%  Similarity=0.334  Sum_probs=63.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      .++|++|.|+|+++++.+++|++        ...+.|++|.+++...+.+  ++.+.|++||.|.++|++++. .+.+.|
T Consensus       444 ~~~G~~v~g~V~~v~~~G~fV~l--------~~~~~Glv~~s~l~~~~~~--~~~~~~~~Gd~v~~~V~~id~~~~~i~l  513 (516)
T TIGR00717       444 YKVGSVVKGKVTEIKDFGAFVEL--------PGGVEGLIRNSELSENRDE--DKTDEIKVGDEVEAKVVDIDKKNRKVSL  513 (516)
T ss_pred             cCcceEEEEEEEEEecceEEEEc--------CCCeEEEEEHHHcCccccc--cccccCCCCCEEEEEEEEEeCCCCEEEE
Confidence            46899999999999999999999        5679999999999876654  788999999999999999973 467888


Q ss_pred             EEe
Q 029155          153 STA  155 (198)
Q Consensus       153 St~  155 (198)
                      |++
T Consensus       514 s~k  516 (516)
T TIGR00717       514 SVK  516 (516)
T ss_pred             EEC
Confidence            874

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=98.20  E-value=7.6e-06  Score=78.29  Aligned_cols=75  Identities=19%  Similarity=0.298  Sum_probs=65.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      .++|++|.|+|+++.+.+++|++        ...+.|++|.++++..+..  ++.+.|++||.|.|+|++++. .+.+.|
T Consensus       560 ~~~G~~v~g~V~~i~~~G~fV~l--------~~~i~Gli~~sel~~~~~~--~~~~~~kvGd~V~vkV~~id~e~~rI~l  629 (647)
T PRK00087        560 YPVGSIVLGKVVRIAPFGAFVEL--------EPGVDGLVHISQISWKRID--KPEDVLSEGEEVKAKILEVDPEEKRIRL  629 (647)
T ss_pred             ccCCeEEEEEEEEEECCeEEEEE--------CCCCEEEEEhhhcCccccC--CHhhcCCCCCEEEEEEEEEeCCCCEEEE
Confidence            46899999999999999999999        5679999999999865544  677899999999999999974 578999


Q ss_pred             EEecCC
Q 029155          153 STAKND  158 (198)
Q Consensus       153 St~~~~  158 (198)
                      |++...
T Consensus       630 slk~~~  635 (647)
T PRK00087        630 SIKEVE  635 (647)
T ss_pred             EEeecc
Confidence            998653

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=98.17  E-value=7.7e-06  Score=80.39  Aligned_cols=74  Identities=18%  Similarity=0.205  Sum_probs=62.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      ..+|++|.|+|+.+.+.+++|++        ..+..|+||.+|++..... ....+.|++||.|.++|++++. .+.+.|
T Consensus       663 ~~vG~~v~G~V~~i~~~G~fV~l--------~~gV~GlIh~sels~~~~~-~~~~~~~kvGq~VkvkVl~ID~e~rrI~L  733 (863)
T PRK12269        663 YPVGARFTRRIVKVTNAGAFIEM--------EEGIDGFLHVDDLSWVKRT-RPADHELEVGKEIECMVIECDPQARRIRL  733 (863)
T ss_pred             CCCCCEEEEEEEEEecceEEEEe--------CCCcEEEEEhHHhhccccc-cchhhccCCCCEEEEEEEEEeccCCEEEE
Confidence            46899999999999999999999        6789999999999753322 2445689999999999999984 477999


Q ss_pred             EEec
Q 029155          153 STAK  156 (198)
Q Consensus       153 St~~  156 (198)
                      |++.
T Consensus       734 S~K~  737 (863)
T PRK12269        734 GVKQ  737 (863)
T ss_pred             Eecc
Confidence            9874

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=98.09  E-value=8.3e-06  Score=78.37  Aligned_cols=77  Identities=21%  Similarity=0.283  Sum_probs=68.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF  151 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~  151 (198)
                      -+++|.++.|.|+.+.+++++|+|        .-.-.|++|+|+++.....  +..+.+++||+|.++|++++. ...+.
T Consensus       655 dLk~Gm~leg~Vrnv~~fgafVdI--------gv~qDglvHis~ls~~fv~--~P~~vv~vGdiV~v~V~~vD~~r~rI~  724 (780)
T COG2183         655 DLKPGMILEGTVRNVVDFGAFVDI--------GVHQDGLVHISQLSDKFVK--DPNEVVKVGDIVKVKVIEVDTARKRIA  724 (780)
T ss_pred             hccCCCEEEEEEEEeeeccceEEe--------ccccceeeeHHHhhhhhcC--ChHHhcccCCEEEEEEEEEecccCeee
Confidence            469999999999999999999999        5567899999999877776  679999999999999999984 46799


Q ss_pred             EEEecCCC
Q 029155          152 LSTAKNDL  159 (198)
Q Consensus       152 LSt~~~~l  159 (198)
                      ||++..+.
T Consensus       725 Lsmr~~~~  732 (780)
T COG2183         725 LSMRLDEE  732 (780)
T ss_pred             eEeeccCC
Confidence            99998765

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

Probab=98.07  E-value=2e-05  Score=63.86  Aligned_cols=86  Identities=17%  Similarity=0.141  Sum_probs=64.4

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccc-ccc---c------cccccCCCCCCEEEEE
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT-EID---K------VDMHLSFRPGDIVRAS  140 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~-~~d---~------~~~~~~~~~GDiV~Ak  140 (198)
                      .+.|-.|++|.|+|+++...++++++.         ++++.+|.+++... .-|   .      .+-...++.||.|++|
T Consensus        76 vFrPf~gEVv~g~V~~v~~~G~~v~~G---------p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~r  146 (176)
T PTZ00162         76 VFKPFKDEVLDAIVTDVNKLGFFAQAG---------PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLR  146 (176)
T ss_pred             EEecCCCCEEEEEEEEEecceEEEEee---------CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEE
Confidence            345889999999999999999999993         67788888877521 100   0      0113568999999999


Q ss_pred             EEEeC-C--CccEEEEEecCCCeeeEEe
Q 029155          141 VLSLG-D--ARAYFLSTAKNDLGVVSAE  165 (198)
Q Consensus       141 V~s~~-~--~~~~~LSt~~~~lGvv~a~  165 (198)
                      |.++. +  ......|++++.||.+.|+
T Consensus       147 V~~v~~~~~~~~~i~T~~~~~LG~~~~~  174 (176)
T PTZ00162        147 LQGVRYDASNLFAIATINSDYLGPIESS  174 (176)
T ss_pred             EEEEEecCCCcEEEEEecCCCcCccccc
Confidence            98874 2  2346789999999999654

>TIGR00717 rpsA ribosomal protein S1

Probab=98.06  E-value=1.9e-05  Score=73.29  Aligned_cols=73  Identities=18%  Similarity=0.205  Sum_probs=63.0

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF  151 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~  151 (198)
                      -+++|++|.|+|+++.+.+++|++        . .+.|++|.++++.....  ++.+.|++||.|.|+|++++. .+.+.
T Consensus       184 ~l~~G~~v~g~V~~i~~~G~~V~l--------~-g~~g~lp~~e~s~~~~~--~~~~~~~vG~~v~v~Vl~~d~~~~~i~  252 (516)
T TIGR00717       184 NLKEGDVVKGVVKNITDFGAFVDL--------G-GVDGLLHITDMSWKRVK--HPSEYVKVGQEVKVKVIKFDKEKGRIS  252 (516)
T ss_pred             hccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHcCCCCCC--CHHHhccCCCEEEEEEEEEECCCCcEE
Confidence            478999999999999999999998        3 47899999999765544  677889999999999999974 46799


Q ss_pred             EEEec
Q 029155          152 LSTAK  156 (198)
Q Consensus       152 LSt~~  156 (198)
                      ||++.
T Consensus       253 lS~k~  257 (516)
T TIGR00717       253 LSLKQ  257 (516)
T ss_pred             EEEEe
Confidence            99885

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=97.99  E-value=3.2e-05  Score=74.11  Aligned_cols=77  Identities=26%  Similarity=0.324  Sum_probs=65.3

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY  150 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~  150 (198)
                      ..+++|++|.|+|.++.+++++|++        .....|+|+.+++......  ++.+.|++||.|.++|+++++ .+.+
T Consensus       298 ~~l~~G~iV~G~V~~v~~~gv~Vdi--------g~~~~G~lp~~els~~~~~--~~~~~~~vGd~V~v~V~~vd~~~g~i  367 (647)
T PRK00087        298 KQIRRGDIVKGTVVSVNENEVFVDV--------GYKSEGVIPLRELTLDEIS--SLKESVKVGDEIEVKVLKLEDEDGYV  367 (647)
T ss_pred             hhccCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcccccC--ChhhccCCCCEEEEEEEEEECCCCcE
Confidence            3479999999999999999999999        5667899999998754333  677889999999999999864 4679


Q ss_pred             EEEEecCC
Q 029155          151 FLSTAKND  158 (198)
Q Consensus       151 ~LSt~~~~  158 (198)
                      .||.+..+
T Consensus       368 ~LS~k~~~  375 (647)
T PRK00087        368 VLSKKEAD  375 (647)
T ss_pred             EEEeehhc
Confidence            99999775

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

Probab=97.80  E-value=5.2e-05  Score=72.02  Aligned_cols=75  Identities=16%  Similarity=0.224  Sum_probs=67.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFL  152 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~L  152 (198)
                      -+++|.+-.|+|+++.+.+++|++        ..+-.|++|+|++...+.+  +..+.++.||.|+.||+.+++.+.+.|
T Consensus       616 e~evg~iy~G~V~ri~~fGaFv~l--------~~gkdgl~hiS~~~~~rv~--kv~dvlk~Gd~v~Vkv~~iD~~Gri~l  685 (692)
T COG1185         616 EVEVGEVYEGTVVRIVDFGAFVEL--------LPGKDGLVHISQLAKERVE--KVEDVLKEGDEVKVKVIEIDKQGRIRL  685 (692)
T ss_pred             hcccccEEEEEEEEEeecceEEEe--------cCCcceeEEehhhhhhhhh--cccceeecCceEEEEEeeecccCCccc
Confidence            479999999999999999999999        5677899999999877776  677999999999999999998788999


Q ss_pred             EEecC
Q 029155          153 STAKN  157 (198)
Q Consensus       153 St~~~  157 (198)
                      |++..
T Consensus       686 s~~~~  690 (692)
T COG1185         686 SIKAV  690 (692)
T ss_pred             eehhc
Confidence            98753

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=97.74  E-value=8.2e-05  Score=68.78  Aligned_cols=71  Identities=23%  Similarity=0.329  Sum_probs=59.8

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC---Cc
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD---AR  148 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~---~~  148 (198)
                      |..+.|++|.|+|.++....++|++        . ...|+||.++..        .++.|++||.|+|.|+.++.   +.
T Consensus       130 yk~~~GeIV~G~V~ri~~~giiVDL--------g-gvea~LP~sE~i--------p~E~~~~GdrIka~I~~Vd~~~kg~  192 (470)
T PRK09202        130 YKDRVGEIITGVVKRVERGNIIVDL--------G-RAEAILPRKEQI--------PRENFRPGDRVRAYVYEVRKEARGP  192 (470)
T ss_pred             HHhhcCCEEEEEEEEEecCCEEEEE--------C-CeEEEecHHHcC--------CCccCCCCCEEEEEEEEEecCCCCC
Confidence            5567999999999999999999999        2 579999998863        35789999999999999974   34


Q ss_pred             cEEEEEecCCC
Q 029155          149 AYFLSTAKNDL  159 (198)
Q Consensus       149 ~~~LSt~~~~l  159 (198)
                      ++.||-+.++|
T Consensus       193 qIilSRt~p~~  203 (470)
T PRK09202        193 QIILSRTHPEF  203 (470)
T ss_pred             eEEEEeCcHHH
Confidence            68899888754

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=97.58  E-value=0.0002  Score=64.23  Aligned_cols=72  Identities=15%  Similarity=0.287  Sum_probs=58.6

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC---C
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD---A  147 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~---~  147 (198)
                      .|..+.|++|.|+|.++..+.++|+|        . ...|+||.++...        ++.|++||.|+|.|.+++.   +
T Consensus       129 ef~~k~GeiV~G~V~~~~~~~~~Vdl--------g-~vEa~LP~~E~ip--------~e~~~~Gd~Ika~V~~V~~~~kg  191 (362)
T PRK12327        129 EFSEREGDIVTGVVQRRDNRFVYVNL--------G-KIEAVLPPAEQIP--------GETYKHGDRIKVYVVKVEKTTKG  191 (362)
T ss_pred             HHHHhcCCEEEEEEEEEeCCcEEEEe--------C-CeEEEecHHHcCC--------CCCCCCCCEEEEEEEEEecCCCC
Confidence            36679999999999999999999999        3 3789999766432        5779999999999999973   3


Q ss_pred             ccEEEEEecCCC
Q 029155          148 RAYFLSTAKNDL  159 (198)
Q Consensus       148 ~~~~LSt~~~~l  159 (198)
                      ..+.||-..++|
T Consensus       192 p~IivSRt~p~~  203 (362)
T PRK12327        192 PQIFVSRTHPGL  203 (362)
T ss_pred             CeEEEEeCCHHH
Confidence            458888877654

>TIGR01953 NusA transcription termination factor NusA

Probab=97.55  E-value=0.00025  Score=63.18  Aligned_cols=72  Identities=21%  Similarity=0.319  Sum_probs=58.5

Q ss_pred             CCCCCCCCEEEEEEEEEecce-EEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC---
Q 029155           71 GPVPEPGSVVIARVTKVMTRM-ASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD---  146 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~-~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~---  146 (198)
                      .|..+.|++|.|+|.++..++ |+|+|        . ...|+||.++...        .+.|++||.|+|.|.++++   
T Consensus       126 ey~~k~GeiV~G~V~~v~~~g~v~Vdi--------G-~~ea~LP~~E~ip--------~E~~~~Gd~ik~~V~~V~~~~k  188 (341)
T TIGR01953       126 EFSSKEGEIISGTVKRVNRRGNLYVEL--------G-KTEGILPKKEQIP--------GEKFRIGDRIKAYVYEVRKTAK  188 (341)
T ss_pred             HHHhhcCCEEEEEEEEEecCCcEEEEE--------C-CeEEEecHHHcCC--------CcCCCCCCEEEEEEEEEEcCCC
Confidence            355689999999999998865 79999        3 5789999888642        3559999999999999974   


Q ss_pred             CccEEEEEecCCC
Q 029155          147 ARAYFLSTAKNDL  159 (198)
Q Consensus       147 ~~~~~LSt~~~~l  159 (198)
                      +.++.||.+.++|
T Consensus       189 g~qIivSRt~~~~  201 (341)
T TIGR01953       189 GPQIILSRTHPEF  201 (341)
T ss_pred             CCeEEEEeCcHHH
Confidence            3568999988765

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.

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

Probab=97.52  E-value=0.00097  Score=48.05  Aligned_cols=74  Identities=22%  Similarity=0.183  Sum_probs=47.8

Q ss_pred             CCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccc-----------cccccccccCCCCCCEEEEEEEEe
Q 029155           76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT-----------EIDKVDMHLSFRPGDIVRASVLSL  144 (198)
Q Consensus        76 vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~-----------~~d~~~~~~~~~~GDiV~AkV~s~  144 (198)
                      +|+++.|+|+++...++++.+.         ++.+++|.+++.+.           ..+  +-...+++||.|++||+++
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G---------pl~~f~~~~~ip~~~~~~~~~~~~~~~~--~~~~~i~~g~~VR~rV~~v   69 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG---------PLSIFISRHLIPSDMEFDPNASPPCFTS--NEDIVIKKDTEVRLKIIGT   69 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc---------CceEEEEeeecCccceECCcCCCCeEeC--CCcEEECCCCEEEEEEEEE
Confidence            5899999999999999999995         23333333332210           111  1145689999999999987


Q ss_pred             C-CCcc--EEEEEecCCCe
Q 029155          145 G-DARA--YFLSTAKNDLG  160 (198)
Q Consensus       145 ~-~~~~--~~LSt~~~~lG  160 (198)
                      . +.+.  ..-|++++.||
T Consensus        70 ~~~~~~~~~igt~~~~~LG   88 (88)
T cd04462          70 RVDATDIFAIGTIKDDYLG   88 (88)
T ss_pred             EEccCceEEEEEccCCCCC
Confidence            4 2222  23366666665

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.

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=97.40  E-value=0.00091  Score=47.73  Aligned_cols=73  Identities=11%  Similarity=0.131  Sum_probs=60.4

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEe-ccccccccccccccccCCCCCCEEEEEEEEeCC-Cc
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR-QQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-AR  148 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~-~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~  148 (198)
                      ...|++||+|. .|..+.+..+.|.++       .++.+|.|. .++++.....  ++++.+ +|=.+.++|+.++. ++
T Consensus        11 y~~P~v~dvv~-~Vv~i~d~~~YV~Ll-------eY~iegmIl~~selsr~rir--si~kll-VGk~e~v~ViRVDk~KG   79 (86)
T PHA02858         11 YVFPNINEVTK-GIVFVKDNIFYVKLI-------DYGLEALIVNYVNVNADRAE--KLKKKL-VGKTINVQVIRTDKLKG   79 (86)
T ss_pred             EecCCCCeEEE-EEEEEeccEEEEEEe-------cCccceEEecHHHHhHHHHH--hhhhhh-cCCeeEEEEEEECCCCC
Confidence            34699999999 899999999999995       556888888 8888776666  788888 99999999999984 35


Q ss_pred             cEEEEE
Q 029155          149 AYFLST  154 (198)
Q Consensus       149 ~~~LSt  154 (198)
                      -+-||.
T Consensus        80 YIDLs~   85 (86)
T PHA02858         80 YIDVRH   85 (86)
T ss_pred             EEEeEc
Confidence            566763

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.22  E-value=0.0024  Score=58.31  Aligned_cols=74  Identities=22%  Similarity=0.280  Sum_probs=55.7

Q ss_pred             CCCCCEEEEEEEEEecc--eEEEEEeeeccccccCcceeEEecccccccc----------ccccccccCCCCCCEEEEEE
Q 029155           74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE----------IDKVDMHLSFRPGDIVRASV  141 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~--~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~----------~d~~~~~~~~~~GDiV~AkV  141 (198)
                      ..+|++..|+|+++.+.  .|||+|        ...-.|+||.+|+....          ....++.+.+++||.|.++|
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            56899999999999998  899999        66778999999985321          01124667899999999999


Q ss_pred             EEeC-CCccEEEEEe
Q 029155          142 LSLG-DARAYFLSTA  155 (198)
Q Consensus       142 ~s~~-~~~~~~LSt~  155 (198)
                      ..-. ......||+.
T Consensus        95 ~Ke~~~~Kgp~lT~~  109 (414)
T TIGR00757        95 VKEPRGNKGARLTTD  109 (414)
T ss_pred             eeCCcCCCCCeEEEE
Confidence            9832 1233555553

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.

>TIGR02063 RNase_R ribonuclease R

Probab=97.04  E-value=0.003  Score=61.18  Aligned_cols=74  Identities=14%  Similarity=0.152  Sum_probs=57.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEeccccccccc--cc-------cccccCCCCCCEEEEEEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEI--DK-------VDMHLSFRPGDIVRASVL  142 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~~--d~-------~~~~~~~~~GDiV~AkV~  142 (198)
                      ..++|.++.|+|++|++.+++|++        .. ..+|++|++++...+.  +.       ......|++||.|.++|.
T Consensus       624 ~~~iG~~~~g~V~~v~~fGifV~L--------~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~  695 (709)
T TIGR02063       624 SEKIGEEFEGVISGVTSFGLFVEL--------ENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVV  695 (709)
T ss_pred             hccCCcEEEEEEEEEEeCCEEEEe--------cCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEE
Confidence            357899999999999999999999        33 5899999999863221  10       122467999999999999


Q ss_pred             EeCC-CccEEEEE
Q 029155          143 SLGD-ARAYFLST  154 (198)
Q Consensus       143 s~~~-~~~~~LSt  154 (198)
                      +++. .+.+.+++
T Consensus       696 ~vd~~~~~I~~~l  708 (709)
T TIGR02063       696 KADLDTGKIDFEL  708 (709)
T ss_pred             EEecccCeEEEEE
Confidence            9974 46677764

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.

>PRK11642 exoribonuclease R; Provisional

Probab=96.81  E-value=0.0068  Score=59.72  Aligned_cols=74  Identities=18%  Similarity=0.207  Sum_probs=57.5

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEecccccccc--cccc-------ccccCCCCCCEEEEEEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATE--IDKV-------DMHLSFRPGDIVRASVLS  143 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~--~d~~-------~~~~~~~~GDiV~AkV~s  143 (198)
                      .++|+++.|+|++|++.+++|+|        .. ..+|++|++++...+  .+..       .....|++||.|.++|.+
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            36899999999999999999999        33 489999999886321  1110       224679999999999999


Q ss_pred             eCC-CccEEEEEe
Q 029155          144 LGD-ARAYFLSTA  155 (198)
Q Consensus       144 ~~~-~~~~~LSt~  155 (198)
                      ++. .+.+.|++.
T Consensus       713 vD~~~rkI~f~l~  725 (813)
T PRK11642        713 VNMDERKIDFSLI  725 (813)
T ss_pred             eecCCCeEEEEEe
Confidence            873 467888874

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.70  E-value=0.0044  Score=55.72  Aligned_cols=72  Identities=17%  Similarity=0.201  Sum_probs=56.2

Q ss_pred             CCCCCCCCEEEEEEEEEec-ceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC---
Q 029155           71 GPVPEPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD---  146 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~-~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~---  146 (198)
                      .|..++|++|.|+|.++.. ..++|++        . ...|+|+.++.-        ..+.|++||.|+|-|..+..   
T Consensus       133 ey~~~~Geiv~g~V~r~~~~~~i~vdl--------g-~~ea~LP~~eqi--------p~E~~~~Gdrik~~i~~V~~~~k  195 (374)
T PRK12328        133 KYKKKVGKIVFGTVVRVDNEENTFIEI--------D-EIRAVLPMKNRI--------KGEKFKVGDVVKAVLKRVKIDKN  195 (374)
T ss_pred             HHHHhcCcEEEEEEEEEecCCCEEEEc--------C-CeEEEeCHHHcC--------CCCcCCCCCEEEEEEEEEecCCC
Confidence            4778999999999999986 4578888        3 478999877643        25779999999999999863   


Q ss_pred             -CccEEEEEecCCC
Q 029155          147 -ARAYFLSTAKNDL  159 (198)
Q Consensus       147 -~~~~~LSt~~~~l  159 (198)
                       +..+.||-..++|
T Consensus       196 ~gp~IilSRt~p~~  209 (374)
T PRK12328        196 NGILIELSRTSPKF  209 (374)
T ss_pred             CCCEEEEEcCCHHH
Confidence             2457777766544

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

Probab=96.69  E-value=0.0085  Score=61.18  Aligned_cols=76  Identities=18%  Similarity=0.223  Sum_probs=67.2

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      .+.||+|.|.|..+.+++.++.+        +..+.|..++++...+...  .-+..|.+|+++.++|.+++. .+.+.|
T Consensus      1160 lk~g~iv~G~V~nv~~~glfi~l--------s~~v~a~v~is~~~ds~~k--~w~k~~~~gklv~~rv~~ve~~s~riel 1229 (1710)
T KOG1070|consen 1160 LKIGDIVRGFVKNVETKGLFIAL--------SRKVEAFVPISGLSDSFEK--EWEKHLPVGKLVTGRVLSVEEDSKRIEL 1229 (1710)
T ss_pred             cccCceeEEEEEEecCCcEEEEE--------ccceEEEEEccccccchhh--hhhccCCccceeeeEEEEeeccCceEEE
Confidence            58899999999999999999999        7899999999999877755  677899999999999999974 467999


Q ss_pred             EEecCCC
Q 029155          153 STAKNDL  159 (198)
Q Consensus       153 St~~~~l  159 (198)
                      +++..+-
T Consensus      1230 ~Lk~s~~ 1236 (1710)
T KOG1070|consen 1230 SLKNSDI 1236 (1710)
T ss_pred             EEecccc
Confidence            9987654

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.60  E-value=0.0063  Score=55.77  Aligned_cols=77  Identities=12%  Similarity=0.146  Sum_probs=58.1

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC---
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD---  146 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~---  146 (198)
                      -|..++|++|.|+|.++..+.+.|++.+-    +.. ...|+|+.++.-        ..+.|++||.|+|-|..+..   
T Consensus       147 ef~~~~GeIV~G~V~r~e~~~viv~l~~~----~g~~~~EaiLP~~Eqi--------p~E~y~~Gdrika~i~~V~~~~~  214 (449)
T PRK12329        147 EFQDLEDTVLTARVLRFERQSVIMAVSSG----FGQPEVEAELPKREQL--------PNDNYRANATFKVFLKEVSEGPR  214 (449)
T ss_pred             HHHHhcCcEEEEEEEEEcCCCEEEEeccc----CCCcceEEEecHHHcC--------CCCcCCCCCEEEEEEEEeecCCC
Confidence            46789999999999999999899888310    011 378899877642        25779999999999999953   


Q ss_pred             -CccEEEEEecCCC
Q 029155          147 -ARAYFLSTAKNDL  159 (198)
Q Consensus       147 -~~~~~LSt~~~~l  159 (198)
                       +..+.||-..++|
T Consensus       215 kGpqIilSRt~p~l  228 (449)
T PRK12329        215 RGPQLFVSRANAGL  228 (449)
T ss_pred             CCCEEEEEcCCHHH
Confidence             2457788776654

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

Probab=96.52  E-value=0.0036  Score=63.79  Aligned_cols=77  Identities=19%  Similarity=0.145  Sum_probs=64.9

Q ss_pred             CCCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCcc
Q 029155           70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARA  149 (198)
Q Consensus        70 ~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~  149 (198)
                      ..+-..+|++|.|.|++|.+++..|..        ...+.|-||++++-.+...-.++.+-|+.||-|.|||+.-.|-.+
T Consensus       879 ~~~~~~igsiv~a~v~svKp~~L~v~l--------~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~~D~k~  950 (1710)
T KOG1070|consen  879 STEDLSIGSIVRAYVKSVKPDQLNVLL--------AANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGGHDVKD  950 (1710)
T ss_pred             cccceeeeeEEEEEEeeecccceEEec--------cccccCceehHHhhccccccCChhhhcccCCeEEEEEEcCCcccc
Confidence            457789999999999999999999998        678999999999987666666789999999999999998765444


Q ss_pred             EEEEE
Q 029155          150 YFLST  154 (198)
Q Consensus       150 ~~LSt  154 (198)
                      +-.|+
T Consensus       951 lpith  955 (1710)
T KOG1070|consen  951 LPITH  955 (1710)
T ss_pred             Ccccc
Confidence            43333

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

Probab=96.47  E-value=0.015  Score=56.02  Aligned_cols=73  Identities=14%  Similarity=0.203  Sum_probs=56.2

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeecccccc-CcceeEEecccccccc--ccc-------cccccCCCCCCEEEEEEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATE--IDK-------VDMHLSFRPGDIVRASVLS  143 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~-~~~~G~l~~s~v~~~~--~d~-------~~~~~~~~~GDiV~AkV~s  143 (198)
                      -++|++..|+|+++++.+++|+|        . ...+|++|.+++...+  .|+       ......|++||.|.++|.+
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            36799999999999999999999        4 4689999999986432  111       1123679999999999999


Q ss_pred             eCC-CccEEEEE
Q 029155          144 LGD-ARAYFLST  154 (198)
Q Consensus       144 ~~~-~~~~~LSt  154 (198)
                      ++. .+.+.+++
T Consensus       642 vd~~~~~I~f~l  653 (654)
T TIGR00358       642 VNMETRSIIFEL  653 (654)
T ss_pred             EecccCeEEEEE
Confidence            973 35666654

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.

>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=96.41  E-value=0.017  Score=40.21  Aligned_cols=70  Identities=19%  Similarity=0.177  Sum_probs=53.7

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEE-EEEEEEeCCCccEEEEE
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIV-RASVLSLGDARAYFLST  154 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV-~AkV~s~~~~~~~~LSt  154 (198)
                      |++|.|+|.+-+.+...|++.       ..+..|.|+..+++........+...+++||.+ .+-|++. ..+.+.||.
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~-------~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL~~-~~r~i~lt~   71 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAIL-------PEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSN-YKGRIILTK   71 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEec-------CCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEEec-cccEEEEec
Confidence            789999999999999999994       457889998877765333334567889999999 8888832 235566653

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.

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

Probab=96.16  E-value=0.0093  Score=56.07  Aligned_cols=74  Identities=9%  Similarity=0.130  Sum_probs=61.9

Q ss_pred             CCCCCCEE-----EEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC
Q 029155           73 VPEPGSVV-----IARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA  147 (198)
Q Consensus        73 ~p~vGDiV-----iG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~  147 (198)
                      .++++|+.     .|+|+.+++.+++|++        ...-.|+||.+|+.+....  +.++.+.+||.|..+-+..+..
T Consensus       660 ~~~~~~l~~g~vy~~tIt~~rd~G~~V~l--------~p~~~~Llh~sqL~~e~ia--kpsd~levGq~I~vk~ie~d~~  729 (760)
T KOG1067|consen  660 DDQVQDLEFGGVYTATITEIRDTGVMVEL--------YPMQQGLLHNSQLDQEKIA--KPSDLLEVGQEIQVKYIERDPR  729 (760)
T ss_pred             CccccceEeeeEEEEEEeeecccceEEEe--------cCCchhhccchhccccccc--ChHHHHhhcceeEEEEEeecCc
Confidence            35556655     5899999999999999        4567899999999877766  7889999999999999999877


Q ss_pred             ccEEEEEec
Q 029155          148 RAYFLSTAK  156 (198)
Q Consensus       148 ~~~~LSt~~  156 (198)
                      +.+.||-|.
T Consensus       730 g~~~ls~ra  738 (760)
T KOG1067|consen  730 GGIMLSSRA  738 (760)
T ss_pred             cceeehhhh
Confidence            778887664

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

Probab=95.94  E-value=0.033  Score=48.05  Aligned_cols=63  Identities=17%  Similarity=0.167  Sum_probs=47.8

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEec
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAK  156 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~  156 (198)
                      ++.|-|.|.++...+.+|-+        ...+.|+||.|++.          ...+.|+.+.|+|+.+.+.+++.||++.
T Consensus       156 nq~v~~tVYr~~~~G~fv~~--------e~~~~GfIh~sEr~----------~~prlG~~l~~rVi~~reDg~lnLSl~p  217 (287)
T COG2996         156 NQEVDATVYRLLESGTFVIT--------ENGYLGFIHKSERF----------AEPRLGERLTARVIGVREDGKLNLSLRP  217 (287)
T ss_pred             cCeeeeEEEEEeccceEEEE--------cCCeEEEEcchhhc----------ccccCCceEEEEEEEEccCCeeeccccc
Confidence            55566666666665555555        56789999988753          3467999999999999877899999975


Q ss_pred             C
Q 029155          157 N  157 (198)
Q Consensus       157 ~  157 (198)
                      -
T Consensus       218 ~  218 (287)
T COG2996         218 R  218 (287)
T ss_pred             c
Confidence            3

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

Probab=95.86  E-value=0.012  Score=59.07  Aligned_cols=81  Identities=20%  Similarity=0.239  Sum_probs=63.5

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF  151 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~  151 (198)
                      ...+|.+|.+.|++++.....| +    ...|..+..|+|+.++++.....  .+.+-+++|+.|.+||++++. .-...
T Consensus       982 t~~~g~iV~~~V~~vt~rr~~C-v----~v~ld~G~~g~i~~~~~Sd~~v~--~p~~~v~vgq~v~~kvi~id~e~f~v~ 1054 (1299)
T KOG1856|consen  982 TFYEGAIVPVTVTKVTHRRGIC-V----RVRLDCGVTGFILAKNLSDRDVR--RPENRVKVGQTVYCKVIKIDKERFSVE 1054 (1299)
T ss_pred             HhccCceEEEeeeEEEecccce-e----EEEecCCCceeeeccccChhhcc--CHHHhhccCceEEEEeeeeeHhhhhhh
Confidence            3578999999999999998555 1    11236789999999998764444  778889999999999999974 34578


Q ss_pred             EEEecCCCe
Q 029155          152 LSTAKNDLG  160 (198)
Q Consensus       152 LSt~~~~lG  160 (198)
                      ||++..+|-
T Consensus      1055 Ls~r~sdlk 1063 (1299)
T KOG1856|consen 1055 LSCRTSDLK 1063 (1299)
T ss_pred             hhhhhHHhh
Confidence            888877764

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=95.69  E-value=0.007  Score=33.26  Aligned_cols=21  Identities=24%  Similarity=0.518  Sum_probs=18.6

Q ss_pred             CCCceeEEcc-CCeEEeCCCCC
Q 029155          167 TAGGTMVPIS-WTEMQCPLTGQ  187 (198)
Q Consensus       167 ~~g~~m~~~~-~~~~~c~~cg~  187 (198)
                      .||..|.|.. ...+.||+||.
T Consensus         3 sC~~~i~~r~~~v~f~CPnCG~   24 (24)
T PF07754_consen    3 SCGRPIAPREQAVPFPCPNCGF   24 (24)
T ss_pred             cCCCcccCcccCceEeCCCCCC
Confidence            7899999887 78999999994

It is likely to bind zinc via its four well-conserved cysteine residues.

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

Probab=95.38  E-value=0.016  Score=49.74  Aligned_cols=77  Identities=18%  Similarity=0.228  Sum_probs=65.8

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-ccE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAY  150 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~~  150 (198)
                      ..|.++|+|++.|..|..-+|.|.++-.+      ..+|.|-.|+++..++.  .++...++|-.=.+-|+.++.. +-+
T Consensus        12 kyPev~e~VmvnV~sIaemGayv~LlEYn------niEGmiLlsELSrRRIR--SI~klirVGr~E~vvVlrVDkekGYI   83 (304)
T KOG2916|consen   12 KYPEVEEIVMVNVRSIAEMGAYVKLLEYN------NIEGMILLSELSRRRIR--SIQKLIRVGRNEPVVVLRVDKEKGYI   83 (304)
T ss_pred             cCCCcccEEEEEeeEehhccceEeeeecC------CcccchhhhHHHHHHHH--HHHHHHhcCCcceEEEEEEcCCCCce
Confidence            46999999999999999999999996432      47899999999876766  8889999999999999999854 567


Q ss_pred             EEEEec
Q 029155          151 FLSTAK  156 (198)
Q Consensus       151 ~LSt~~  156 (198)
                      .||.|.
T Consensus        84 DLSkrr   89 (304)
T KOG2916|consen   84 DLSKRR   89 (304)
T ss_pred             echhcc
Confidence            899875

>PRK11712 ribonuclease G; Provisional

Probab=95.13  E-value=0.089  Score=49.14  Aligned_cols=73  Identities=19%  Similarity=0.188  Sum_probs=53.1

Q ss_pred             CCCCCEEEEEEEEEecc--eEEEEEeeeccccccCcceeEEecccccccc----------ccccccccCCCCCCEEEEEE
Q 029155           74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE----------IDKVDMHLSFRPGDIVRASV  141 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~--~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~----------~d~~~~~~~~~~GDiV~AkV  141 (198)
                      ..+|+|-.|+|.+|.+.  .|||||        ...-.|+||.+|+....          .....+.+.+++||.|...|
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            46899999999999775  699999        67788999999874210          00113566799999999999


Q ss_pred             EEeCC-CccEEEEE
Q 029155          142 LSLGD-ARAYFLST  154 (198)
Q Consensus       142 ~s~~~-~~~~~LSt  154 (198)
                      ..-.- .....||+
T Consensus       108 ~Ke~~~~KG~~lT~  121 (489)
T PRK11712        108 VKDPLGTKGARLTT  121 (489)
T ss_pred             EeCCcCCCCCeEEE
Confidence            98431 23345555

>PRK10811 rne ribonuclease E; Reviewed

Probab=95.04  E-value=0.095  Score=52.34  Aligned_cols=74  Identities=12%  Similarity=0.165  Sum_probs=54.0

Q ss_pred             CCCCCEEEEEEEEEec--ceEEEEEeeeccccccCcceeEEecccccccc-cc------ccccccCCCCCCEEEEEEEEe
Q 029155           74 PEPGSVVIARVTKVMT--RMASADIMCVGAKSVREKFSGIIRQQDVRATE-ID------KVDMHLSFRPGDIVRASVLSL  144 (198)
Q Consensus        74 p~vGDiViG~V~~v~~--~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~-~d------~~~~~~~~~~GDiV~AkV~s~  144 (198)
                      +.+|+|-.|+|.+|-+  +.+||+|        ...-.|+||.+|+.... ..      ...+.+.+++||.|...|..-
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDI--------G~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE  107 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE  107 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEe--------cCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence            4689999999999966  4699999        66788999999984211 11      113456799999999999984


Q ss_pred             C-CCccEEEEEe
Q 029155          145 G-DARAYFLSTA  155 (198)
Q Consensus       145 ~-~~~~~~LSt~  155 (198)
                      . .++...||++
T Consensus       108 a~gtKGp~LTt~  119 (1068)
T PRK10811        108 ERGNKGAALTTF  119 (1068)
T ss_pred             ccCCCCCceeee
Confidence            3 2234555554

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=94.54  E-value=0.044  Score=31.87  Aligned_cols=25  Identities=20%  Similarity=0.341  Sum_probs=15.0

Q ss_pred             ec-CCCceeEEccC-CeEEeCCCCCEE
Q 029155          165 ES-TAGGTMVPISW-TEMQCPLTGQTE  189 (198)
Q Consensus       165 ~~-~~g~~m~~~~~-~~~~c~~cg~~e  189 (198)
                      .| +||.+|.+..+ -.++||.||...
T Consensus         5 fC~~CG~~t~~~~~g~~r~C~~Cg~~~   31 (32)
T PF09297_consen    5 FCGRCGAPTKPAPGGWARRCPSCGHEH   31 (32)
T ss_dssp             B-TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred             ccCcCCccccCCCCcCEeECCCCcCEe
Confidence            47 89999988753 379999999764

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

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

Probab=94.39  E-value=0.077  Score=37.73  Aligned_cols=47  Identities=17%  Similarity=0.308  Sum_probs=38.4

Q ss_pred             eeccCCcEEecCCccCC--CCCeeeCCCEEEeCCceEEEEeEeeeEEEcC
Q 029155            3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLS   50 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~--~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~   50 (198)
                      +|..+.+.|.||+.|..  ...|-||.++..-.+ .+|||.+-|.|....
T Consensus        22 vK~~~G~~V~~G~IivRQRgtk~hPG~NVg~GrD-~TLfAl~~G~V~f~~   70 (81)
T PF01016_consen   22 VKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGRD-HTLFALVDGRVKFTK   70 (81)
T ss_dssp             ESSSTTCEESSTSEEEEBSSSSSEEBTTEEEETT-SEEEESSSCEEEEEE
T ss_pred             EEEeCCEEEcCCCEEEEeCCCcCcCCCCEEECCC-CcEEEecCEEEEEEE
Confidence            57788999999999874  246999999987743 359999999999864

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 ....

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=94.20  E-value=0.027  Score=41.39  Aligned_cols=29  Identities=24%  Similarity=0.424  Sum_probs=24.8

Q ss_pred             ec-CCCceeEEccCCeEEeCCCCCEEeeeeC
Q 029155          165 ES-TAGGTMVPISWTEMQCPLTGQTEQRKVA  194 (198)
Q Consensus       165 ~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva  194 (198)
                      .| .||++|.|.+ +.+.|+.||..+.++.+
T Consensus         2 fC~~Cg~~l~~~~-~~~~C~~C~~~~~~~~~   31 (104)
T TIGR01384         2 FCPKCGSLMTPKN-GVYVCPSCGYEKEKKPE   31 (104)
T ss_pred             CCcccCcccccCC-CeEECcCCCCccccccc
Confidence            47 8999999876 68999999999998744

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]

Probab=93.44  E-value=0.19  Score=45.91  Aligned_cols=61  Identities=20%  Similarity=0.356  Sum_probs=41.3

Q ss_pred             ccccCCCCCCEEEEE--E----EEeCCCccEEEEEecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEEe
Q 029155          126 DMHLSFRPGDIVRAS--V----LSLGDARAYFLSTAKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTEQ  190 (198)
Q Consensus       126 ~~~~~~~~GDiV~Ak--V----~s~~~~~~~~LSt~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e~  190 (198)
                      ++-.-+.+||.|.+-  |    +++.   .+++..-.. +-...-+| .||..|.-.+.+-++|++||++-+
T Consensus       311 ~~a~~L~pGD~i~~~G~~~~~~~n~e---k~~v~~l~~-~~~~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~  378 (421)
T COG1571         311 ELARKLIPGDEITVYGSVKPGTLNLE---KFQVLKLAR-YERVNPVCPRCGGRMKSAGRNGFRCKKCGTRAR  378 (421)
T ss_pred             HHHHhcCCCCEEEEecCccccceeEE---EEEEEEeee-eEEcCCCCCccCCchhhcCCCCcccccccccCC
Confidence            334567899998542  1    2221   233333344 77777899 999999877766899999998743

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=93.26  E-value=0.84  Score=30.30  Aligned_cols=60  Identities=17%  Similarity=0.080  Sum_probs=31.3

Q ss_pred             CCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEE
Q 029155           76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLST  154 (198)
Q Consensus        76 vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt  154 (198)
                      +|+++..+|.++++.+|+++.        ...-.-+||.+++.          ..+.+||.|.+-|=. +..+.+..||
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~--------~~~~~vlLp~~e~~----------~~~~~Gd~v~VFvY~-D~~~rl~AT~   60 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDD--------GEGKEVLLPKSEVP----------EPLKVGDEVEVFVYL-DKEGRLVATT   60 (61)
T ss_dssp             --------EEEE-SSEEEEEE--------TT-EEEEEEGGG----------------TTSEEEEEEEE--TTS-EEEE-
T ss_pred             CCCCcceEEEEEeCCEEEEEC--------CCCCEEEechHHcC----------CCCCCCCEEEEEEEE-CCCCCEEEec
Confidence            589999999999999999987        44456677766542          447899999998875 2234565555

>PRK05435 rpmA 50S ribosomal protein L27; Validated

Probab=93.09  E-value=0.24  Score=35.26  Aligned_cols=46  Identities=20%  Similarity=0.278  Sum_probs=36.8

Q ss_pred             eeccCCcEEecCCccCCC--CCeeeCCCEEEeCCceEEEEeEeeeEEEc
Q 029155            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTL   49 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~~g~~~i~asv~G~v~~~   49 (198)
                      +|....+.|.||+.|..-  ..|-||.++-.-.+ .+|||.+.|.|...
T Consensus        23 vK~~~g~~V~~G~IivRQRGtk~~PG~nVg~GrD-~TlfA~~~G~V~f~   70 (82)
T PRK05435         23 VKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKD-HTLFALVDGVVKFE   70 (82)
T ss_pred             eEecCCEEEcCCcEEEEeCCCeECCCCCEeecCC-ceEEEecceEEEEE
Confidence            567788999999998743  35899999976532 35999999999985

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=92.97  E-value=0.083  Score=35.28  Aligned_cols=30  Identities=17%  Similarity=0.347  Sum_probs=23.2

Q ss_pred             ec-CCCceeEEcc-CCeEEeCCCCCEEeeeeC
Q 029155          165 ES-TAGGTMVPIS-WTEMQCPLTGQTEQRKVA  194 (198)
Q Consensus       165 ~~-~~g~~m~~~~-~~~~~c~~cg~~e~RKva  194 (198)
                      .| .||..|.|.+ ...+.||+||..+-+..+
T Consensus         9 ~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~   40 (59)
T PRK14890          9 KCTSCGIEIAPREKAVKFLCPNCGEVIIYRCE   40 (59)
T ss_pred             cccCCCCcccCCCccCEeeCCCCCCeeEeech
Confidence            46 7999998887 678999999987554443

>CHL00121 rpl27 ribosomal protein L27; Reviewed

Probab=92.95  E-value=0.19  Score=35.99  Aligned_cols=59  Identities=20%  Similarity=0.288  Sum_probs=42.9

Q ss_pred             eeccCCcEEecCCccCCC--CCeeeCCCEEEe-CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecC
Q 029155            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~-~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~   67 (198)
                      +|....+.|.||+.|..-  ..|-||.++-.- |.  +|||...|.|....    ...+++.|+|.|.
T Consensus        23 vK~~~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~--TlfAl~~G~V~f~~----~~~~~~~vsv~~~   84 (86)
T CHL00121         23 VKRFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDF--TLYALIDGFVKFKK----KNKKQKSINVINI   84 (86)
T ss_pred             eEEcCCEEEcCCcEEEEcCCCeECCCCcccccCCc--eEEEccceEEEEEE----eCCCCEEEEEeec
Confidence            467788999999998743  358899987544 43  59999999999853    1223456777764

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=92.89  E-value=0.096  Score=33.33  Aligned_cols=26  Identities=19%  Similarity=0.351  Sum_probs=21.1

Q ss_pred             ec-CCCceeEEccC---CeEEeCCCCCEEe
Q 029155          165 ES-TAGGTMVPISW---TEMQCPLTGQTEQ  190 (198)
Q Consensus       165 ~~-~~g~~m~~~~~---~~~~c~~cg~~e~  190 (198)
                      .| .||+.|.+..+   +.+.||.||..+.
T Consensus         2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~   31 (52)
T smart00661        2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEP   31 (52)
T ss_pred             CCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence            47 89999988765   3799999998764

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=92.09  E-value=0.13  Score=39.83  Aligned_cols=29  Identities=24%  Similarity=0.424  Sum_probs=22.0

Q ss_pred             eeEEe-c-CCCceeEEccCCeEEeCCCCCEEe
Q 029155          161 VVSAE-S-TAGGTMVPISWTEMQCPLTGQTEQ  190 (198)
Q Consensus       161 vv~a~-~-~~g~~m~~~~~~~~~c~~cg~~e~  190 (198)
                      +..+. | .||.||.... .+..||.||+++.
T Consensus        25 kML~~hCp~Cg~PLF~Kd-G~v~CPvC~~~~~   55 (131)
T COG1645          25 KMLAKHCPKCGTPLFRKD-GEVFCPVCGYREV   55 (131)
T ss_pred             HHHHhhCcccCCcceeeC-CeEECCCCCceEE
Confidence            33444 6 8999999866 4899999996553

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

Probab=91.83  E-value=0.96  Score=36.27  Aligned_cols=85  Identities=20%  Similarity=0.115  Sum_probs=52.2

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeecccccc------CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR------EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG  145 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~------~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~  145 (198)
                      ..|-.|++|-|.|+.+...++++++...+-..++      ..|.   +-++- +.+.. .+++ ....|+.|+.+|+.+.
T Consensus        77 FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~---p~~n~-P~f~~-~d~s-~I~~~~~VR~kiigtr  150 (170)
T KOG3298|consen   77 FKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFD---PGENP-PNFQT-EDES-VIQKGVEVRLKIIGTR  150 (170)
T ss_pred             EeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccC---CCCCC-Ccccc-cccc-eeeeCcEEEEEEEEEE
Confidence            4577899999999999999999999654432111      1121   22221 11111 1222 6889999999999864


Q ss_pred             -CCcc-E-EEEEecCCCeee
Q 029155          146 -DARA-Y-FLSTAKNDLGVV  162 (198)
Q Consensus       146 -~~~~-~-~LSt~~~~lGvv  162 (198)
                       +... + .=|+.++-||.+
T Consensus       151 ~~~~~i~algtl~~D~LG~i  170 (170)
T KOG3298|consen  151 VDETEIFALGTLKGDYLGPI  170 (170)
T ss_pred             EeeeeEEEEEEecCcccccC
Confidence             2222 3 335566667754

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=91.52  E-value=0.19  Score=31.11  Aligned_cols=29  Identities=34%  Similarity=0.558  Sum_probs=20.9

Q ss_pred             ec-CCCce---eEEccC-CeEEeCCCCCEEeeee
Q 029155          165 ES-TAGGT---MVPISW-TEMQCPLTGQTEQRKV  193 (198)
Q Consensus       165 ~~-~~g~~---m~~~~~-~~~~c~~cg~~e~RKv  193 (198)
                      +| +||+.   +.+.+. ....||+||..+-||+
T Consensus         7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~   40 (42)
T PF09723_consen    7 RCEECGHEFEVLQSISEDDPVPCPECGSTEVRRV   40 (42)
T ss_pred             EeCCCCCEEEEEEEcCCCCCCcCCCCCCCceEEe
Confidence            46 78854   566653 6899999999666554

The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=91.00  E-value=0.36  Score=30.29  Aligned_cols=30  Identities=17%  Similarity=-0.002  Sum_probs=23.5

Q ss_pred             Eec-CCCceeEEccCCeEEeCCCCCEEeeee
Q 029155          164 AES-TAGGTMVPISWTEMQCPLTGQTEQRKV  193 (198)
Q Consensus       164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKv  193 (198)
                      -.| +||......+...++||+||..-.-|.
T Consensus         3 Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~   33 (44)
T smart00659        3 YICGECGRENEIKSKDVVRCRECGYRILYKK   33 (44)
T ss_pred             EECCCCCCEeecCCCCceECCCCCceEEEEe
Confidence            367 899987665667999999998766554

present in RNA polymerase I, II and III

>PRK05054 exoribonuclease II; Provisional

Probab=90.70  E-value=1.6  Score=42.22  Aligned_cols=72  Identities=11%  Similarity=0.243  Sum_probs=51.6

Q ss_pred             CCCC--EEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccc---cc---c--cccc--ccCCCCCCEEEEEEE
Q 029155           75 EPGS--VVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT---EI---D--KVDM--HLSFRPGDIVRASVL  142 (198)
Q Consensus        75 ~vGD--iViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~---~~---d--~~~~--~~~~~~GDiV~AkV~  142 (198)
                      ++|+  ...|.|++++..+.+|+|.       .....|++|.+.+...   +.   +  ...+  ...|++||-|..+|.
T Consensus       558 ~~G~~~~f~g~I~~v~~~G~fV~l~-------~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~  630 (644)
T PRK05054        558 KAGTDTRFAAEIIDISRGGMRVRLL-------ENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLA  630 (644)
T ss_pred             ccCCCeEEEEEEEeeecCcEEEEEe-------CCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEE
Confidence            4555  9999999999999999994       3467899999887431   10   0  0111  246999999999999


Q ss_pred             EeCC-CccEEEE
Q 029155          143 SLGD-ARAYFLS  153 (198)
Q Consensus       143 s~~~-~~~~~LS  153 (198)
                      +++. .+.+..+
T Consensus       631 ~vd~~~~~i~~~  642 (644)
T PRK05054        631 EVRMETRSIIAR  642 (644)
T ss_pred             EEccccCeEEEE
Confidence            9973 3445443

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=90.66  E-value=0.35  Score=28.78  Aligned_cols=26  Identities=19%  Similarity=0.313  Sum_probs=19.6

Q ss_pred             ec-CCCceeEEcc--CCeEEeCCCCCEEe
Q 029155          165 ES-TAGGTMVPIS--WTEMQCPLTGQTEQ  190 (198)
Q Consensus       165 ~~-~~g~~m~~~~--~~~~~c~~cg~~e~  190 (198)
                      .| +||+.|+|..  +....|+.|+..++
T Consensus         3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~   31 (35)
T PF02150_consen    3 FCPECGNLLYPKEDKEKRVACRTCGYEEP   31 (35)
T ss_dssp             BETTTTSBEEEEEETTTTEEESSSS-EEE
T ss_pred             eCCCCCccceEcCCCccCcCCCCCCCccC
Confidence            47 8999999985  33347999999886

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=90.59  E-value=0.53  Score=29.43  Aligned_cols=33  Identities=15%  Similarity=0.205  Sum_probs=23.4

Q ss_pred             EEec-CCCceeEEccCC-eEEeCCCCCEEeeeeCC
Q 029155          163 SAES-TAGGTMVPISWT-EMQCPLTGQTEQRKVAK  195 (198)
Q Consensus       163 ~a~~-~~g~~m~~~~~~-~~~c~~cg~~e~RKva~  195 (198)
                      .-.| .||..+.-.... .+.||.||.....|...
T Consensus         3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~   37 (46)
T PRK00398          3 EYKCARCGREVELDEYGTGVRCPYCGYRILFKERP   37 (46)
T ss_pred             EEECCCCCCEEEECCCCCceECCCCCCeEEEccCC
Confidence            3468 899987554433 79999999977665443

>PRK00420 hypothetical protein; Validated

Probab=89.77  E-value=0.26  Score=37.21  Aligned_cols=27  Identities=19%  Similarity=0.368  Sum_probs=21.7

Q ss_pred             Eec-CCCceeEEccCCeEEeCCCCCEEe
Q 029155          164 AES-TAGGTMVPISWTEMQCPLTGQTEQ  190 (198)
Q Consensus       164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~  190 (198)
                      ..| .||.+|........+||.||....
T Consensus        24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~   51 (112)
T PRK00420         24 KHCPVCGLPLFELKDGEVVCPVHGKVYI   51 (112)
T ss_pred             CCCCCCCCcceecCCCceECCCCCCeee
Confidence            567 899999875556899999998643

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=89.64  E-value=0.34  Score=29.13  Aligned_cols=28  Identities=29%  Similarity=0.463  Sum_probs=19.1

Q ss_pred             ec-CCCce---eEEcc-CCeEEeCCCCCEEeeee
Q 029155          165 ES-TAGGT---MVPIS-WTEMQCPLTGQTEQRKV  193 (198)
Q Consensus       165 ~~-~~g~~---m~~~~-~~~~~c~~cg~~e~RKv  193 (198)
                      +| .||+.   +.+.+ .....||.||. +-||+
T Consensus         7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~-~~~r~   39 (41)
T smart00834        7 RCEDCGHTFEVLQKISDDPLATCPECGG-DVRRL   39 (41)
T ss_pred             EcCCCCCEEEEEEecCCCCCCCCCCCCC-cceec
Confidence            67 78884   34433 56789999999 44443

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

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

Probab=88.82  E-value=1.2  Score=34.64  Aligned_cols=62  Identities=21%  Similarity=0.276  Sum_probs=43.7

Q ss_pred             eeccCCcEEecCCccCCCC--CeeeCCCEEEe-CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCC
Q 029155            3 VKEEEMVLVTPGEVLGKAT--EVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK   68 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~~--e~~~G~Gty~~-~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~   68 (198)
                      +|.++++.|.||+.|..--  .|-||.++=.- |.  +|||..-|.|+......+  ..++.|.|.|..
T Consensus        50 vKk~egq~V~~G~IIvrQRgtkfHPG~nVGiGKDh--tifaL~eG~Vrf~k~~~~--~~Rk~i~V~~~~  114 (144)
T KOG4600|consen   50 VKKYEGQSVIPGNIIVRQRGTKFHPGDNVGIGKDH--TIFALEEGRVRFEKSKIT--PPRKWIGVDPRG  114 (144)
T ss_pred             ceecCCeeeecccEEEEecccccCCCcccccCCcc--eEEEeeccEEEEEEccCC--CCcceEEEeecC
Confidence            5788899999999997643  46677665433 43  599999999998653211  135678888754

>TIGR00062 L27 ribosomal protein L27

Probab=88.57  E-value=0.87  Score=32.49  Aligned_cols=45  Identities=20%  Similarity=0.353  Sum_probs=36.4

Q ss_pred             eeccCCcEEecCCccCCC--CCeeeCCCEEEe-CCceEEEEeEeeeEEEc
Q 029155            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTL   49 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~-~g~~~i~asv~G~v~~~   49 (198)
                      +|....+.|.||+.|..-  ..|-||.++-.- |.  +|||.+.|.|...
T Consensus        23 vK~~~gq~V~~G~IivRQRGtk~hPG~nVg~GrD~--TlfAl~~G~V~f~   70 (83)
T TIGR00062        23 VKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGKDH--TLFALSDGVVKFE   70 (83)
T ss_pred             eEecCCEEEcCCcEEEEcCCceECCCCcccccCCC--eEEEecceEEEEE
Confidence            577788999999998743  358899998665 54  5999999999985

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

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=88.12  E-value=0.39  Score=32.12  Aligned_cols=31  Identities=19%  Similarity=0.408  Sum_probs=19.4

Q ss_pred             EEec-CCCceeEEcc-CCeEEeCCCCCEEeeee
Q 029155          163 SAES-TAGGTMVPIS-WTEMQCPLTGQTEQRKV  193 (198)
Q Consensus       163 ~a~~-~~g~~m~~~~-~~~~~c~~cg~~e~RKv  193 (198)
                      ...| .||..+-|.. ...+.||+||..+-...
T Consensus         9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc   41 (61)
T COG2888           9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRC   41 (61)
T ss_pred             CceeccCCCEeccCCceeEeeCCCCCceeeehh
Confidence            3456 6777775543 45777888886665443

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=87.39  E-value=0.52  Score=30.01  Aligned_cols=32  Identities=22%  Similarity=0.345  Sum_probs=20.9

Q ss_pred             ec-CCCc---eeEEccC-CeEEeCCCCCEEe-eeeCCC
Q 029155          165 ES-TAGG---TMVPISW-TEMQCPLTGQTEQ-RKVAKV  196 (198)
Q Consensus       165 ~~-~~g~---~m~~~~~-~~~~c~~cg~~e~-RKva~~  196 (198)
                      +| +||+   .+.+.+- ....||.||..+- |-+|.|
T Consensus         7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~s~~   44 (52)
T TIGR02605         7 RCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLLSAV   44 (52)
T ss_pred             EeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEeccc
Confidence            57 7888   4554442 3567999999654 556644

This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.

>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors []

Probab=87.36  E-value=0.87  Score=26.80  Aligned_cols=26  Identities=15%  Similarity=0.190  Sum_probs=20.4

Q ss_pred             ec-CCCceeEE-ccCCeEEeCCCCCEEe
Q 029155          165 ES-TAGGTMVP-ISWTEMQCPLTGQTEQ  190 (198)
Q Consensus       165 ~~-~~g~~m~~-~~~~~~~c~~cg~~e~  190 (198)
                      .| .||+.++- .....+.|+.||....
T Consensus         5 ~C~~C~~~~i~~~~~~~~~C~~Cg~~~~   32 (33)
T PF08792_consen    5 KCSKCGGNGIVNKEDDYEVCIFCGSSFP   32 (33)
T ss_pred             EcCCCCCCeEEEecCCeEEcccCCcEee
Confidence            57 69988876 4557999999998764

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=87.34  E-value=3.2  Score=40.48  Aligned_cols=74  Identities=16%  Similarity=0.092  Sum_probs=53.8

Q ss_pred             CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc---------cccccccCCCCCCEEEEEEEEeC
Q 029155           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI---------DKVDMHLSFRPGDIVRASVLSLG  145 (198)
Q Consensus        75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~---------d~~~~~~~~~~GDiV~AkV~s~~  145 (198)
                      .+|+.-.|.|+++..++.+|.|.       ...++|.+|++.+...+-         ........|+.||-|.++|.+++
T Consensus       621 ~vg~~f~g~V~~v~~~g~~V~l~-------~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~  693 (706)
T COG0557         621 RVGEEFDGVVTGVTSFGFFVELP-------ELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVD  693 (706)
T ss_pred             hcCCEEEEEEEEEEeccEEEEec-------ccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEc
Confidence            67899999999999999999993       234788888887752110         01123457999999999999986


Q ss_pred             C-CccEEEEEe
Q 029155          146 D-ARAYFLSTA  155 (198)
Q Consensus       146 ~-~~~~~LSt~  155 (198)
                      . .+.+.++..
T Consensus       694 ~~~~~i~~~~v  704 (706)
T COG0557         694 LDERKIDFELV  704 (706)
T ss_pred             ccccceEEEec
Confidence            3 355655543

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

Probab=87.30  E-value=1.3  Score=41.44  Aligned_cols=74  Identities=19%  Similarity=0.234  Sum_probs=54.1

Q ss_pred             CCCCCEEEEEEEEEecc--eEEEEEeeeccccccCcceeEEecccccccccc--ccccccCCCCCCEEEEEEEEeCCC-c
Q 029155           74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATEID--KVDMHLSFRPGDIVRASVLSLGDA-R  148 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~--~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d--~~~~~~~~~~GDiV~AkV~s~~~~-~  148 (198)
                      -.+|++-.|+|++|.+.  .|+|||        ...-.|+||.+++.+....  ...++..++.|+.+...|..-..+ .
T Consensus        35 ~~~gniy~grv~~i~p~~~aafvdi--------g~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~K  106 (487)
T COG1530          35 QIVGNIYKGRVTRVLPSLEAAFVDI--------GLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVKEPRGTK  106 (487)
T ss_pred             eeecCceEEEecccCccchhheeec--------cCCccceEEecccchhhhhcccccceeeecCCceEEEEEEeecCccc
Confidence            46899999999999876  599999        5567899999998752111  113567999999999999986432 2


Q ss_pred             cEEEEEe
Q 029155          149 AYFLSTA  155 (198)
Q Consensus       149 ~~~LSt~  155 (198)
                      ...||+.
T Consensus       107 ga~lT~~  113 (487)
T COG1530         107 GARLTTD  113 (487)
T ss_pred             cccceeE
Confidence            2444443

>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]

Probab=87.30  E-value=0.64  Score=36.25  Aligned_cols=34  Identities=18%  Similarity=0.335  Sum_probs=26.7

Q ss_pred             CeeeEEec-CCCceeEEccCCeEEeCCCCCE---EeeeeCC
Q 029155          159 LGVVSAES-TAGGTMVPISWTEMQCPLTGQT---EQRKVAK  195 (198)
Q Consensus       159 lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~---e~RKva~  195 (198)
                      ..-+-++| +||+...|-.   ..||.||..   |...+|.
T Consensus        25 ~kl~g~kC~~CG~v~~PPr---~~Cp~C~~~~~~E~vels~   62 (140)
T COG1545          25 GKLLGTKCKKCGRVYFPPR---AYCPKCGSETELEWVELSG   62 (140)
T ss_pred             CcEEEEEcCCCCeEEcCCc---ccCCCCCCCCceEEEEeCC
Confidence            34455679 8999999954   889999998   7777765

>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins

Probab=87.22  E-value=0.45  Score=32.05  Aligned_cols=28  Identities=21%  Similarity=0.236  Sum_probs=22.7

Q ss_pred             ec-CCCceeEE-ccCCeEEeCCCCCEEeee
Q 029155          165 ES-TAGGTMVP-ISWTEMQCPLTGQTEQRK  192 (198)
Q Consensus       165 ~~-~~g~~m~~-~~~~~~~c~~cg~~e~RK  192 (198)
                      .| .||..+.. .++..+.||+||....|=
T Consensus        30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD   59 (69)
T PF07282_consen   30 TCPRCGHRNKKRRSGRVFTCPNCGFEMDRD   59 (69)
T ss_pred             CccCcccccccccccceEEcCCCCCEECcH
Confidence            36 79998876 577899999999987763

More information about these proteins can be found at Protein of the Month: Transposase [].

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=87.03  E-value=0.32  Score=36.42  Aligned_cols=37  Identities=22%  Similarity=0.419  Sum_probs=28.8

Q ss_pred             ecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEEeee
Q 029155          155 AKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTEQRK  192 (198)
Q Consensus       155 ~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e~RK  192 (198)
                      ..++||. .-.| .||...|=...+-..||.||.....-
T Consensus         2 akpelGt-KR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~   39 (108)
T PF09538_consen    2 AKPELGT-KRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE   39 (108)
T ss_pred             CccccCC-cccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence            4567776 3468 89999888888899999999876543

The function of members of this family is unknown.

>PRK07218 replication factor A; Provisional

Probab=86.32  E-value=2.8  Score=38.57  Aligned_cols=41  Identities=17%  Similarity=0.249  Sum_probs=30.6

Q ss_pred             EEEEEEEEeCCCccEEEEEecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEEeeee
Q 029155          136 IVRASVLSLGDARAYFLSTAKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTEQRKV  193 (198)
Q Consensus       136 iV~AkV~s~~~~~~~~LSt~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKv  193 (198)
                      .|.+.|+++..+.            -+..+| .|+..|..     -+||.||..|..+.
T Consensus       282 ev~G~Iv~i~~gs------------gli~rCP~C~r~v~~-----~~C~~hG~ve~~~d  323 (423)
T PRK07218        282 ELVGNIISVRDGS------------GLIERCPECGRVIQK-----GQCRSHGAVEGEDD  323 (423)
T ss_pred             EEEEEEEEeccCC------------cceecCcCccccccC-----CcCCCCCCcCCeee
Confidence            4788888886542            236699 99999954     47999999987653

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=86.31  E-value=0.91  Score=29.24  Aligned_cols=28  Identities=21%  Similarity=0.245  Sum_probs=22.3

Q ss_pred             EEec-CCCc-eeEEccCCeEEeCCCCCEEee
Q 029155          163 SAES-TAGG-TMVPISWTEMQCPLTGQTEQR  191 (198)
Q Consensus       163 ~a~~-~~g~-~m~~~~~~~~~c~~cg~~e~R  191 (198)
                      +..| +||. .|.+-. +.+.|..||.++-.
T Consensus        20 ~~fCP~Cg~~~m~~~~-~r~~C~~Cgyt~~~   49 (50)
T PRK00432         20 NKFCPRCGSGFMAEHL-DRWHCGKCGYTEFK   49 (50)
T ss_pred             cCcCcCCCcchheccC-CcEECCCcCCEEec
Confidence            4467 8999 887765 78999999998754

>COG1656 Uncharacterized conserved protein [Function unknown]

Probab=84.69  E-value=0.33  Score=38.97  Aligned_cols=28  Identities=21%  Similarity=0.442  Sum_probs=22.9

Q ss_pred             eeEEec-CCCceeEEccCCeEE----------------eCCCCCE
Q 029155          161 VVSAES-TAGGTMVPISWTEMQ----------------CPLTGQT  188 (198)
Q Consensus       161 vv~a~~-~~g~~m~~~~~~~~~----------------c~~cg~~  188 (198)
                      --+++| .|++++.+++-.+.+                ||+||+.
T Consensus        95 ~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki  139 (165)
T COG1656          95 PEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI  139 (165)
T ss_pred             cccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence            348899 999999999866644                9999985

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=84.62  E-value=0.88  Score=28.15  Aligned_cols=24  Identities=13%  Similarity=0.228  Sum_probs=18.6

Q ss_pred             EEec-CCCceeEEccCCeEEeCCCC
Q 029155          163 SAES-TAGGTMVPISWTEMQCPLTG  186 (198)
Q Consensus       163 ~a~~-~~g~~m~~~~~~~~~c~~cg  186 (198)
                      ...| .||.||.+.......|+.|+
T Consensus        17 ~~~Cp~C~~PL~~~k~g~~~Cv~C~   41 (41)
T PF06677_consen   17 DEHCPDCGTPLMRDKDGKIYCVSCG   41 (41)
T ss_pred             cCccCCCCCeeEEecCCCEECCCCC
Confidence            3467 89999987444689999996

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=83.40  E-value=0.63  Score=27.24  Aligned_cols=28  Identities=18%  Similarity=0.246  Sum_probs=18.9

Q ss_pred             ec-CCCceeEEccCCeEEeCCCCCEEeee
Q 029155          165 ES-TAGGTMVPISWTEMQCPLTGQTEQRK  192 (198)
Q Consensus       165 ~~-~~g~~m~~~~~~~~~c~~cg~~e~RK  192 (198)
                      .| +||....-...+.++|++||.+-.-|
T Consensus         2 ~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   30 (32)
T PF03604_consen    2 ICGECGAEVELKPGDPIRCPECGHRILYK   30 (32)
T ss_dssp             BESSSSSSE-BSTSSTSSBSSSS-SEEBE
T ss_pred             CCCcCCCeeEcCCCCcEECCcCCCeEEEe
Confidence            46 78888764456789999999865433

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function

Probab=82.96  E-value=0.74  Score=35.95  Aligned_cols=32  Identities=25%  Similarity=0.468  Sum_probs=24.9

Q ss_pred             CCeeeEEec-CCCceeEEccCCe----------------EEeCCCCCEE
Q 029155          158 DLGVVSAES-TAGGTMVPISWTE----------------MQCPLTGQTE  189 (198)
Q Consensus       158 ~lGvv~a~~-~~g~~m~~~~~~~----------------~~c~~cg~~e  189 (198)
                      ++..++++| .|.+++.+++..+                .+||.||++.
T Consensus        86 ~~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy  134 (147)
T PF01927_consen   86 RLDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY  134 (147)
T ss_pred             ccCCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence            345678999 8999998887553                4899999864

The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.

>TIGR02062 RNase_B exoribonuclease II

Probab=82.89  E-value=7.2  Score=37.73  Aligned_cols=65  Identities=9%  Similarity=0.168  Sum_probs=48.1

Q ss_pred             CCCC--EEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccc---c---ccc--cccc--cCCCCCCEEEEEEE
Q 029155           75 EPGS--VVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT---E---IDK--VDMH--LSFRPGDIVRASVL  142 (198)
Q Consensus        75 ~vGD--iViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~---~---~d~--~~~~--~~~~~GDiV~AkV~  142 (198)
                      ++|+  .-.|.|+++...+.+|++.       ...+.|++|.+.+...   +   .+.  ..+.  ..|+.||-|..+|.
T Consensus       554 ~~g~~~~f~g~I~~v~~~g~~v~l~-------~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~  626 (639)
T TIGR02062       554 KAAKNTRFAAEIVDISRGGMRVRLL-------ENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLT  626 (639)
T ss_pred             ccCCCcEEEEEEEeeeCCcEEEEEe-------cCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEE
Confidence            4554  8899999999999999994       4568999998887531   1   011  1221  25999999999999


Q ss_pred             EeCC
Q 029155          143 SLGD  146 (198)
Q Consensus       143 s~~~  146 (198)
                      +++.
T Consensus       627 ~vd~  630 (639)
T TIGR02062       627 EVRM  630 (639)
T ss_pred             Eecc
Confidence            9973

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.

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

Probab=82.43  E-value=7.4  Score=29.65  Aligned_cols=70  Identities=17%  Similarity=0.150  Sum_probs=38.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccC----cceeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVRE----KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSL  144 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~----~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~  144 (198)
                      |-+|+++.|+|.+-+..+..|.+...++--+..    .-...=+.+++=-...+ .+-.-+|..|+.|+=||.+.
T Consensus         1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~-~~~~l~~d~ge~IRFRV~~~   74 (122)
T PF08292_consen    1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYD-EEQELFFDIGEEIRFRVESE   74 (122)
T ss_dssp             --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEES-SSEEEEE-TT-EEEEEEEEE
T ss_pred             CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECC-CCceeEccCCCEEEEEEeEE
Confidence            568999999999999999999996555421110    00011011111001110 13345679999999999985

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

>PF01959 DHQS: 3-dehydroquinate synthase (EC 4

Probab=82.42  E-value=15  Score=33.07  Aligned_cols=96  Identities=18%  Similarity=0.371  Sum_probs=65.4

Q ss_pred             EEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEec
Q 029155           10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMT   89 (198)
Q Consensus        10 iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~   89 (198)
                      +.+||+.=...+|...|.-+..-+..|.-+..++|++++.        +++.+.|+-.    +   -|    -++.-+..
T Consensus       246 v~~pg~kT~YLSEL~sG~~VlvVd~~G~tR~~~VGRvKIE--------~RPLllIeA~----~---~g----~~~svilQ  306 (354)
T PF01959_consen  246 VLMPGGKTRYLSELRSGDEVLVVDADGRTRTAIVGRVKIE--------RRPLLLIEAE----A---DG----KRISVILQ  306 (354)
T ss_pred             EEcCCCceeehhhhcCCCEEEEEeCCCCEEEEEeeEEEEe--------ecceEEEEEE----e---CC----eEEEEEEe
Confidence            4678888777788889988776654455999999999994        4677777642    1   12    23444567


Q ss_pred             ceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC
Q 029155           90 RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD  146 (198)
Q Consensus        90 ~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~  146 (198)
                      +-|.|.+...++.+++                      --.+++||.|.+.+..-+.
T Consensus       307 naetIRlv~p~G~~vs----------------------Vt~Lk~GD~vL~~~~~~~R  341 (354)
T PF01959_consen  307 NAETIRLVGPDGEPVS----------------------VTELKPGDEVLVYLEEAGR  341 (354)
T ss_pred             cCcEEEEECCCCCEee----------------------eeecCCCCEEEEEecCCCc
Confidence            8888888543322111                      1236899999999987543

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

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=82.28  E-value=1.1  Score=26.61  Aligned_cols=24  Identities=25%  Similarity=0.501  Sum_probs=13.0

Q ss_pred             ec-CCCceeE---E--ccCCeEEeCCCCCE
Q 029155          165 ES-TAGGTMV---P--ISWTEMQCPLTGQT  188 (198)
Q Consensus       165 ~~-~~g~~m~---~--~~~~~~~c~~cg~~  188 (198)
                      .| .||++|.   |  -+..-+.|+.||++
T Consensus         2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I   31 (34)
T PF14803_consen    2 FCPQCGGPLERRIPEGDDRERLVCPACGFI   31 (34)
T ss_dssp             B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred             ccccccChhhhhcCCCCCccceECCCCCCE
Confidence            46 7898873   4  23457999999986

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=82.28  E-value=1.1  Score=33.79  Aligned_cols=32  Identities=16%  Similarity=0.120  Sum_probs=22.1

Q ss_pred             eEEec-CCCceeEEccCCeEEeCCCCCEEeeee
Q 029155          162 VSAES-TAGGTMVPISWTEMQCPLTGQTEQRKV  193 (198)
Q Consensus       162 v~a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKv  193 (198)
                      ..++| .||...-...+..+.||.||....+=+
T Consensus        69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~  101 (114)
T PRK03681         69 AECWCETCQQYVTLLTQRVRRCPQCHGDMLRIV  101 (114)
T ss_pred             cEEEcccCCCeeecCCccCCcCcCcCCCCcEEc
Confidence            37889 799765444555588999997654433

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=81.63  E-value=0.81  Score=34.56  Aligned_cols=30  Identities=13%  Similarity=0.083  Sum_probs=21.4

Q ss_pred             eEEec-CCCceeEEccCCeEEeCCCCCEEee
Q 029155          162 VSAES-TAGGTMVPISWTEMQCPLTGQTEQR  191 (198)
Q Consensus       162 v~a~~-~~g~~m~~~~~~~~~c~~cg~~e~R  191 (198)
                      ..++| .||...-+..+..+.||.||....+
T Consensus        70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~  100 (117)
T PRK00564         70 VELECKDCSHVFKPNALDYGVCEKCHSKNVI  100 (117)
T ss_pred             CEEEhhhCCCccccCCccCCcCcCCCCCceE
Confidence            37889 7997765544555679999986544

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=81.15  E-value=0.75  Score=35.40  Aligned_cols=36  Identities=25%  Similarity=0.350  Sum_probs=28.2

Q ss_pred             ecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEEee
Q 029155          155 AKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTEQR  191 (198)
Q Consensus       155 ~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e~R  191 (198)
                      ..++||. .-.| .||...+=....-..||.||.....
T Consensus         2 ~k~elGt-Kr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~   38 (129)
T TIGR02300         2 AKPDLGT-KRICPNTGSKFYDLNRRPAVSPYTGEQFPP   38 (129)
T ss_pred             CchhhCc-cccCCCcCccccccCCCCccCCCcCCccCc
Confidence            3456775 3467 9999999888889999999987643

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.

>PRK02290 3-dehydroquinate synthase; Provisional

Probab=81.09  E-value=17  Score=32.66  Aligned_cols=95  Identities=17%  Similarity=0.362  Sum_probs=63.5

Q ss_pred             EEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEec
Q 029155           10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMT   89 (198)
Q Consensus        10 iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~   89 (198)
                      +.+||+.=...+|...|.-+-.-+..|.-+..++|++++.        .++.+-|+-.    +   -|    -++.-+..
T Consensus       236 v~~pgg~T~YLsEL~sG~eVlvVd~~G~tR~~~VGRvKIE--------~RPL~lIeAe----~---~g----~~~~viLQ  296 (344)
T PRK02290        236 VRVPGDKTRYLSELRSGDEVLVVDADGNTREAIVGRVKIE--------KRPLLLIEAE----Y---GG----KRIRTILQ  296 (344)
T ss_pred             EEcCCCcchhhHhhcCCCEEEEEeCCCCEEEEEeeEEEEe--------eccEEEEEEE----e---CC----eEEEEEEe
Confidence            4678998888788888988765544444999999999994        4677777642    1   13    23334467


Q ss_pred             ceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC
Q 029155           90 RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG  145 (198)
Q Consensus        90 ~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~  145 (198)
                      +-|.+.+...++++        +.+              -.+++||.|.+++...+
T Consensus       297 naetIrlv~~dG~~--------vsV--------------t~Lk~GD~VL~~~~~~~  330 (344)
T PRK02290        297 NAETIRLVTPDGKP--------VSV--------------VDLKPGDEVLGYLEEAA  330 (344)
T ss_pred             cCcEEEEECCCCCE--------eee--------------eecCCCCEEEEEecCCc
Confidence            77888885332221        111              23689999999998644

>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]

Probab=80.98  E-value=0.94  Score=39.38  Aligned_cols=25  Identities=20%  Similarity=0.264  Sum_probs=19.9

Q ss_pred             ec-CCCceeEEcc-CCeEEeCCCCCEE
Q 029155          165 ES-TAGGTMVPIS-WTEMQCPLTGQTE  189 (198)
Q Consensus       165 ~~-~~g~~m~~~~-~~~~~c~~cg~~e  189 (198)
                      .| +||++|.+.. .-.++|++||+..
T Consensus       113 FCg~CG~~~~~~~~g~~~~C~~cg~~~  139 (279)
T COG2816         113 FCGRCGTKTYPREGGWARVCPKCGHEH  139 (279)
T ss_pred             CCCCCCCcCccccCceeeeCCCCCCcc
Confidence            46 7999998874 2379999999864

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=80.69  E-value=2.5  Score=37.44  Aligned_cols=101  Identities=13%  Similarity=0.173  Sum_probs=58.5

Q ss_pred             CCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEE
Q 029155           14 GEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMAS   93 (198)
Q Consensus        14 Gd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~~~~~   93 (198)
                      ||.+-..-.-+.-.|.|++=+.   |--+=|++.+++           ++-.......-..++||.|.++|.+|....-.
T Consensus        18 GdvV~g~V~~I~d~GafV~L~E---Y~gvEGlIhiSE-----------lS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~   83 (319)
T PTZ00248         18 DDLVMVKVVRITEMGAYVSLLE---YDDIEGMILMSE-----------LSKRRIRSINKLIRVGRHEVVVVLRVDKEKGY   83 (319)
T ss_pred             CCEEEEEEEEEeCCeEEEEecC---CCCcEEEEEHHH-----------hcccccCCHHHhcCCCCEEEEEEEEEeCCCCE
Confidence            6655332223445567755321   123456676642           11122223334579999999999999776555


Q ss_pred             EEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC
Q 029155           94 ADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD  146 (198)
Q Consensus        94 V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~  146 (198)
                      +++        +        ..++....  ...+.+.|..|++|.++|..+-+
T Consensus        84 IdL--------S--------~K~v~~~p--w~~~~e~~~~g~~v~~~V~~ia~  118 (319)
T PTZ00248         84 IDL--------S--------KKRVSPED--IEACEEKFSKSKKVHSIMRHIAQ  118 (319)
T ss_pred             EEE--------E--------eeecccch--HHHHHHhCcCCCEEEEEEEEchh
Confidence            555        1        11222221  12556889999999999999843

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=80.03  E-value=0.99  Score=29.65  Aligned_cols=30  Identities=17%  Similarity=0.256  Sum_probs=24.5

Q ss_pred             Eec-CCCceeEEccCCeEEeCCCCCEEeeeeC
Q 029155          164 AES-TAGGTMVPISWTEMQCPLTGQTEQRKVA  194 (198)
Q Consensus       164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva  194 (198)
                      .+| .||.++.+.+ +.+.||.||...-|-..
T Consensus         6 ~~C~~Cg~~~~~~d-DiVvCp~CgapyHR~C~   36 (54)
T PF14446_consen    6 CKCPVCGKKFKDGD-DIVVCPECGAPYHRDCW   36 (54)
T ss_pred             ccChhhCCcccCCC-CEEECCCCCCcccHHHH
Confidence            467 7999998765 79999999998877544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	198
2nn6_I	209	Structure Of The Human Rna Exosome Composed Of Rrp4		8e-37
4ifd_I	301	Crystal Structure Of An 11-subunit Eukaryotic Exoso		8e-25

>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 =  149 bits (377), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 84/185 (45%), Positives = 113/185 (61%), Gaps = 7/185 (3%)
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 PGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQR 191
           PGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G  MVPISW EMQCP T   E R
Sbjct: 138 PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTKEFR 197
Query: 192 KVAKV 196
           KVA+V
Sbjct: 198 KVARV 202

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

Iteration: 1
 Score =  109 bits (273), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 66/179 (36%), Positives = 91/179 (50%), Gaps = 36/179 (20%)
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 ASVLSLGDARAYFLSTAKNDLGVVSAEST--AGGTMVPISWTEMQCPLTGQTEQRKVAK 195
           A VLSLGD   Y+L+TA+NDLGVV A +   AGG M    W  M  P+TG TE+RK AK
Sbjct: 241 AQVLSLGDGTNYYLTTARNDLGVVFARAANGAGGLMYATDWQMMTSPVTGATEKRKCAK 299

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	198
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	7e-61
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	2e-46
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	5e-24
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	1e-21
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	5e-15
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	3e-13

>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 =  187 bits (477), Expect = 7e-61
 Identities = 83/188 (44%), Positives = 111/188 (59%), Gaps = 7/188 (3%)

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 SFRPGDIVRASVLSLGDAR-AYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQT 188
           SFRPGDIV A V+SLGDA+  Y L+TA+N+LGVV A S +G  MVPISW EMQCP T   
Sbjct: 135 SFRPGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTK 194

Query: 189 EQRKVAKV 196
           E RKVA+V
Sbjct: 195 EFRKVARV 202

>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 =  149 bits (378), Expect = 2e-46
 Identities = 42/190 (22%), Positives = 76/190 (40%), Gaps = 20/190 (10%)

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 DMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLT 185
                    DI++A V+         LST + ++GV+ A  +   T +      ++CP  
Sbjct: 109 SEA--VGYLDILKARVIG----DNLRLSTKEEEMGVLRALCSNCKTEMVREGDILKCPEC 162

Query: 186 GQTEQRKVAK 195
           G+ E+RK++ 
Sbjct: 163 GRVEKRKIST 172

>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 = 95.2 bits (236), Expect = 5e-24
 Identities = 33/178 (18%), Positives = 67/178 (37%), Gaps = 17/178 (9%)

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 KVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQ 181
           ++ M    + GD++ A V ++    A  L T     G +       G +V +S + ++
Sbjct: 143 ELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLG-----QGVLVQVSPSLVK 195

>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 = 87.9 bits (217), Expect = 1e-21
 Identities = 33/162 (20%), Positives = 55/162 (33%), Gaps = 19/162 (11%)

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 IDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS 163
               D+      GD V A + +   +    LS    DLG VS
Sbjct: 113 NVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVS 154

>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 = 69.7 bits (170), Expect = 5e-15
 Identities = 37/160 (23%), Positives = 57/160 (35%), Gaps = 21/160 (13%)

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 IDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGV 161
               DM    + GD ++A V++    R+  L+     LG 
Sbjct: 106 PAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGEGLGR 145

>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 = 64.7 bits (157), Expect = 3e-13
 Identities = 36/167 (21%), Positives = 56/167 (33%), Gaps = 27/167 (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 SFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPIS 176
               GD + A VL++       L+        +       G +V I+
Sbjct: 102 VLDIGDAIIAKVLNIDPKMKVTLTMKDRICRPIR-----FGRIVAIN 143

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	198
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	100.0
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	100.0
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	100.0
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	99.98
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	99.97
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	99.97
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	99.96
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	99.73
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.26
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.25
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.22
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.2
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.2
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.2
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.18
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.17
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.08
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.05
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.04
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	98.96
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.96
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.94
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.87
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.77
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.69
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	98.62
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.59
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.58
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.58
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	98.55
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.39
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.37
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.36
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.29
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	98.23
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.05
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	98.0
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.82
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.68
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.59
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	97.43
2bh8_A	101	1B11; transcription, molecular evolution, unique a	96.61
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	96.56
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	95.84
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	95.75
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	95.3
3v2d_0	85	50S ribosomal protein L27; ribosome associated inh	93.31
3r8s_W	76	50S ribosomal protein L27; protein biosynthesis, R	91.83
2zjr_T	91	50S ribosomal protein L27; ribosome, large ribosom	91.33
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	90.74
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	86.16
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	85.33
2ftc_O	69	L27MT, MRP-L27, mitochondrial 39S ribosomal protei	83.52
1y71_A	130	Kinase-associated protein B; structural genomics,	82.93
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	81.73

>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=8.8e-54  Score=353.45  Aligned_cols=186  Identities=45%  Similarity=0.703  Sum_probs=164.5

Q ss_pred             cCCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 029155            6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT   85 (198)
Q Consensus         6 ~~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~   85 (198)
                      +++++|+|||.|+..++|++|+|||.++|+  ||||++|.+....    .++.+++|+|.|++..+|.|++||+|+|+|+
T Consensus        17 ~~~~iV~PGd~l~~~~~~~~G~Gty~~~g~--I~Asv~G~v~~~~----~~~~~~vi~V~p~~~~~y~p~vGDvV~G~V~   90 (209)
T 2nn6_I           17 PPVRYCIPGERLCNLEEGSPGSGTYTRHGY--IFSSLAGCLMKSS----ENGALPVVSVVRETESQLLPDVGAIVTCKVS   90 (209)
T ss_dssp             ---CCCCTTCEEEETTTCCCSSSCEEETTE--EECCSCSCBCCCB----CTTSSBC-CBCCSCCCCCCCCTTCEEEEEEE
T ss_pred             CCCcEEcCCCCCCCCCCeeecCCEEEECCE--EEEEEEEEEEEec----cCCcccEEEEecCCCCcCCCCCCCEEEEEEE
Confidence            457899999999998899999999999999  9999999987631    1123467899998766799999999999999


Q ss_pred             EEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCc-cEEEEEecCCCeeeEE
Q 029155           86 KVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDAR-AYFLSTAKNDLGVVSA  164 (198)
Q Consensus        86 ~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~-~~~LSt~~~~lGvv~a  164 (198)
                      ++++++|+|+|.++++++|..+|+|+||++|+++++.++.+|+++|++||+|+|+|+++++.+ .+.|||++++||||+|
T Consensus        91 ~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i~LS~k~~~lGVv~A  170 (209)
T 2nn6_I           91 SINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAENELGVVVA  170 (209)
T ss_dssp             EECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEEECCSSSCEECCC
T ss_pred             EEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeEEEEEecCCCcEEEE
Confidence            999999999999999999999999999999999999888899999999999999999998754 6999999999999999


Q ss_pred             ecCCCceeEEccCCeEEeCCCCCEEeeeeCCCC
Q 029155          165 ESTAGGTMVPISWTEMQCPLTGQTEQRKVAKVG  197 (198)
Q Consensus       165 ~~~~g~~m~~~~~~~~~c~~cg~~e~RKva~~~  197 (198)
                      +|..|++|+|.+|++|+||+||++|+||+|++.
T Consensus       171 ~c~~g~~m~~~~~~~m~cp~cg~~E~RKva~~~  203 (209)
T 2nn6_I          171 HSESGIQMVPISWCEMQCPKTHTKEFRKVARVQ  203 (209)
T ss_dssp             BCSSSCBCEEEETTEEECTTTTCCBCCCC----
T ss_pred             EcCCCCEEEEccCCEEECCCCCCEEeeccCCCC
Confidence            996699999999999999999999999999974

>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=2.1e-51  Score=331.88  Aligned_cols=170  Identities=24%  Similarity=0.390  Sum_probs=159.7

Q ss_pred             CcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEE
Q 029155            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV   87 (198)
Q Consensus         8 ~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v   87 (198)
                      |++|+|||.|+.+++|.+|+|||.++++  ||||++|.+++.         ++.++|+|++..+|.|+ ||+|+|+|++|
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 MRFVMPGDRIGSAEEYVKGEGVYEEGGE--LFAAVAGKLIIK---------DRVAKVESISPIPEIVK-GDVVLGRVVDL   68 (179)
T ss_dssp             CCEECTTCEEEETTTSEECTTEEEETTE--EEESSSEEEEEE---------TTEEEEEESSCCCCCCT-TCEEEEEEEEE
T ss_pred             CeEEcCCCCCCCCCCEeccCCEEEeCCE--EEEEEEEEEEEe---------CCEEEEEECCCCcccCC-CCEEEEEEEEE
Confidence            3799999999998999999999999988  999999999983         47999999877789999 99999999999


Q ss_pred             ecceEEEEEeee--ccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCeeeEEe
Q 029155           88 MTRMASADIMCV--GAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAE  165 (198)
Q Consensus        88 ~~~~~~V~I~~v--~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a~  165 (198)
                      .+++|+|+|.++  +++++..+++|+||+||+++.+.+  +|+++|++||+|+|+|++    +++.|||++++||||+|+
T Consensus        69 ~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~--~~~~~~~~GD~V~akVi~----~~i~LS~k~~~lGvv~a~  142 (179)
T 3m7n_A           69 RNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVK--EISEAVGYLDILKARVIG----DNLRLSTKEEEMGVLRAL  142 (179)
T ss_dssp             CSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCS--SGGGTCCTTCEEEEEEEE----TTTEEECCSTTCEEEECB
T ss_pred             eCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhh--CHhhcCCCCCEEEEEEEC----CeEEEEEecCCCCEEEec
Confidence            999999999988  557788899999999999988776  999999999999999998    579999999999999999


Q ss_pred             c-CCCceeEEccCCeEEeCCCCCEEeeeeCCC
Q 029155          166 S-TAGGTMVPISWTEMQCPLTGQTEQRKVAKV  196 (198)
Q Consensus       166 ~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~~  196 (198)
                      | +||++|+|.+ ++|+||+||++|+||+|+.
T Consensus       143 ~~~~g~~m~~~~-~~~~cp~~g~~e~RKva~~  173 (179)
T 3m7n_A          143 CSNCKTEMVREG-DILKCPECGRVEKRKISTD  173 (179)
T ss_dssp             CTTTCCBCEECS-SSEECSSSCCEECCCBCTT
T ss_pred             ccccCCceEECC-CEEECCCCCCEEEEecccc
Confidence            9 8999999999 9999999999999999985

>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=100.00  E-value=4.2e-36  Score=260.08  Aligned_cols=166  Identities=20%  Similarity=0.298  Sum_probs=133.1

Q ss_pred             ccCCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 029155            5 EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV   84 (198)
Q Consensus         5 ~~~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V   84 (198)
                      .+++++|+|||.|+..++|.+|+|||.++|+  ||||++|.+...         ++.++|.|.+ .+|+|++||+|+|+|
T Consensus        36 ~~~~~iVlPGd~L~~~~~~~~G~Gty~~~g~--I~Asv~G~v~~~---------~~~vsV~p~~-~rY~P~vGDvViG~V  103 (308)
T 2nn6_H           36 DTKKHLVVPGDTITTDTGFMRGHGTYMGEEK--LIASVAGSVERV---------NKLICVKALK-TRYIGEVGDIVVGRI  103 (308)
T ss_dssp             ----CBCCTTCBCCCCTTCCBCTTEEECSSS--EEECSSEEEEEE---------TTEEEEEESS-CCCCCCSSBCCCEEE
T ss_pred             CCCCcEEeCCCCCCCCCCEeecCCeEEECCE--EEEEEEEEEEec---------CCEEEEeeCC-CccCCCCCCEEEEEE
Confidence            4567899999999988999999999999999  999999999873         4689999986 579999999999999


Q ss_pred             EEEecceEEEEEeeeccccc--cC-cc-eeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCe
Q 029155           85 TKVMTRMASADIMCVGAKSV--RE-KF-SGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLG  160 (198)
Q Consensus        85 ~~v~~~~~~V~I~~v~~~~l--~~-~~-~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lG  160 (198)
                      +++.+++|+|+|.+..+..+  +. .| .|++|.++.    .|..+|+++|++||+|+|||+++++...+.|||++++||
T Consensus       104 t~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~----~D~~~m~~~l~vGDlV~ArVisv~~~~~i~LStr~~~LG  179 (308)
T 2nn6_H          104 TEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSA----EDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYG  179 (308)
T ss_dssp             EEEETTEEEEECSSSSCEEEESSCCC-----------------CHHHHHHSCSSCEECCEEEEEETTTEEEEECCSSTTC
T ss_pred             EEEeCceEEEEECCCcCCceechhhccccceeecccc----hhhhhhhccCCCCCEEEEEEEEcCCCCCEEEEecCcCCc
Confidence            99999999999965433221  11 23 244444432    234589999999999999999998777899999999999


Q ss_pred             eeEEec--CCCceeEEccCCeEEeCCCC
Q 029155          161 VVSAES--TAGGTMVPISWTEMQCPLTG  186 (198)
Q Consensus       161 vv~a~~--~~g~~m~~~~~~~~~c~~cg  186 (198)
                      ++.+.|  .+...|+|..|++|+|+.||
T Consensus       180 kL~~G~v~~vs~~lv~r~~~~l~~l~~g  207 (308)
T 2nn6_H          180 KLGQGVLVQVSPSLVKRQKTHFHDLPCG  207 (308)
T ss_dssp             EECSSCEEECCTTSCCCSTTCSCCCBTT
T ss_pred             ccCCeEEEEEChhheechhheEecCCCC
Confidence            999988  45778999999999999998

>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=99.98  E-value=7.4e-32  Score=227.89  Aligned_cols=141  Identities=21%  Similarity=0.259  Sum_probs=127.0

Q ss_pred             cCCcEEecCCccCCCCCeeeCC--CEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEE
Q 029155            6 EEMVLVTPGEVLGKATEVKAGK--GAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIAR   83 (198)
Q Consensus         6 ~~~~iV~PGd~l~~~~e~~~G~--Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~   83 (198)
                      .++++|+|||.|+. ++|.+|+  |||.++++  |||+++|.+...         ++.++|.|+...+|.|++||+|+|+
T Consensus        14 ~~~~iV~PGd~l~~-~~~~~G~~~Gty~~~g~--i~as~~G~v~~~---------~~~v~V~p~~~~~y~p~~GDiV~G~   81 (251)
T 2je6_I           14 QPRSIVVPGELLAE-GEFQIPWSPYILKINSK--YYSTVVGLFDVK---------DTQFEVIPLEGSFYYPKINDIVIGL   81 (251)
T ss_dssp             CSSCEECTTCEEEE-ECCCCCCCTTEEEETTE--EEECSSEEEEEE---------TTEEEEEESCCSCCCCCTTCEEEEE
T ss_pred             CCCcEEcCCCCCcc-CCeeeCCCCCEEEECCE--EEEEEEEEEEEe---------CCEEEEEECCCcccCCCCCCEEEEE
Confidence            35789999999996 6799999  99999999  999999999984         3589999998768999999999999


Q ss_pred             EEEEecceEEEEEeeeccccccCcceeEEeccccccccccc-cccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCe--
Q 029155           84 VTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDK-VDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLG--  160 (198)
Q Consensus        84 V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~-~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lG--  160 (198)
                      |+++.+++|+|+|        ..+++|+||+++++..+.+. .+|+++|++||+|+|+|+++++.+.+.||+++++||  
T Consensus        82 V~~v~~~ga~VdI--------~~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~~~lG~L  153 (251)
T 2je6_I           82 VEDVEIYGWVVDI--------KAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRV  153 (251)
T ss_dssp             EEEECSSEEEEEC--------SSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCSTTCEEC
T ss_pred             EEEEeCceEEEEc--------CCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECCCCcEEEEEccccCCcc
Confidence            9999999999999        67899999999998655533 699999999999999999998777899999999999  


Q ss_pred             ---eeEEec
Q 029155          161 ---VVSAES  166 (198)
Q Consensus       161 ---vv~a~~  166 (198)
                         ++++.|
T Consensus       154 ~~G~v~~vs  162 (251)
T 2je6_I          154 SNGIVIDIM  162 (251)
T ss_dssp             CSSCEEECC
T ss_pred             cCCEEEEEC
Confidence               777766

>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=99.97  E-value=2e-31  Score=222.51  Aligned_cols=133  Identities=23%  Similarity=0.299  Sum_probs=119.4

Q ss_pred             CcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEE
Q 029155            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV   87 (198)
Q Consensus         8 ~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v   87 (198)
                      +++|+|||.|+. ++|.+|+|||.++++  ||||++|.+...         ++.++|.|.+ .+|.|++||+|+|+|+++
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-NPRAAGYGTYVEGGK--VYAKIIGLFDQT---------ETHVRVIPLK-GRYTPSVGDVVIGIIREV   68 (229)
T ss_dssp             CCEECTTCEEES-CTTSBCTTEEEETTE--EEECSSEEEEEC---------SSCEEEEECS-SSCCCCTTCEEEEEEEEE
T ss_pred             CCEEcCCCCccc-CCeEecCCEEEeCCE--EEEEEEEEEEEe---------CCEEEEEeCC-CcccCCCCCEEEEEEEEE
Confidence            579999999995 679999999999999  999999999983         2479999986 469999999999999999


Q ss_pred             ecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCeee
Q 029155           88 MTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVV  162 (198)
Q Consensus        88 ~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv  162 (198)
                      .+++|+|+|        ..+++|+||+++++. +.+..+|+++|++||+|+|+|+++++.+.+.|||++++||++
T Consensus        69 ~~~~a~V~I--------~~~~~g~l~isev~~-~~~~~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~~~lG~L  134 (229)
T 2ba0_A           69 AANGWAVDI--------YSPYQAFLPVSENPE-MKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRICRPI  134 (229)
T ss_dssp             CSSEEEEEC--------SSSSCEEEEGGGCTT-CCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCSSSCEEE
T ss_pred             eCCeEEEEe--------CCCeEEEEEHHHccc-cccccchhcccCCCCEEEEEEEEECCCCcEEEEEccccCCcc
Confidence            999999999        678999999999983 223458999999999999999999877889999999999954

>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=99.97  E-value=8.1e-31  Score=219.58  Aligned_cols=136  Identities=24%  Similarity=0.265  Sum_probs=76.5

Q ss_pred             CcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEE
Q 029155            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV   87 (198)
Q Consensus         8 ~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v   87 (198)
                      +++|+|||.|+. ++|.+|+|||.++++  |||+++|.+...       +++..++|+|.+ .+|.|++||+|+|+|+++
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-EVEASPPYVIDYKGV--KRATVVGLLREK-------GDGGGRAFVKLK-EIYVPQAGDVVIGLIQSV   77 (235)
T ss_dssp             --------------------------------------------------------------CCCCCCTTCCEEEEEEEE
T ss_pred             CcEEeCCCCccc-CceEcCCCEEEECCE--EEEEEeEEEEEe-------CCccEEEEEeCC-CccCCCCCCEEEEEEEEE
Confidence            479999999996 669999999999988  999999998873       233579999986 469999999999999999


Q ss_pred             ecceEEEEEeeeccccccCcceeEEecccccc--ccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCeee
Q 029155           88 MTRMASADIMCVGAKSVREKFSGIIRQQDVRA--TEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVV  162 (198)
Q Consensus        88 ~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~--~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv  162 (198)
                      .+++|+|+|        ..+++|+||+++++.  ++.+..+|+++|++||+|+|+|+++++.+.+.||++++.||++
T Consensus        78 ~~~~~~V~I--------~~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k~~~lG~l  146 (235)
T 2z0s_A           78 GIMNWFVDI--------NSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGEGLGRI  146 (235)
T ss_dssp             CSSEEEEEC--------SSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSSSCEEC
T ss_pred             eCCeEEEEe--------CCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECCCCcEEEEEecccCccc
Confidence            999999999        778999999999964  3345569999999999999999999877789999999999944

>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=99.96  E-value=1.8e-29  Score=216.70  Aligned_cols=139  Identities=21%  Similarity=0.209  Sum_probs=109.1

Q ss_pred             CCcEEecCCccCCCC-----------------------Ceee--CCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCe
Q 029155            7 EMVLVTPGEVLGKAT-----------------------EVKA--GKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPT   61 (198)
Q Consensus         7 ~~~iV~PGd~l~~~~-----------------------e~~~--G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~   61 (198)
                      -+++|+|||.|+..+                       +|.+  |+|||.++++  |||+++|.++.....  +....+.
T Consensus        38 ~~~iVlPGD~L~~~~~~~~~~~g~~~~~~l~~~~~~~~~~~~~~G~Gty~~~~~--I~as~aG~l~~~~~~--~~~~~~~  113 (289)
T 2nn6_G           38 LGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDR--LLVTKCGRLRHKEPG--SGSGGGV  113 (289)
T ss_dssp             GSSBCCSSEEECCSCSCCEECSSEEECC-----------------------CCC--EEECSCCEEEEECCT--TTSSCCE
T ss_pred             CCcEEeCCCCcCccccccccccccccccccccccccCcceEEccCCCeEEECCE--EEEEEeEeEEeccCC--ccCccce
Confidence            357899999999876                       7999  9999999999  999999999985210  0001148


Q ss_pred             EEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccc-cccccccccccCCCCCCEEEEE
Q 029155           62 VEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVR-ATEIDKVDMHLSFRPGDIVRAS  140 (198)
Q Consensus        62 i~V~p~~~~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~-~~~~d~~~~~~~~~~GDiV~Ak  140 (198)
                      ++|.|.+ .+|+|++||+|+|+|+++..++|.|+|        ..++.|+||.++++ ++    .+|+++|++||+|+||
T Consensus       114 v~V~~~~-~rYiP~vGDiVIG~Vt~v~~~~~~VdI--------~s~~~a~L~~~~f~Gat----k~~r~~f~~GDlV~Ar  180 (289)
T 2nn6_G          114 YWVDSQQ-KRYVPVKGDHVIGIVTAKSGDIFKVDV--------GGSEPASLSYLSFEGAT----KRNRPNVQVGDLIYGQ  180 (289)
T ss_dssp             EEEECCC-SSCCCCSSEEEEEEEEEEETTEEEEEC--------SSSSCCCEESCSSSCCS----SCSSSSSCTTCEEEEE
T ss_pred             EEEEecC-CCCCCCCCCEEEEEEEEEeCcEEEEEE--------CCCceeEEehhhcCcch----hhhhhhcCCCCEEEEE
Confidence            8999986 579999999999999999999999999        56799999999987 33    2789999999999999


Q ss_pred             EEEeCCCccEEEEE-----ecCCCeee
Q 029155          141 VLSLGDARAYFLST-----AKNDLGVV  162 (198)
Q Consensus       141 V~s~~~~~~~~LSt-----~~~~lGvv  162 (198)
                      |+++++...+.||+     ++++||+|
T Consensus       181 V~s~~~~~~~eLsc~~~~~k~~~lG~L  207 (289)
T 2nn6_G          181 FVVANKDMEPEMVCIDSCGRANGMGVI  207 (289)
T ss_dssp             EEECCTTSCCEEECSBTTTTBCCCCSC
T ss_pred             EEEcCCCCceEEEecccccccccCCEe
Confidence            99998777899999     99999998

>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=99.73  E-value=2.3e-17  Score=132.31  Aligned_cols=83  Identities=12%  Similarity=0.153  Sum_probs=74.5

Q ss_pred             CCCCCCCCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCc
Q 029155           70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDAR  148 (198)
Q Consensus        70 ~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~  148 (198)
                      ++|+|++||+|+|+|+++..+.|+|+|        .+ ++.|+||.+++...   ..+|++.|++||+|+|||++++...
T Consensus         1 krY~P~~gDvViG~V~~v~~~~~~VdI--------~~~~~~a~L~~s~~~g~---~k~~r~~l~~GDlV~ArV~~~~~~~   69 (175)
T 2ja9_A            1 KRYIPSVNDFVIGVIIGTFSDSYKVSL--------QNFSSSVSLSYMAFPNA---SKKNRPTLQVGDLVYARVCTAEKEL   69 (175)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEES--------STTSCCEEEETTSSTTC---CSSSCCCCCTTCEEEEEEEECCTTS
T ss_pred             CCccCCCcCEEEEEEEEEECcEEEEEE--------CCCCccEEEEHHHCCch---hhhhhccCCCCCEEEEEEEEecCCC
Confidence            379999999999999999999999999        66 89999999998621   2379999999999999999998767


Q ss_pred             cEEEE------EecCCCeeeE
Q 029155          149 AYFLS------TAKNDLGVVS  163 (198)
Q Consensus       149 ~~~LS------t~~~~lGvv~  163 (198)
                      .+.||      +++++||++.
T Consensus        70 ~~~Ltc~~~~~~r~~~lG~L~   90 (175)
T 2ja9_A           70 EAEIECFDSTTGRDAGFGILE   90 (175)
T ss_dssp             CCEEESSCTTTCSCTTCEEEC
T ss_pred             ceEEEecccccccccCCcCcC
Confidence            89999      9999999984

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

Probab=99.26  E-value=4.7e-11  Score=83.41  Aligned_cols=70  Identities=19%  Similarity=0.274  Sum_probs=61.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-ccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~~~L  152 (198)
                      +++||++.|+|+++.+.+|+|+|        ...+.|+||.+++...+.      +.|++||.|.|+|++++.. +.+.|
T Consensus         3 ~~~G~iv~G~V~~v~~~G~fV~l--------~~~~~Gllh~sel~~~~~------~~~~~Gd~V~v~V~~vd~~~~~i~l   68 (80)
T 2k52_A            3 VEPGKFYKGVVTRIEKYGAFINL--------NEQVRGLLRPRDMISLRL------ENLNVGDEIIVQAIDVRPEKREIDF   68 (80)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE--------ETTEEEEECGGGCSSCCG------GGCCTTCEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEE--------CCCCEEEEEHHHCCcccc------eeeCCCCEEEEEEEEEECCCCEEEE
Confidence            68999999999999999999999        557899999999864331      7899999999999999854 78999


Q ss_pred             EEecC
Q 029155          153 STAKN  157 (198)
Q Consensus       153 St~~~  157 (198)
                      |++..
T Consensus        69 sl~~~   73 (80)
T 2k52_A           69 KYIPL   73 (80)
T ss_dssp             EECSC
T ss_pred             EEeec
Confidence            98754

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

Probab=99.25  E-value=3.5e-11  Score=91.69  Aligned_cols=73  Identities=25%  Similarity=0.293  Sum_probs=65.9

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      +++|++|.|+|++|.+.+|+|+|        ...+.|+||++++...+..  ++.+.|++||.|.|+|++++. .+.+.|
T Consensus         5 ~~vG~iv~G~V~~i~~~G~FV~l--------~~~~~Glihisel~~~~~~--~~~~~~~vGd~V~vkV~~vd~~~~kI~L   74 (130)
T 2k4k_A            5 FEVGSVYTGKVTGLQAYGAFVAL--------DEETQGLVHISEVTHGFVK--DINEHLSVGDEVQVKVLAVDEEKGKISL   74 (130)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE--------ETTEEEEEEGGGTSSSCCS--CGGGTCCTTCEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEE--------CCCcEEEEEHHHCCccccc--CccccCCCCCEEEEEEEEEeCCCCEEEE
Confidence            68999999999999999999999        5679999999999876655  788999999999999999975 678999


Q ss_pred             EEec
Q 029155          153 STAK  156 (198)
Q Consensus       153 St~~  156 (198)
                      |++.
T Consensus        75 Slk~   78 (130)
T 2k4k_A           75 SIRA   78 (130)
T ss_dssp             ESHH
T ss_pred             EEee
Confidence            9975

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

Probab=99.22  E-value=8.4e-11  Score=87.64  Aligned_cols=87  Identities=18%  Similarity=0.176  Sum_probs=68.5

Q ss_pred             eEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccc-cccccccccCCCCCCEEEE
Q 029155           61 TVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT-EIDKVDMHLSFRPGDIVRA  139 (198)
Q Consensus        61 ~i~V~p~~~~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~-~~d~~~~~~~~~~GDiV~A  139 (198)
                      .+.+.|.....+.+++|+++.|+|+++.+.+++|+|        ...+.|+||++++... +..  ++.+.|++||.|.+
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            456667665556799999999999999999999999        5679999999999642 222  67889999999999


Q ss_pred             EEEEeCC-CccEEEEEecC
Q 029155          140 SVLSLGD-ARAYFLSTAKN  157 (198)
Q Consensus       140 kV~s~~~-~~~~~LSt~~~  157 (198)
                      +|++++. .+.+.||++..
T Consensus        85 kV~~vd~~~~rI~lslk~~  103 (115)
T 2khi_A           85 MVLDIDEERRRISLGLKQC  103 (115)
T ss_dssp             EEEEEETTTTEEEECCCCC
T ss_pred             EEEEEECCCCEEEEEEEec
Confidence            9999975 46899998853

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

Probab=99.20  E-value=5.6e-11  Score=87.02  Aligned_cols=77  Identities=19%  Similarity=0.317  Sum_probs=63.5

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccc-ccccccccccccCCCCCCEEEEEEEEeCCCccE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV-RATEIDKVDMHLSFRPGDIVRASVLSLGDARAY  150 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v-~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~  150 (198)
                      ..+++|+++.|+|++|.+++|+|+|...     ....+|+||++++ ...+..  ++.+.|++||.|.++|++++. +.+
T Consensus         8 ~~~~vG~i~~G~V~~v~~fG~FV~l~~~-----~~~~~Glvhisel~~~~~~~--~~~~~~~~Gd~V~VkV~~vd~-~~i   79 (103)
T 2eqs_A            8 EEPTIGDIYNGKVTSIMQFGCFVQLEGL-----RKRWEGLVHISELRREGRVA--NVADVVSKGQRVKVKVLSFTG-TKT   79 (103)
T ss_dssp             SSCCTTCEEEEEEEEECSSCEEEEECSS-----SSCCEEEECGGGTSSSSCCC--CHHHHCCTTCEEEEEEEEEET-TEE
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCC-----CCCeEEEEEHHHCCCCcccC--CcccEeCCCCEEEEEEEEEEC-Cee
Confidence            4589999999999999999999999210     0268999999999 333333  677899999999999999976 579


Q ss_pred             EEEEec
Q 029155          151 FLSTAK  156 (198)
Q Consensus       151 ~LSt~~  156 (198)
                      .||++.
T Consensus        80 ~LSlk~   85 (103)
T 2eqs_A           80 SLSMKD   85 (103)
T ss_dssp             EEESTT
T ss_pred             EEEEee
Confidence            999886

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

Probab=99.20  E-value=4.2e-11  Score=88.35  Aligned_cols=77  Identities=23%  Similarity=0.369  Sum_probs=66.8

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-cc
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RA  149 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~  149 (198)
                      ...+++||+|.|+|+++.+++|+|+|        ...+.|+||.+++...+.+  ++.+.|++||.|.|+|++++.. +.
T Consensus        26 ~~~~~~G~iv~G~V~~v~~~G~fV~l--------~~~~~Gll~~sel~~~~~~--~~~~~~~vGd~V~v~V~~vd~~~~k   95 (109)
T 2khj_A           26 VALNKKGAIVTGKVTAVDAKGATVEL--------ADGVEGYLRASEASRDRVE--DATLVLSVGDEVEAKFTGVDRKNRA   95 (109)
T ss_dssp             TTTCCSSSEEEEEEEEECSSCEEEEC--------STTCBCCBCTTCCCSSSSS--SGGGSCCTTCEEEEEEEEEETTTTE
T ss_pred             hhcCCCCCEEEEEEEEEECCeEEEEE--------CCCCEEEEEHHHcCccccc--ChhhccCCCCEEEEEEEEEECCCCE
Confidence            34689999999999999999999999        5678999999999765554  7789999999999999999753 57


Q ss_pred             EEEEEecC
Q 029155          150 YFLSTAKN  157 (198)
Q Consensus       150 ~~LSt~~~  157 (198)
                      +.||++..
T Consensus        96 i~LS~k~~  103 (109)
T 2khj_A           96 ISLSVRAK  103 (109)
T ss_dssp             EEEETTSS
T ss_pred             EEEEEeec
Confidence            99998763

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5

Probab=99.20  E-value=7.1e-11  Score=95.00  Aligned_cols=79  Identities=18%  Similarity=0.206  Sum_probs=58.1

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY  150 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~  150 (198)
                      +.|++||+|.|+|++|++.+|+|+|..      ..+.+|+||+|+++..+..  ++++.|++||.|.|+|++++. .+.+
T Consensus        11 ~~p~~G~iv~G~V~~I~~fGaFV~L~e------~~g~eGLvhiSels~~~v~--~~~~~~~vGd~V~VkVl~vD~~~~rI   82 (182)
T 1kl9_A           11 KFPEVEDVVMVNVRSIAEMGAYVSLLE------YNNIEGMILLSELSRRRIR--SINKLIRIGRNECVVVIRVDKEKGYI   82 (182)
T ss_dssp             SSCCTTCEEEEEEEEECSSEEEEEETT------TTTEEEEEEGGGC--------------CTTCEEEEEEEEEETTTTEE
T ss_pred             cCCCCCCEEEEEEEEEeccEEEEEEcc------CCCcEEEEEHHHCCCcccC--CHHHhcCCCCEEEEEEEEEECCCCEE
Confidence            457999999999999999999999920      1358999999999876665  789999999999999999974 5679


Q ss_pred             EEEEecCC
Q 029155          151 FLSTAKND  158 (198)
Q Consensus       151 ~LSt~~~~  158 (198)
                      .||++...
T Consensus        83 ~LSlk~~~   90 (182)
T 1kl9_A           83 DLSKRRVS   90 (182)
T ss_dssp             EEESTTCC
T ss_pred             EEEEeecC
Confidence            99998653

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A

Probab=99.18  E-value=1.2e-10  Score=93.11  Aligned_cols=77  Identities=19%  Similarity=0.238  Sum_probs=61.6

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeecccccc--CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-Cc
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-AR  148 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~--~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~  148 (198)
                      +.|++||+|.|+|++|.+.+|+|+|        .  ...+|+||+|+++..+..  ++++.|++||.|.|+|++++. .+
T Consensus        11 ~~p~~G~iv~G~V~~i~~fGaFV~L--------~e~~gveGLvhiSels~~~v~--~~~~~~~vGd~V~vkVl~vd~~~~   80 (175)
T 2a19_A           11 KYPEIDDIVMVNVQQIAEMGAYVKL--------LEYDNIEGMILLSELSRRRIR--SIQKLIRVGKNDVAVVLRVDKEKG   80 (175)
T ss_dssp             SSCCTTCEEEEEEEEEETTEEEEEE--------TTTTTCEEEEECC----------CCCCCCCTTSEEEEEEEEEETTTT
T ss_pred             cCCCCCCEEEEEEEEEecceEEEEE--------cCCCCcEEEEEHHHcCCcccC--CHHHcCCCCCEEEEEEEEEECCCC
Confidence            5688999999999999999999999        3  468999999999876655  788999999999999999974 56


Q ss_pred             cEEEEEecCC
Q 029155          149 AYFLSTAKND  158 (198)
Q Consensus       149 ~~~LSt~~~~  158 (198)
                      .+.||++...
T Consensus        81 ~I~LSlk~~~   90 (175)
T 2a19_A           81 YIDLSKRRVS   90 (175)
T ss_dssp             EEEEESTTCC
T ss_pred             eEEEEEEecC
Confidence            7999998653

>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.17  E-value=7.6e-11  Score=88.60  Aligned_cols=77  Identities=16%  Similarity=0.120  Sum_probs=65.6

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC--
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA--  147 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~--  147 (198)
                      .+.|++|+++.|+|++|.+++|+|+|        .. ...|+||++++...+.+  ++.+.|++||.|.|+|++++..  
T Consensus        17 ~~~~~vG~iv~G~V~~I~~fGaFV~l--------~g~~~~Glvhisel~~~~~~--~~~~~~~~Gd~V~VkV~~vd~~~~   86 (119)
T 2cqo_A           17 ENLPALYTIFQGEVAMVTDYGAFIKI--------PGCRKQGLVHRTHMSSCRVD--KPSEIVDVGDKVWVKLIGREMKND   86 (119)
T ss_dssp             CCSCCTTCEEEEEEEEEETTEEEEEC--------TTCSSCEEEEHHHHCSSCCS--CHHHHCCTTCEEEEEEEEEEECSS
T ss_pred             hcccCCCCEEEEEEEEEeCceEEEEE--------CCCcEEEEEEHHHCCccccc--ChhhcCCCCCEEEEEEEEEecccc
Confidence            46789999999999999999999999        32 36999999999766554  7788999999999999999732  


Q ss_pred             -ccEEEEEecC
Q 029155          148 -RAYFLSTAKN  157 (198)
Q Consensus       148 -~~~~LSt~~~  157 (198)
                       +.+.||++..
T Consensus        87 ~~~i~LSlk~~   97 (119)
T 2cqo_A           87 RIKVSLSMKVV   97 (119)
T ss_dssp             CEEEEEESTTB
T ss_pred             CceEEEEEeec
Confidence             4799998864

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

Probab=99.08  E-value=2.4e-10  Score=81.54  Aligned_cols=73  Identities=14%  Similarity=0.211  Sum_probs=62.5

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccC--cceeEEecc-ccccccccccccccCCCCCCEEEEEEEEeCC-C
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE--KFSGIIRQQ-DVRATEIDKVDMHLSFRPGDIVRASVLSLGD-A  147 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~--~~~G~l~~s-~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~  147 (198)
                      -.|++|+++.|+|+ +.+.+|+|+|        ..  ..+|++|+| +++..+..  ++++.| +||.|.++|++++. .
T Consensus         7 ~~~~vG~~~~G~V~-v~~fG~FVel--------~~~~~~eGLvhis~el~~~~~~--~~~~~~-~Gd~V~VkV~~vd~~~   74 (88)
T 1luz_A            7 SLPNAGDVIKGRVY-EKDYALYIYL--------FDYPHFEAILAESVKMHMDRYV--EYRDKL-VGKTVKVKVIRVDYTK   74 (88)
T ss_dssp             CCCCTTCEEEEEEE-EETTEEEEEE--------TTCTTSEEEEGGGSSCCHHHHH--HHHHHH-TTCEEEEEEEEEETTT
T ss_pred             cCCCCCCEEEEEEE-EEccEEEEEE--------CCCCCeEEEEEeeHHhCccccc--CHhHEe-CCCEEEEEEEEEECCC
Confidence            34899999999999 9999999999        32  589999999 99755544  667888 99999999999975 5


Q ss_pred             ccEEEEEec
Q 029155          148 RAYFLSTAK  156 (198)
Q Consensus       148 ~~~~LSt~~  156 (198)
                      +.+.||++.
T Consensus        75 ~kI~lslk~   83 (88)
T 1luz_A           75 GYIDVNYKR   83 (88)
T ss_dssp             TEEEEEEEE
T ss_pred             CEEEEEEee
Confidence            789999875

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

Probab=99.05  E-value=6.4e-10  Score=89.21  Aligned_cols=82  Identities=17%  Similarity=0.236  Sum_probs=68.1

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccc--c-------cccccCCCCCCEEEEEEE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID--K-------VDMHLSFRPGDIVRASVL  142 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d--~-------~~~~~~~~~GDiV~AkV~  142 (198)
                      +.|.+|+++.|+|+++.+.+++|+|        . +++|++|++++...+..  .       .+..+.|++||.|+++|+
T Consensus        77 ~~~~~Gev~~G~V~~v~~~G~fV~l--------~-~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~  147 (187)
T 1go3_E           77 YIPEMYELIEGEVVDVVEFGSFVRL--------G-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIV  147 (187)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEC--------S-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEE
T ss_pred             EccCCCCEEEEEEEEEeCcEEEEEE--------c-CccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEE
Confidence            4589999999999999999999999        3 38999999998643321  0       145688999999999999


Q ss_pred             EeCCC------ccEEEEEecCCCeee
Q 029155          143 SLGDA------RAYFLSTAKNDLGVV  162 (198)
Q Consensus       143 s~~~~------~~~~LSt~~~~lGvv  162 (198)
                      +++..      ..+.||++++.||++
T Consensus       148 ~vd~~~~~p~~~~I~lS~k~~~LG~~  173 (187)
T 1go3_E          148 AISLKAERKRGSKIALTMRQPYLGKL  173 (187)
T ss_dssp             EEECCC-----CEEEEECCSTTCEEH
T ss_pred             EEEcccCCCCccEEEEEEcCCCCCcH
Confidence            99742      379999999999986

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

Probab=99.04  E-value=1.1e-09  Score=93.18  Aligned_cols=77  Identities=19%  Similarity=0.235  Sum_probs=67.4

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeecccccc--CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-C
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-A  147 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~--~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~  147 (198)
                      .+.|++||+|.|+|+++.+.+|+|+|        .  .+..|+||+|+++..+..  ++++.|++||.|.++|++++. .
T Consensus         6 ~~~p~~Gdiv~G~V~~I~~fGaFV~L--------~e~~gieGlIhiSels~~~v~--~~~~~~kvGd~V~vkVi~vD~~~   75 (275)
T 3aev_A            6 REYPEEGEFVVATVKRIHNYGAFLEL--------DEYPGKEAFMHISEVASTWVR--NIRDYLKEGQKVVAKVIRVDPRK   75 (275)
T ss_dssp             -CCCCTTCEEEEEEEEEETTEEEEEE--------TTSTTCEEEEEGGGSCSSCCS--CGGGTCCTTCEEEEEEEEEETTT
T ss_pred             ccCCCCCCEEEEEEEEEECcEEEEEE--------CCCCCeEEEEEHHHcCccccc--CHHhccCCCCEEEEEEEEEECCC
Confidence            35689999999999999999999999        4  368999999999866655  788999999999999999975 5


Q ss_pred             ccEEEEEecC
Q 029155          148 RAYFLSTAKN  157 (198)
Q Consensus       148 ~~~~LSt~~~  157 (198)
                      +.+.||++..
T Consensus        76 ~~I~LSlk~~   85 (275)
T 3aev_A           76 GHIDLSLRRV   85 (275)
T ss_dssp             TEEEEESTTC
T ss_pred             CEEEEEEeec
Confidence            7899999874

>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=98.96  E-value=2.2e-09  Score=92.69  Aligned_cols=76  Identities=18%  Similarity=0.227  Sum_probs=66.8

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeecccccc--CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-Cc
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-AR  148 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~--~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~  148 (198)
                      ..|++||+|.|+|++|.+++|+|+|        .  .+..|+||+|+++..+..  ++.+.|++||.|.++|++++. .+
T Consensus         9 ~~~~vG~iv~G~V~~I~~fGaFV~L--------~ey~gveGLvhiSels~~~i~--~~~~~~kvGd~V~VkVl~vD~~~~   78 (308)
T 1q8k_A            9 KFPEVEDVVMVNVRSIQEMGAYVSL--------LEYNNIEGMIHLSELSRRRIR--SINKLIRIGRNECVKVIRVDKEKG   78 (308)
T ss_dssp             CCCSSCCEEEEEEEEEETTEEEEES--------CTTTSCCEEECGGGTSCSSCS--CCTTTCSSSCEEEEEEEEEETTTT
T ss_pred             cCCCCCCEEEEEEEEEeCcEEEEEE--------CCCCCeEEEEEhHHcCccccc--CHHHhcCCCCEEEEEEEEEeCCCC
Confidence            3578999999999999999999999        4  468999999999865554  788999999999999999975 57


Q ss_pred             cEEEEEecC
Q 029155          149 AYFLSTAKN  157 (198)
Q Consensus       149 ~~~LSt~~~  157 (198)
                      .+.||++..
T Consensus        79 rI~LSlK~~   87 (308)
T 1q8k_A           79 YIDLSKRRV   87 (308)
T ss_dssp             EEEEECSSC
T ss_pred             EEEEEEEec
Confidence            899999865

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

Probab=98.96  E-value=1.9e-09  Score=80.54  Aligned_cols=86  Identities=12%  Similarity=0.127  Sum_probs=65.7

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF  151 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~  151 (198)
                      -+++|+++.|+|++|.+++|+|+|.       .....|+++.++..... ...+..+.|++||.|.++|++++. .+.+.
T Consensus        18 ~l~~G~i~~G~V~~v~~fG~fV~l~-------~~~~~~l~~~~~~~~~~-~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~   89 (119)
T 1wi5_A           18 ALKPGMLLTGTVSSLEDHGYLVDIG-------VDGTRAFLPLLKAQEYI-RQKNKGAKLKVGQYLNCIVEKVKGNGGVVS   89 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECC-------CSSCEEEEEHHHHHHHH-HHHSSSCCCCTTCEEEEEEEECCTTSCEEE
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEEC-------CCCeEEEEEEecccccc-cccCccCEeCCCCEEEEEEEEEeCCCCEEE
Confidence            4799999999999999999999992       12345666555432111 111567899999999999999985 46899


Q ss_pred             EEEecCCCeeeEEec
Q 029155          152 LSTAKNDLGVVSAES  166 (198)
Q Consensus       152 LSt~~~~lGvv~a~~  166 (198)
                      ||++..++|.-.+..
T Consensus        90 Lslk~~~l~~~~~~~  104 (119)
T 1wi5_A           90 LSVGHSEVSTAIATE  104 (119)
T ss_dssp             EECCCCCSCCCCCCS
T ss_pred             EEEchhhcccceeec
Confidence            999999999766554

>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=98.94  E-value=5.3e-09  Score=83.40  Aligned_cols=82  Identities=21%  Similarity=0.261  Sum_probs=67.0

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccc--c-------cccccCCCCCCEEEEEEE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID--K-------VDMHLSFRPGDIVRASVL  142 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d--~-------~~~~~~~~~GDiV~AkV~  142 (198)
                      ..|.+|+++.|+|+++++.+++|++        . +++|++|++++...+..  .       .+-.+.|++||.|++||+
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--------G-PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVI  147 (180)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEC--------S-SSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEE
T ss_pred             eeccCCCEEEEEEeeeccceEEEEE--------C-CccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEE
Confidence            4589999999999999999999998        3 58999999998754321  0       134578999999999999


Q ss_pred             EeCC-----CccEEEEEecCCCeee
Q 029155          143 SLGD-----ARAYFLSTAKNDLGVV  162 (198)
Q Consensus       143 s~~~-----~~~~~LSt~~~~lGvv  162 (198)
                      +++.     ...+.||++++.||.+
T Consensus       148 ~v~~~~~~~~~rI~ls~k~~gLG~~  172 (180)
T 4ayb_E          148 SVASTVTGRLPRIALTMRQPYLGKL  172 (180)
T ss_dssp             EECC-------CEEEECCSTTCEEH
T ss_pred             EEeCCCCcccCcEEEEcCCCCCCCC
Confidence            9973     2369999999999975

>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=98.87  E-value=1.7e-09  Score=91.63  Aligned_cols=78  Identities=14%  Similarity=0.214  Sum_probs=68.1

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeecccccc--CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-C
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-A  147 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~--~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~  147 (198)
                      .+.|++||++.|+|+++.+.+|+|+|        .  ....|+||+|+++..+..  ++++.|++||.|.++|++++. .
T Consensus         6 ~~~~~vG~iv~G~V~~I~~~GaFV~l--------~e~~~~~GlihiSels~~~v~--~~~~~~~vGd~V~VkVi~vd~~~   75 (266)
T 3cw2_C            6 SKLPSEGEILIATVKQVFDYGSYVSL--------DEYGGLQAFLPWSEVSSKWVK--NIRDVLKENRKVIVKVIRVDRRK   75 (266)
T ss_dssp             SSSCCTTCEEEEEEEECCSSSBEEEE--------TTTTSEECBBCGGGSSCSSCC--CHHHHSCTTCEEEEEECCCCSSS
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEE--------cCCCCeEEEEEhHHcCccccc--CHHHhCcCCCEEEEEEEEEeCCC
Confidence            46789999999999999999999999        4  468999999999766655  788999999999999999975 5


Q ss_pred             ccEEEEEecCC
Q 029155          148 RAYFLSTAKND  158 (198)
Q Consensus       148 ~~~~LSt~~~~  158 (198)
                      +.+.||++...
T Consensus        76 g~I~LSlk~~~   86 (266)
T 3cw2_C           76 GTVDVSLKKVT   86 (266)
T ss_dssp             CCCBEESTTSC
T ss_pred             CEEEEEEEecc
Confidence            78999998653

>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=98.77  E-value=2.4e-08  Score=79.03  Aligned_cols=83  Identities=23%  Similarity=0.176  Sum_probs=63.9

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc-ccc---------ccccCCCCCCEEEEE
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKV---------DMHLSFRPGDIVRAS  140 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~-d~~---------~~~~~~~~GDiV~Ak  140 (198)
                      ...|.+|+++.|+|+++++.+|+|+|        . +++|++|++++...+. +..         .-.+.|++||.|++|
T Consensus        76 ~~~~~~Gev~~G~V~~v~~fG~fV~l--------~-~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vk  146 (172)
T 2c35_B           76 VFRPFKGEVVDAVVTQVNKVGLFTEI--------G-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLK  146 (172)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEE--------T-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEE
T ss_pred             EeeCCCCCEEEEEEEEEeCCEEEEEE--------C-CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEE
Confidence            34589999999999999999999999        3 5789999999853211 110         114579999999999


Q ss_pred             EEEeCCC-c--cEEEEEecCCCeee
Q 029155          141 VLSLGDA-R--AYFLSTAKNDLGVV  162 (198)
Q Consensus       141 V~s~~~~-~--~~~LSt~~~~lGvv  162 (198)
                      |++++.. +  ...-|++++.||.+
T Consensus       147 V~~vd~~~~~~~~igsm~~~~LG~~  171 (172)
T 2c35_B          147 IVGTRVDKNDIFAIGSLMDDYLGLV  171 (172)
T ss_dssp             EEEEEEETTEEEEEEECCSTTCEEC
T ss_pred             EEEEEcCCCCcEEEEEecCCCCCCC
Confidence            9998632 2  23348999999986

>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=98.69  E-value=5.8e-08  Score=76.87  Aligned_cols=80  Identities=13%  Similarity=0.055  Sum_probs=61.8

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc-ccccc-------ccCCCCCCEEEEEEEEe
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKVDM-------HLSFRPGDIVRASVLSL  144 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~-d~~~~-------~~~~~~GDiV~AkV~s~  144 (198)
                      .|.+|+++.|+|+++++.+++|+|        .. .+|++|+|++...+. +..+.       ++.|++||.|++||+++
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            478999999999999999999999        44 899999999853211 11111       26799999999999998


Q ss_pred             CC-C---ccEEEEEecCCCeee
Q 029155          145 GD-A---RAYFLSTAKNDLGVV  162 (198)
Q Consensus       145 ~~-~---~~~~LSt~~~~lGvv  162 (198)
                      +- .   ..+. |++++.||.+
T Consensus       151 d~~~~~~~~ig-sm~~~~LG~~  171 (171)
T 1y14_B          151 ISQVSSIHAIG-SIKEDYLGAI  171 (171)
T ss_dssp             EEETTEEEEEE-ECCSTTCEEC
T ss_pred             EcCCCCcEEEE-EcCCCCCCCC
Confidence            63 2   2344 7899999974

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

Probab=98.62  E-value=1.4e-07  Score=80.66  Aligned_cols=73  Identities=15%  Similarity=0.102  Sum_probs=63.7

Q ss_pred             CCCCCCCEEEEEEEEEecceEEE-EEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-Ccc
Q 029155           72 PVPEPGSVVIARVTKVMTRMASA-DIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARA  149 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V-~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~  149 (198)
                      .-.++||+|.|+|.++++.+++| +|        ...+.|+||.||+.          +.|++||.|.|+|+++++ .+.
T Consensus       148 ~~~~~G~~V~g~V~~i~~~G~fV~~i--------~~g~~Glih~SEl~----------~~l~~Gd~v~~~V~~id~~d~k  209 (285)
T 3go5_A          148 YNNMQNQNWPAIVYRLKLSGTFVYLP--------ENNMLGFIHPSERY----------AEPRLGQVLDARVIGFREVDRT  209 (285)
T ss_dssp             CSCCTTCEEEEEEEEEETTEEEEEET--------TTTEEEEECGGGCS----------SCCCTTCEEEEEEEEEETTTTE
T ss_pred             hhCCCCCEEEEEEEEEeCCcEEEEEe--------CCCeEEEEEHHHcc----------ccCCCCCEEEEEEEEEECCCCe
Confidence            34578999999999999999999 88        67899999999874          458999999999999986 678


Q ss_pred             EEEEEecCCCeee
Q 029155          150 YFLSTAKNDLGVV  162 (198)
Q Consensus       150 ~~LSt~~~~lGvv  162 (198)
                      +.||++...+..+
T Consensus       210 I~LSlk~~~~~~~  222 (285)
T 3go5_A          210 LNLSLKPRSFEML  222 (285)
T ss_dssp             EEEECSCCCCCCC
T ss_pred             EEEEeChhhhhcc
Confidence            9999998876543

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

Probab=98.59  E-value=5.6e-09  Score=99.14  Aligned_cols=75  Identities=17%  Similarity=0.221  Sum_probs=0.0

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYF  151 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~  151 (198)
                      ..|++|+++.|+|++|.+++|+|+|        ....+|++|+|++...+.+  ++.+.|++||.|.+||++++..+.+.
T Consensus       633 ~~~~vG~v~~G~V~~I~~fGaFVel--------~~g~eGLvHiSels~~rv~--~~~d~~kvGD~V~VkVi~iD~~grI~  702 (726)
T 4aid_A          633 DEAEVGKIYDGKVVKVVDFGAFVNF--------FGAKDGLVHVSQISNERVA--KPSDVLKEGQMVKVKLLGFDDRGKTK  702 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhcCCcEEEEEEEEEeccEEEEEE--------CCCcEEEEEHHHcCccccc--CccccCCCCCEEEEEEEEECCCCcEE
Confidence            3589999999999999999999999        5578999999999876666  78899999999999999998667899


Q ss_pred             EEEec
Q 029155          152 LSTAK  156 (198)
Q Consensus       152 LSt~~  156 (198)
                      ||++.
T Consensus       703 LS~K~  707 (726)
T 4aid_A          703 LSMKV  707 (726)
T ss_dssp             -----
T ss_pred             EEEee
Confidence            99885

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

Probab=98.58  E-value=4.3e-08  Score=77.81  Aligned_cols=81  Identities=22%  Similarity=0.113  Sum_probs=64.2

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccc-c-------cccccCCCCCCEEEEEEEE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-K-------VDMHLSFRPGDIVRASVLS  143 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d-~-------~~~~~~~~~GDiV~AkV~s  143 (198)
                      ..|.+|+++.|+|+++++.+++|++        . +++|++|++++...+.. .       .+..+.|++||.|++||++
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--------G-PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVG  150 (172)
T ss_dssp             ECCCTTCEEECCCCEEETTEEECCB--------T-TBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEE
T ss_pred             eccCCCCEEEEEEEEEEcceEEEEe--------C-CeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEE
Confidence            4589999999999999999999999        3 57899999998533211 0       1224689999999999999


Q ss_pred             eCCC----ccEEEEEecCCCeee
Q 029155          144 LGDA----RAYFLSTAKNDLGVV  162 (198)
Q Consensus       144 ~~~~----~~~~LSt~~~~lGvv  162 (198)
                      ++..    ..+. |++++.||.+
T Consensus       151 vd~~~~~~~~Ig-tm~~~~LG~~  172 (172)
T 3h0g_G          151 TRTDATEIFAIA-TMKEDYLGVL  172 (172)
T ss_dssp             EEESSSCEEEEE-ECCSTTCEEC
T ss_pred             EECCCCCceEEE-EcCCCCCCCC
Confidence            8732    2466 8899999975

>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=98.58  E-value=1.2e-07  Score=77.93  Aligned_cols=84  Identities=14%  Similarity=0.056  Sum_probs=64.3

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc-ccccc-------ccCCCCCCEEEEEEEE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKVDM-------HLSFRPGDIVRASVLS  143 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~-d~~~~-------~~~~~~GDiV~AkV~s  143 (198)
                      ..|++|+++.|+|+++++.+++|+|        .. .+|++|++++...+. +..+.       ++.|++||.|++||++
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            4489999999999999999999999        44 899999999863321 11111       2679999999999999


Q ss_pred             eCCC----ccEEEEEecCCCeeeEEe
Q 029155          144 LGDA----RAYFLSTAKNDLGVVSAE  165 (198)
Q Consensus       144 ~~~~----~~~~LSt~~~~lGvv~a~  165 (198)
                      ++..    ..+. |++++.||.+.+.
T Consensus       150 vd~~~~~i~~Ig-Smk~~~LG~~~~~  174 (215)
T 2b8k_G          150 CISQVSSIHAIG-SIKEDYLGAISHE  174 (215)
T ss_dssp             EEEETTEEEEEE-ECCSTTCEEC---
T ss_pred             EEcCCCccEEEE-EcCCCCCCCcchh
Confidence            8732    2466 8999999998643

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

Probab=98.55  E-value=8.4e-08  Score=95.46  Aligned_cols=79  Identities=13%  Similarity=0.113  Sum_probs=68.9

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccc-ccccccccCCCCCCEEEEEEEEeC-CCcc
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE-IDKVDMHLSFRPGDIVRASVLSLG-DARA  149 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~-~d~~~~~~~~~~GDiV~AkV~s~~-~~~~  149 (198)
                      -.+++|++|.|+|++|.+++++|+|        .....|++|+|+++..+ ..  +..+.|++||.|.|+|++++ +.+.
T Consensus       898 ~~l~~G~iv~G~V~~V~~fGaFV~L--------~~gveGLVHiSelsd~~~v~--~p~~v~kvGd~V~vkVl~VD~~~~r  967 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWHNDIICTT--------NSEVECVVNAQRHAGAQLRR--PANEIYEIGKTYPAKVIYIDYANIT  967 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEEC--------TTSCEEEECTTSSSSTTSCS--CSTTTSCTTCEEEEEEEEEEGGGTE
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEe--------CCCceEEEEHHHcCCCcccC--CHHHcCCCCCEEEEEEEEEECCCCE
Confidence            4579999999999999999999999        56789999999998655 33  67899999999999999997 4578


Q ss_pred             EEEEEecCCCe
Q 029155          150 YFLSTAKNDLG  160 (198)
Q Consensus       150 ~~LSt~~~~lG  160 (198)
                      +.||++..++-
T Consensus       968 I~LSlk~~dl~  978 (1219)
T 3psi_A          968 AEVSLLDHDVK  978 (1219)
T ss_dssp             EEEECCHHHHC
T ss_pred             EEEEecHHHhc
Confidence            99999987663

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

Probab=98.39  E-value=3.8e-08  Score=96.51  Aligned_cols=79  Identities=13%  Similarity=0.113  Sum_probs=0.0

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccc-ccccccccCCCCCCEEEEEEEEeC-CCcc
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE-IDKVDMHLSFRPGDIVRASVLSLG-DARA  149 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~-~d~~~~~~~~~~GDiV~AkV~s~~-~~~~  149 (198)
                      --+++|++|.|+|++|.+++++|+|        .....|++|+|+++..+ ..  +..+.|++||.|.|+|++++ +.+.
T Consensus       901 ~~l~~G~iv~G~V~~V~~fGaFV~L--------~~gveGLVHiSelsd~~~v~--~~~~v~kvGd~V~vkVl~VD~~~~r  970 (1030)
T 3psf_A          901 KTFFKGSIIPVRVERFWHNDIICTT--------NSEVECVVNAQRHAGAQLRR--PANEIYEIGKTYPAKVIYIDYANIT  970 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhcCCCEEEEEEEEEccCeEEEEe--------CCCcEEEEEHHHcCCCcccC--CHHHcCCCCCEEEEEEEEEECCCCE
Confidence            3578999999999999999999999        55789999999998654 33  67899999999999999998 4578


Q ss_pred             EEEEEecCCCe
Q 029155          150 YFLSTAKNDLG  160 (198)
Q Consensus       150 ~~LSt~~~~lG  160 (198)
                      +.||++..++-
T Consensus       971 I~LSlk~~dl~  981 (1030)
T 3psf_A          971 AEVSLLDHDVK  981 (1030)
T ss_dssp             -----------
T ss_pred             EEEEechHHhc
Confidence            99999988773

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

Probab=98.37  E-value=4.5e-08  Score=93.03  Aligned_cols=75  Identities=19%  Similarity=0.216  Sum_probs=0.0

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYF  151 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~  151 (198)
                      ..+++|+++.|+|+++.+++++|+|        .....|++|+|++...+..  +..+.|++||.|.+||++++..+.+.
T Consensus       623 ~~~~vG~i~~G~V~~i~~fGaFVel--------~~g~eGLvHiSel~~~~v~--~~~~~~~vGd~V~VkVi~vd~~grI~  692 (723)
T 3cdi_A          623 AEIEVGRVYTGKVTRIVDFGAFVAI--------GGGKEGLVHISQIADKRVE--KVTDYLQMGQEVPVKVLEVDRQGRIR  692 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhcCcEEEEEEEEEecceEEEEe--------CCCceEEEEHHHcCCcccc--CcccccCCCCEEEEEEEEECCCCcEE
Confidence            3579999999999999999999999        4568999999999866655  78899999999999999998667899


Q ss_pred             EEEec
Q 029155          152 LSTAK  156 (198)
Q Consensus       152 LSt~~  156 (198)
                      ||++.
T Consensus       693 LS~k~  697 (723)
T 3cdi_A          693 LSIKE  697 (723)
T ss_dssp             -----
T ss_pred             EEEEe
Confidence            99885

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

Probab=98.36  E-value=1.6e-07  Score=89.91  Aligned_cols=76  Identities=25%  Similarity=0.252  Sum_probs=66.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF  151 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~  151 (198)
                      -+++|+++.|+|++|.+++++|+|        ....+|++|+|++...+..  +..+.|++||.|.++|++++. .+.+.
T Consensus       651 ~l~vG~iv~G~V~~V~~fGaFV~l--------~~~~eGLVhiS~Lsd~~v~--d~~~~~~vGd~V~VkVi~VD~~~~rI~  720 (785)
T 3bzc_A          651 DLKPGMVLEGVVTNVTNFGAFVDI--------GVHQDGLVHISALSEKFVK--DPYEVVKAGDIVKVKVMEVDIPRNRVG  720 (785)
T ss_dssp             TCCTTCBCCCEEEEEETTEEEEEC--------SSSSEEEEETTTSCSSCCS--CHHHHCCTTCCCCCBEEEEETTTTEEE
T ss_pred             hcCCCCEEEEEEEEEecCCeEEEe--------CCCcEEEEEHHHcCccccC--ChhheeCCCCEEEEEEEEEECCCCEEE
Confidence            478999999999999999999999        4567999999999865554  678999999999999999974 57899


Q ss_pred             EEEecCC
Q 029155          152 LSTAKND  158 (198)
Q Consensus       152 LSt~~~~  158 (198)
                      ||++..+
T Consensus       721 LSlk~~~  727 (785)
T 3bzc_A          721 LSMRMSD  727 (785)
T ss_dssp             ECCSSCC
T ss_pred             EEEecCC
Confidence            9998765

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

Probab=98.29  E-value=2.4e-06  Score=69.44  Aligned_cols=82  Identities=17%  Similarity=0.195  Sum_probs=63.0

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc--cc---------------cccccCCCCC
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DK---------------VDMHLSFRPG  134 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~--d~---------------~~~~~~~~~G  134 (198)
                      ..|.+|+++.|+|++++..+++|++        . .++|++|++++...+.  |.               .+-...|++|
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--------S-FFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDID  147 (203)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEC--------S-SCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTT
T ss_pred             EccCCCCEEEEEEEEEeccEEEEEE--------e-CceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCC
Confidence            4489999999999999999999999        3 5789999998753221  00               1235679999


Q ss_pred             CEEEEEEEEeCCC------------------------ccEEEEEecCCCeee
Q 029155          135 DIVRASVLSLGDA------------------------RAYFLSTAKNDLGVV  162 (198)
Q Consensus       135 DiV~AkV~s~~~~------------------------~~~~LSt~~~~lGvv  162 (198)
                      |.|+.||.+++-.                        ..+.+|++++.||.+
T Consensus       148 d~VrvrV~~v~~~~~~p~~~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~~  199 (203)
T 3ayh_B          148 EEIRFQIESEDFVDISPKRNKNATAITGTEALESVSPYTLIASCSRDGLGIP  199 (203)
T ss_dssp             CEEEEEEEEEEECC--------------------CCSEEEEEEBCSTTCBCG
T ss_pred             CEEEEEEEEEEccccCCCCccccccccccccccCCCCeEEEEEecCCCCcee
Confidence            9999999997521                        117888888888875

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=98.23  E-value=6.1e-08  Score=92.56  Aligned_cols=76  Identities=14%  Similarity=0.219  Sum_probs=36.8

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccc----ccccccccccccCCCCCCEEEEEEEEeCCC
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV----RATEIDKVDMHLSFRPGDIVRASVLSLGDA  147 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v----~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~  147 (198)
                      ..+++|+++.|+|+++.+++++|+|        .....|+||+|++    ...+..  +..+.|++||.|.++|++++..
T Consensus       663 ~~~~vG~i~~G~V~~i~~fGaFV~l--------~~g~eGLvHiSel~~~~s~~rv~--~~~~~~~vGd~V~VkVi~vd~~  732 (757)
T 1e3p_A          663 TSPEVGERILGSVVKTTTFGAFVSL--------LPGKDGLLHISQIRKLAGGKRVE--NVEDVLGVGQKVQVEIAEIDSR  732 (757)
T ss_dssp             ----------CBEEECC-CSCEECC--------C---CCCCC---------------------CCSSCBCCCCCCCCCSS
T ss_pred             hhcccccEEEEEEEEccccEEEEEE--------cCCcEEEEEhHHhccccCCCccc--CcccccCCCCEEEEEEEEECCC
Confidence            4579999999999999999999999        5578999999999    655554  7889999999999999999866


Q ss_pred             ccEEEEEecC
Q 029155          148 RAYFLSTAKN  157 (198)
Q Consensus       148 ~~~~LSt~~~  157 (198)
                      +.+.||++..
T Consensus       733 grI~LS~k~~  742 (757)
T 1e3p_A          733 GKLSLIPVIE  742 (757)
T ss_dssp             CC--------
T ss_pred             CCEEEEEecC
Confidence            7799998753

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=98.05  E-value=1e-05  Score=70.78  Aligned_cols=70  Identities=19%  Similarity=0.230  Sum_probs=57.9

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC---
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA---  147 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~---  147 (198)
                      .|..+.||+|.|+|.++.++.++|+|        . ...|+||.++..        ..+.|++||.|+|.|.++++.   
T Consensus       129 e~~~~~GeIV~G~V~ri~~~~v~VDl--------G-k~EgiLp~sE~i--------p~E~~~vGD~Vkv~V~~V~~~~kg  191 (344)
T 1hh2_P          129 KYSELKGTVTTAEVIRVMGEWADIRI--------G-KLETRLPKKEWI--------PGEEIKAGDLVKVYIIDVVKTTKG  191 (344)
T ss_dssp             CTTCCTTCEEEEEEEEECSSEEEEEE--------T-TEEEEEEGGGSC--------TTCCCCTTCEEEEEEEEEEEETTE
T ss_pred             HHhhcCCCEEEEEEEEEecCcEEEEe--------C-CeEEEEeHHHcC--------CCcCCCCCCEEEEEEEEEEcCCCC
Confidence            35567999999999999999999999        4 689999999874        247899999999999999732   


Q ss_pred             ccEEEEEecC
Q 029155          148 RAYFLSTAKN  157 (198)
Q Consensus       148 ~~~~LSt~~~  157 (198)
                      .++.||-..+
T Consensus       192 ~~I~LSRt~p  201 (344)
T 1hh2_P          192 PKILVSRRVP  201 (344)
T ss_dssp             EEEEEESSSH
T ss_pred             cEEEEEeecc
Confidence            3577777654

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=98.00  E-value=8.7e-06  Score=68.17  Aligned_cols=72  Identities=17%  Similarity=0.218  Sum_probs=59.1

Q ss_pred             CCCCCCCEEEEEEEE----EecceEEEEEeeeccccccC---cceeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 029155           72 PVPEPGSVVIARVTK----VMTRMASADIMCVGAKSVRE---KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSL  144 (198)
Q Consensus        72 ~~p~vGDiViG~V~~----v~~~~~~V~I~~v~~~~l~~---~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~  144 (198)
                      |.-++||+|.|+|.+    +..+.++|+|        ..   ..+|+|+.++..        ..+.|++||.|+|.|..+
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        43   479999988753        257899999999999999


Q ss_pred             CCC---ccEEEEEecCCC
Q 029155          145 GDA---RAYFLSTAKNDL  159 (198)
Q Consensus       145 ~~~---~~~~LSt~~~~l  159 (198)
                      .+.   .++.||-..++|
T Consensus        67 ~~~~~gpqIiLSRt~p~l   84 (251)
T 2asb_A           67 TRGAREPLITLSRTHPNL   84 (251)
T ss_dssp             ECCSSSCEEEEESSCHHH
T ss_pred             EcCCCCCEEEEEeccHHH
Confidence            753   568888877654

>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=97.82  E-value=2.6e-05  Score=68.62  Aligned_cols=72  Identities=15%  Similarity=0.208  Sum_probs=57.8

Q ss_pred             CCCCCCCCEEEEEEEE----EecceEEEEEeeeccccccC---cceeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 029155           71 GPVPEPGSVVIARVTK----VMTRMASADIMCVGAKSVRE---KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLS  143 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~----v~~~~~~V~I~~v~~~~l~~---~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s  143 (198)
                      .|..++||+|.|+|.+    +..+.++|+|        ..   ..+|+||.++..+        .+.|++||-|+|.|.+
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            3567899999999999    9999999999        33   4799999988642        4789999999999999


Q ss_pred             eCCC---ccEEEEEecCC
Q 029155          144 LGDA---RAYFLSTAKND  158 (198)
Q Consensus       144 ~~~~---~~~~LSt~~~~  158 (198)
                      +.+.   .++.||-..++
T Consensus       189 V~~~~kgpqI~LSRT~p~  206 (366)
T 1k0r_A          189 VTRGAREPLITLSRTHPN  206 (366)
T ss_dssp             EECCSSSCEEEEESSCHH
T ss_pred             EecCCCccEEEEEeCChH
Confidence            9753   44777766554

>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=97.68  E-value=0.00017  Score=66.10  Aligned_cols=75  Identities=12%  Similarity=0.164  Sum_probs=60.1

Q ss_pred             CCCCCCEEEEEEEEEecc--eEEEEEeeeccccccCcceeEEecccccccccc-------ccccccCCCCCCEEEEEEEE
Q 029155           73 VPEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATEID-------KVDMHLSFRPGDIVRASVLS  143 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~--~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d-------~~~~~~~~~~GDiV~AkV~s  143 (198)
                      -+.+|++..|+|+++.+.  .|||+|        ..+-.|+||++|+...+..       ..++.+.+++||.|.++|..
T Consensus        42 ~~~vGnIY~GkV~rv~p~~~aAFVdi--------G~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~K  113 (517)
T 2bx2_L           42 EQKKANIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDK  113 (517)
T ss_dssp             CCCTTCEEEEEEEEEETTTTEEEEES--------SSSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEE
T ss_pred             cCCCCCEEEEEEEEeccCCceEEEEe--------CCCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEe
Confidence            368899999999999999  999999        6778899999998644311       22577899999999999999


Q ss_pred             eCC-CccEEEEEe
Q 029155          144 LGD-ARAYFLSTA  155 (198)
Q Consensus       144 ~~~-~~~~~LSt~  155 (198)
                      ... +....||+.
T Consensus       114 e~~g~KGa~lTt~  126 (517)
T 2bx2_L          114 EERGNKGAALTTF  126 (517)
T ss_dssp             CCCTTCCCEEESS
T ss_pred             eccccCCceEEee
Confidence            653 244667765

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

Probab=97.59  E-value=0.00014  Score=59.60  Aligned_cols=67  Identities=15%  Similarity=0.122  Sum_probs=52.5

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc--cc----------cccccCCCCCCEEE
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DK----------VDMHLSFRPGDIVR  138 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~--d~----------~~~~~~~~~GDiV~  138 (198)
                      ...|.+|+++.|+|++++..+++|++        ...++|++|++++...+.  |.          ..-...|++||.|+
T Consensus        76 ~f~p~vGEv~~G~Is~Vt~fGifVeL--------~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~Vr  147 (218)
T 2ckz_B           76 VFKPFLGEIVTGWISKCTAEGIKVSL--------LGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIR  147 (218)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEC--------TTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEE
T ss_pred             EecCCCCCEEEEEEEEEccCcEEEEc--------cCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEE
Confidence            34589999999999999999999999        446799999998753221  00          12246699999999


Q ss_pred             EEEEEeC
Q 029155          139 ASVLSLG  145 (198)
Q Consensus       139 AkV~s~~  145 (198)
                      +||.+++
T Consensus       148 vrV~~v~  154 (218)
T 2ckz_B          148 FRIEREV  154 (218)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEEE
Confidence            9999986

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

Probab=97.43  E-value=0.00074  Score=57.47  Aligned_cols=68  Identities=15%  Similarity=0.037  Sum_probs=55.6

Q ss_pred             CCCCCCEEEEEEEEEe-cceEEEEEeeeccccccC-cceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccE
Q 029155           73 VPEPGSVVIARVTKVM-TRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAY  150 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~-~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~  150 (198)
                      ..++|+++.|+|++++ +.+|+|++        .. ...|++|.++++...      ...+.+||.+.+. +.++..+.+
T Consensus        66 ~~~~G~~~~g~V~~v~~~~GaFVdi--------G~~~~d~lvp~sel~~~~------~~~~~~Gd~v~v~-l~iD~~~Ri  130 (285)
T 3go5_A           66 TATQDQFGWGRVTEVRKDLGVFVDT--------GLPDKEIVVSLDILPELK------ELWPKKGDQLYIR-LEVDKKDRI  130 (285)
T ss_dssp             CSCSSSCEEEEEEEEETTTEEEEEC--------SCTTCCEEEEGGGSCSSG------GGSCCTTCEEEEE-EEECTTSCE
T ss_pred             cccCCCEEEEEEEEEccCceEEEEE--------CCCCcEEEEEHHHCCccc------ccccCCCCEEEEE-EEECCCCcE
Confidence            3588999999999999 79999999        55 478999999986532      2357999999655 688866789


Q ss_pred             EEEEe
Q 029155          151 FLSTA  155 (198)
Q Consensus       151 ~LSt~  155 (198)
                      .||++
T Consensus       131 ~ls~k  135 (285)
T 3go5_A          131 WGLLA  135 (285)
T ss_dssp             EEEEC
T ss_pred             EEEeh
Confidence            99985

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

Probab=96.61  E-value=0.0018  Score=46.66  Aligned_cols=41  Identities=12%  Similarity=0.252  Sum_probs=36.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccc
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE  121 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~  121 (198)
                      .|++|++|.+.|+++.+.+++|+|        ....+|++|+|+++..+
T Consensus        58 ~l~~Ge~V~g~V~~i~~fG~fv~l--------~~~~eGlvhis~i~~~~   98 (101)
T 2bh8_A           58 NPQQGDRVEGKIKSITDFGIFIGL--------DGGIDGLVHLSDISWAQ   98 (101)
T ss_dssp             CCCTTCEEEEEEEECCSEEEEECT--------TSCEEEEEEEEEEEECC
T ss_pred             CCCCCCEEEEEEEEeCCcEEEEEc--------CCCceEEEEHHHCccCc
Confidence            689999999999999999999999        55789999999987543

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

Probab=96.56  E-value=0.0053  Score=57.59  Aligned_cols=75  Identities=9%  Similarity=0.139  Sum_probs=57.4

Q ss_pred             CCCCC--EEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccc--cc--cc--cc----ccccCCCCCCEEEEEE
Q 029155           74 PEPGS--VVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRA--TE--ID--KV----DMHLSFRPGDIVRASV  141 (198)
Q Consensus        74 p~vGD--iViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~--~~--~d--~~----~~~~~~~~GDiV~AkV  141 (198)
                      .++|+  +..|+|++|++.+++|+|.       ....+|++|++++..  .+  .+  ..    .....|++||.|.++|
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            56898  9999999999999999992       246899999999852  11  11  11    2246799999999999


Q ss_pred             EEeCC-CccEEEEEe
Q 029155          142 LSLGD-ARAYFLSTA  155 (198)
Q Consensus       142 ~s~~~-~~~~~LSt~  155 (198)
                      .+++. .+.+.|++.
T Consensus       629 ~~vd~~~~~I~~~l~  643 (644)
T 2id0_A          629 AEVRMETRSIIARPV  643 (644)
T ss_dssp             EEEETTTTEEEEEEC
T ss_pred             EEEeCCCCEEEEEEc
Confidence            99974 467887764

>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=95.84  E-value=0.042  Score=39.42  Aligned_cols=60  Identities=15%  Similarity=0.184  Sum_probs=46.3

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc---cccc-cccCCCCCCEEEEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI---DKVD-MHLSFRPGDIVRAS  140 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~---d~~~-~~~~~~~GDiV~Ak  140 (198)
                      .|..|+...+.|+++.++.+.+.+        .....+.|..++++....   .... ..+.|++||+|+.+
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            467799999999999999988877        444666788888764432   1124 67889999999998

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=95.75  E-value=0.012  Score=56.27  Aligned_cols=70  Identities=21%  Similarity=0.144  Sum_probs=48.3

Q ss_pred             CEEEEEEEEEecceEEEEEeeeccccccC-cceeEEeccccc--ccc--cc--cc-----c----cccCCCCCCEEEEEE
Q 029155           78 SVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVR--ATE--ID--KV-----D----MHLSFRPGDIVRASV  141 (198)
Q Consensus        78 DiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~--~~~--~d--~~-----~----~~~~~~~GDiV~AkV  141 (198)
                      .+..|.|++|+.++++|.|        .. ..+|++|++++.  ..+  -+  ..     .    ....|++||.|.++|
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        44 689999999884  111  01  00     1    247899999999999


Q ss_pred             EEeCCC----ccEEEEEe
Q 029155          142 LSLGDA----RAYFLSTA  155 (198)
Q Consensus       142 ~s~~~~----~~~~LSt~  155 (198)
                      .+++..    +.+.||++
T Consensus       743 ~~vd~~~~~~~kI~lslk  760 (760)
T 2vnu_D          743 RSVMDPITSKRKAELLLK  760 (760)
T ss_dssp             C--------CCEEEC---
T ss_pred             EEEECccccCCcEEEEeC
Confidence            999743    56777753

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

Probab=95.30  E-value=0.028  Score=55.20  Aligned_cols=71  Identities=21%  Similarity=0.144  Sum_probs=54.8

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEeccccc--ccc--ccc--cc---------cccCCCCCCEEEEE
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVR--ATE--IDK--VD---------MHLSFRPGDIVRAS  140 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~--~~~--~d~--~~---------~~~~~~~GDiV~Ak  140 (198)
                      |.+..|.|++|+.++++|.|        .. +.+|++|++++.  ..+  -++  ..         ....|++||.|.++
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            88999999999999999999        43 689999999985  111  010  01         24789999999999


Q ss_pred             EEEeCCC----ccEEEEEe
Q 029155          141 VLSLGDA----RAYFLSTA  155 (198)
Q Consensus       141 V~s~~~~----~~~~LSt~  155 (198)
                      |.+++..    +.+.||++
T Consensus       959 V~~vd~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          959 VRSVMDPITSKRKAELLLK  977 (977)
T ss_dssp             ECCCCCSSSCCCCCCEEEC
T ss_pred             EEEEcCcccCCCceEEEeC
Confidence            9998751    56888764

>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=93.31  E-value=0.12  Score=35.91  Aligned_cols=59  Identities=24%  Similarity=0.285  Sum_probs=45.0

Q ss_pred             eeccCCcEEecCCccCCC--CCeeeCCCEEEe-CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecC
Q 029155            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~-~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~   67 (198)
                      +|..+.+.|.||..|..-  ..|-||.++-.- |..  |||.+-|.|....    ....++.|+|.|.
T Consensus        23 vK~~~Gq~V~aG~IivRQRGtk~hPG~NVg~GkD~T--LfAl~~G~V~f~~----~~~~r~~VsV~p~   84 (85)
T 3v2d_0           23 VKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFT--LFALVDGVVEFQD----RGRLGRYVHVRPL   84 (85)
T ss_dssp             ESSCTTCEECTTCEEEECSSCSEEECTTEEECTTCC--EEESSSEEEEEEE----CGGGCEEEEEEEC
T ss_pred             eEecCCeEEcCCeEEEecCCccCcCCCCEeEcCCCe--EEEecCEEEEEEE----cCCCCEEEEEEEC
Confidence            577889999999998743  368999999765 444  9999999999853    1123567888874

>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=91.83  E-value=0.22  Score=33.92  Aligned_cols=59  Identities=20%  Similarity=0.300  Sum_probs=44.0

Q ss_pred             eeccCCcEEecCCccCCC--CCeeeCCCEEEe-CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEec
Q 029155            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTG   66 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~-~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p   66 (198)
                      +|....+.|.||..|..-  ..|-||.++-.- |.  +|||.+-|.|.....   ....++.|+|.|
T Consensus        14 vK~~~Gq~V~aG~IivRQRGtk~hPG~NVG~GkD~--TLfAl~~G~V~f~~~---~~~~r~~VsV~p   75 (76)
T 3r8s_W           14 VKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDH--TLFAKADGKVKFEVK---GPKNRKFISIEA   75 (76)
T ss_dssp             ESSCTTCEECTTCEEEECSSCSSEECTTEEECTTS--CEEESSSEEEEEEEE---TTTTEEEEEEEC
T ss_pred             EEecCCeEEecCcEEEeccCccCcCCCCeeecCCC--eEEEccCEEEEEEEe---CCCCCEEEEEEe
Confidence            577889999999998753  358999999766 44  499999999998520   012356788876

>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=91.33  E-value=0.19  Score=35.37  Aligned_cols=59  Identities=22%  Similarity=0.317  Sum_probs=44.8

Q ss_pred             eeccCCcEEecCCccCCC--CCeeeCCCEEEe-CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecC
Q 029155            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~-~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~   67 (198)
                      +|....+.|.||..|..-  ..|-||.++-.- |.  +|||.+-|.|....    ...+++.|+|.|.
T Consensus        23 vK~~gGq~V~aG~IivRQRGtk~hPG~NVg~GkD~--TLfAl~~G~V~f~~----~~~~r~~V~V~p~   84 (91)
T 2zjr_T           23 VKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDH--TLFALSDGKVVFIN----KGKGARFISIEAA   84 (91)
T ss_dssp             CSSCTTCEECSSCEEECCSSSSSEECTTEECCTTS--CEEESSCEEEEEEE----ETTTEEEEEECCC
T ss_pred             EEecCCeEEcCCeEEEecCCCEEcCCCCEEEcCCC--cEEeccceEEEEEE----cCCCcEEEEEEeC
Confidence            577889999999998753  358999998665 44  49999999999852    1124567899874

>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=90.74  E-value=0.74  Score=37.13  Aligned_cols=75  Identities=12%  Similarity=0.084  Sum_probs=47.0

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc---c------ccccc-cCCCCCCEEEEEEE
Q 029155           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI---D------KVDMH-LSFRPGDIVRASVL  142 (198)
Q Consensus        73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~---d------~~~~~-~~~~~GDiV~AkV~  142 (198)
                      .|.+|+++.|+|+.++.....+-+        -..|...|+...+++...   +      ..... +--++|+.|+-||.
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            489999999999999998877765        235666777666531110   0      00000 11136999999999


Q ss_pred             EeCCCccEEEEEec
Q 029155          143 SLGDARAYFLSTAK  156 (198)
Q Consensus       143 s~~~~~~~~LSt~~  156 (198)
                      ++.-.+.+ ||+.+
T Consensus       198 ~~~~~~~~-lsI~G  210 (214)
T 2rf4_A          198 NVHTTGRV-VSVDG  210 (214)
T ss_dssp             EEECCSSS-CEEEE
T ss_pred             EEEecCCE-EEEEE
Confidence            98643222 55543

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=86.16  E-value=0.72  Score=28.76  Aligned_cols=27  Identities=22%  Similarity=0.206  Sum_probs=21.2

Q ss_pred             EEec-CCCc--eeEEccCCeEEeCCCCCEEe
Q 029155          163 SAES-TAGG--TMVPISWTEMQCPLTGQTEQ  190 (198)
Q Consensus       163 ~a~~-~~g~--~m~~~~~~~~~c~~cg~~e~  190 (198)
                      +-.| +||.  .|.+-. +.+.|+.||.++-
T Consensus        19 ~k~CP~CG~~~fm~~~~-~R~~C~kCG~t~~   48 (50)
T 3j20_Y           19 NKFCPRCGPGVFMADHG-DRWACGKCGYTEW   48 (50)
T ss_dssp             SEECSSSCSSCEEEECS-SEEECSSSCCEEE
T ss_pred             cccCCCCCCceEEecCC-CeEECCCCCCEEE
Confidence            4567 8987  777654 7899999999874

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=85.33  E-value=0.24  Score=32.59  Aligned_cols=29  Identities=10%  Similarity=0.097  Sum_probs=22.4

Q ss_pred             eeEEec-CCCceeEEccCCeEEeCCCCCEE
Q 029155          161 VVSAES-TAGGTMVPISWTEMQCPLTGQTE  189 (198)
Q Consensus       161 vv~a~~-~~g~~m~~~~~~~~~c~~cg~~e  189 (198)
                      .+.-+| .||..........++||+||.+-
T Consensus        19 ~v~Y~C~~Cg~~~~l~~~~~iRC~~CG~RI   48 (63)
T 3h0g_L           19 TMIYLCADCGARNTIQAKEVIRCRECGHRV   48 (63)
T ss_dssp             CCCCBCSSSCCBCCCCSSSCCCCSSSCCCC
T ss_pred             CeEEECCCCCCeeecCCCCceECCCCCcEE
Confidence            355678 89988765566789999999764

>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=83.52  E-value=1.1  Score=29.96  Aligned_cols=43  Identities=23%  Similarity=0.349  Sum_probs=34.4

Q ss_pred             eeccCCcEEecCCccCCC--CCeeeCCCEEEe-CCceEEEEeEeeeEE
Q 029155            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLR   47 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~-~g~~~i~asv~G~v~   47 (198)
                      +|..+.+.|.||..|..-  ..|-||.++-.- |.  +|||.+.|.|+
T Consensus        23 vK~~~Gq~V~aG~IivrQRgtk~hPG~nVg~GkD~--TLfAl~~G~V~   68 (69)
T 2ftc_O           23 IKKMEGHYVHAGNIIATQRHFRWHPGAHVGVGKNK--CLYALEEGIVR   68 (69)
T ss_pred             EEecCCeEecCCeEEEecCCCeEcCCCCeeecCCC--cEEEccceEEe
Confidence            577889999999998753  358899998655 44  49999999986

>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=82.93  E-value=2.2  Score=31.78  Aligned_cols=36  Identities=22%  Similarity=0.269  Sum_probs=26.5

Q ss_pred             CCCCCEE---------EEEEEEEecceEEEEEeeeccccccCcceeEEe
Q 029155           74 PEPGSVV---------IARVTKVMTRMASADIMCVGAKSVREKFSGIIR  113 (198)
Q Consensus        74 p~vGDiV---------iG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~  113 (198)
                      .++||+|         +|.|++.+++.+.|.|++|-    ..|-+|-||
T Consensus         8 ~~~g~~v~~~yKTG~YigeI~e~~~~~~lVkVlaVl----KHP~QGDLH   52 (130)
T 1y71_A            8 FEIGEIVTGIYKTGKYIGEVTNSRPGSYVVKVLAVL----KHPVQGDLH   52 (130)
T ss_dssp             CCTTCEEEEEETTEEEEEEEEEEETTEEEEEEEEEE----ECCCC----
T ss_pred             CCccceeEEEEecceeEEEEEeecCCeEEEEEEEEe----cCCCccCCC
Confidence            5889999         89999999999999998763    344555554

>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...

Probab=81.73  E-value=0.42  Score=32.03  Aligned_cols=27  Identities=7%  Similarity=0.122  Sum_probs=21.0

Q ss_pred             eeEEec-CCCceeEEccCCeEEeCCCCC
Q 029155          161 VVSAES-TAGGTMVPISWTEMQCPLTGQ  187 (198)
Q Consensus       161 vv~a~~-~~g~~m~~~~~~~~~c~~cg~  187 (198)
                      .+.-.| .||........+.+.||+||.
T Consensus        26 ~v~Y~C~~CG~~~e~~~~d~irCp~CG~   53 (70)
T 1twf_L           26 TLKYICAECSSKLSLSRTDAVRCKDCGH   53 (70)
T ss_dssp             CCCEECSSSCCEECCCTTSTTCCSSSCC
T ss_pred             eEEEECCCCCCcceeCCCCCccCCCCCc
Confidence            455678 999995544567899999998

---

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	198
d2nn6i1	125	b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H	6e-50
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	1e-06
d2nn6i2	55	b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Hum	3e-05
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	0.002

>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 =  156 bits (395), Expect = 6e-50
 Identities = 65/122 (53%), Positives = 88/122 (72%), Gaps = 1/122 (0%)

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

Query: 133 PGDIVRASVLSLGDAR-AYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQR 191
           PGDIV A V+SLGDA+  Y L+TA+N+LGVV A S +G  MVPISW EMQCP T   E R
Sbjct: 64  PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTKEFR 123

Query: 192 KV 193
           KV
Sbjct: 124 KV 125

>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 = 43.0 bits (101), Expect = 1e-06
 Identities = 17/88 (19%), Positives = 35/88 (39%)

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

Query: 133 PGDIVRASVLSLGDARAYFLSTAKNDLG 160
            GD++ A V ++    A  L T     G
Sbjct: 65  EGDLISAEVQAVFSDGAVSLHTRSLKYG 92

>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 = 38.2 bits (89), 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

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 87

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 33.8 bits (77), Expect = 0.002
 Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 9/92 (9%)

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKV-DMHLSF 131
            P+   +VI  V  V       DI           +   +   ++    I+   D+    
Sbjct: 4   YPKINDIVIGLVEDVEIYGWVVDIK--------APYKAYLPASNLLGRSINVGEDLRRYL 55

Query: 132 RPGDIVRASVLSLGDARAYFLSTAKNDLGVVS 163
             GD V A + +   +    LS    DLG VS
Sbjct: 56  DVGDYVIARIENFDRSIDPVLSVKGKDLGRVS 87

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	198
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	100.0
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.81
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.77
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	99.77
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.75
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	99.75
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.74
d2ba0a2	51	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.52
d2nn6h2	48	Ribosomal RNA-processing protein 4, RRP4 {Human (H	99.49
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.42
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.41
d2nn6i2	55	Exosome component 1, EXOSC1 {Human (Homo sapiens)	99.4
d2je6i2	59	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.38
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.38
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.22
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.02
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.01
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.79
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.69
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	98.47
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.38
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.72
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.14
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	97.13
d1v8qa_	66	Ribosomal protein L27 {Thermus thermophilus [TaxId	96.52
d2nn6g2	91	Ribosomal RNA-processing protein 40, RRP40 {Human	96.52
d2zjrt1	84	Ribosomal protein L27 {Deinococcus radiodurans [Ta	95.93
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	84.3
d2gycu1	84	Ribosomal protein L27 {Escherichia coli [TaxId: 56	81.6
d1e1oa1	143	Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g	81.56
d1y71a1	124	Kinase-associated protein B {Bacillus cereus [TaxI	80.87

>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=100.00  E-value=7.5e-44  Score=270.62  Aligned_cols=123  Identities=53%  Similarity=0.853  Sum_probs=118.9

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCc-c
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDAR-A  149 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~-~  149 (198)
                      +|+|++||+|+|+|+++++++|.|+|++++++++..+|.|+||.+|+|.++.|+.+|+++|++||+|+|+|+|+++.. +
T Consensus         2 ~~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~   81 (125)
T d2nn6i1           2 QLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSN   81 (125)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTE
T ss_pred             CcCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCcc
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999998764 5


Q ss_pred             EEEEEecCCCeeeEEecCCCceeEEccCCeEEeCCCCCEEeeee
Q 029155          150 YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQRKV  193 (198)
Q Consensus       150 ~~LSt~~~~lGvv~a~~~~g~~m~~~~~~~~~c~~cg~~e~RKv  193 (198)
                      |+|||++++||||+|+|.+|++|+|.+|++|+||+||++|+||+
T Consensus        82 ~~Lst~~~~LGVv~A~c~~g~~m~~~~~~~m~cp~~g~~E~RKV  125 (125)
T d2nn6i1          82 YLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTKEFRKV  125 (125)
T ss_dssp             EEEECCSSSCEECCCBCSSSCBCEEEETTEEECTTTTCCBCCCC
T ss_pred             EEEEecCCCcEEEEEECCCCCEeEeecCCEEECCCCCCeeccCC
Confidence            99999999999999999999999999999999999999999996

>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=99.81  E-value=8.9e-21  Score=136.22  Aligned_cols=85  Identities=19%  Similarity=0.290  Sum_probs=73.9

Q ss_pred             CCCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccc--------cccccccccccCCCCCCEEEEEE
Q 029155           70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVR--------ATEIDKVDMHLSFRPGDIVRASV  141 (198)
Q Consensus        70 ~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~--------~~~~d~~~~~~~~~~GDiV~AkV  141 (198)
                      .+|.|++||+|+|+|+++.+++|+|+|        ...+.|+||++++.        ++..+..+|+++|++||.|.|+|
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        66789999999983        24455668999999999999999


Q ss_pred             EEeCCCccEEEEEecCCCeee
Q 029155          142 LSLGDARAYFLSTAKNDLGVV  162 (198)
Q Consensus       142 ~s~~~~~~~~LSt~~~~lGvv  162 (198)
                      ++++..+.+.||||+..||++
T Consensus        74 ~~v~~dg~i~Ls~r~~~~gkl   94 (95)
T d2nn6h1          74 QAVFSDGAVSLHTRSLKYGKL   94 (95)
T ss_dssp             EEEETTTEEEEECCSSTTCEE
T ss_pred             EEECCCCCEEEEeccccCCcC
Confidence            999876889999999999986

>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=99.77  E-value=7.4e-19  Score=123.87  Aligned_cols=84  Identities=23%  Similarity=0.231  Sum_probs=75.5

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc-cccccccCCCCCCEEEEEEEEeCCCcc
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKVDMHLSFRPGDIVRASVLSLGDARA  149 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~-d~~~~~~~~~~GDiV~AkV~s~~~~~~  149 (198)
                      .|+|++||+|+|+|+++.+++|+|+|        ...++|+||.++++..+. +..++++.|++||.|.|+|++++..+.
T Consensus         2 ~Y~Pk~Gdiv~G~V~~i~~~g~fV~i--------~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~   73 (87)
T d2je6i1           2 FYYPKINDIVIGLVEDVEIYGWVVDI--------KAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSID   73 (87)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEEC--------SSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEE
T ss_pred             cccCCCCCEEEEEEEEEECCEEEEEe--------CCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECCCCC
Confidence            59999999999999999999999999        678999999999975433 234788999999999999999987678


Q ss_pred             EEEEEecCCCeee
Q 029155          150 YFLSTAKNDLGVV  162 (198)
Q Consensus       150 ~~LSt~~~~lGvv  162 (198)
                      +.||+++.+||++
T Consensus        74 i~LS~k~~~lgkl   86 (87)
T d2je6i1          74 PVLSVKGKDLGRV   86 (87)
T ss_dssp             EEEECCSTTCEEC
T ss_pred             EEEEEecCCCccC
Confidence            9999999999987

>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=99.77  E-value=7.3e-19  Score=124.51  Aligned_cols=81  Identities=16%  Similarity=0.171  Sum_probs=72.0

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccE
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAY  150 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~  150 (198)
                      +|+|++||+|+|+|++++.+.|+|||        ++++.|+||.+++. ....  ++++.|++||+|+|||++++..+.+
T Consensus         1 rY~P~~GD~ViG~V~~~~~~~~~VdI--------~s~~~a~L~~~~f~-g~~k--~~r~~l~~GD~V~arV~~v~~~~~~   69 (88)
T d2nn6g1           1 RYVPVKGDHVIGIVTAKSGDIFKVDV--------GGSEPASLSYLSFE-GATK--RNRPNVQVGDLIYGQFVVANKDMEP   69 (88)
T ss_dssp             SCCCCSSEEEEEEEEEEETTEEEEEC--------SSSSCCCEESCSSS-CCSS--CSSSSSCTTCEEEEEEEECCTTSCC
T ss_pred             CCcCCCCCEEEEEEEEEeCCeEEEEc--------CCCeeEEEeHHHcC-cccc--ccCcccCCCCEEEEEEEEeCCCCCE
Confidence            59999999999999999999999999        78899999999984 3333  7899999999999999999877789


Q ss_pred             EEEE-----ecCCCeee
Q 029155          151 FLST-----AKNDLGVV  162 (198)
Q Consensus       151 ~LSt-----~~~~lGvv  162 (198)
                      .||.     ++.+||++
T Consensus        70 ~Lscvd~~~k~~g~G~L   86 (88)
T d2nn6g1          70 EMVCIDSCGRANGMGVI   86 (88)
T ss_dssp             EEECSBTTTTBCCCCSC
T ss_pred             EEEEEcccCcccCCccc
Confidence            9987     67788876

>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=99.75  E-value=1.7e-18  Score=122.18  Aligned_cols=84  Identities=25%  Similarity=0.364  Sum_probs=75.1

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc--cccccccCCCCCCEEEEEEEEeCCCc
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DKVDMHLSFRPGDIVRASVLSLGDAR  148 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~--d~~~~~~~~~~GDiV~AkV~s~~~~~  148 (198)
                      .|.|++||+|.|+|+++++++|+|+|        ...+.|+||.+++.....  +..++++.|++||.|.|+|++++..+
T Consensus         2 ~Y~Pk~GdvV~G~V~~v~~~g~fV~i--------~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~~~   73 (88)
T d2z0sa1           2 IYVPQAGDVVIGLIQSVGIMNWFVDI--------NSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTR   73 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEEC--------SSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTS
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEe--------CCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECCCC
Confidence            49999999999999999999999999        678899999999864432  23478899999999999999998667


Q ss_pred             cEEEEEecCCCeee
Q 029155          149 AYFLSTAKNDLGVV  162 (198)
Q Consensus       149 ~~~LSt~~~~lGvv  162 (198)
                      .+.||+++.+||+|
T Consensus        74 ~i~Ls~k~~~~gkl   87 (88)
T d2z0sa1          74 SPLLTVQGEGLGRI   87 (88)
T ss_dssp             CEEEECCSSSCEEC
T ss_pred             CEEEEEecCCCccc
Confidence            89999999999987

>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=99.75  E-value=2.5e-18  Score=122.17  Aligned_cols=82  Identities=12%  Similarity=0.095  Sum_probs=70.2

Q ss_pred             CCCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCcc
Q 029155           70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARA  149 (198)
Q Consensus        70 ~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~  149 (198)
                      ++|+|++||+|+|+|+++..+.|+|||        .+++.|+||.+........  ++++.|++||+|.|||++++..+.
T Consensus         1 krY~P~~gD~ViG~V~~~~~~~~~vdI--------~~~~~~~L~~~~~f~g~~k--~~r~~l~~GDlV~arV~~v~~~~~   70 (90)
T d2ja9a1           1 KRYIPSVNDFVIGVIIGTFSDSYKVSL--------QNFSSSVSLSYMAFPNASK--KNRPTLQVGDLVYARVCTAEKELE   70 (90)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEES--------STTSCCEEEETTSSTTCCS--SSCCCCCTTCEEEEEEEECCTTSC
T ss_pred             CCccCCCCCEEEEEEEEEeCCcEEEEc--------CCcchhhhhhhhccCcccc--ccCCccCCCCEEEEEEEEECCCCC
Confidence            379999999999999999999999999        7788899887775543333  889999999999999999987788


Q ss_pred             EEEEEecCCCee
Q 029155          150 YFLSTAKNDLGV  161 (198)
Q Consensus       150 ~~LSt~~~~lGv  161 (198)
                      +.||+.++.+|+
T Consensus        71 ~~Lsc~~~~~gK   82 (90)
T d2ja9a1          71 AEIECFDSTTGR   82 (90)
T ss_dssp             CEEESSCTTTCS
T ss_pred             EEEEEeccccCc
Confidence            999987665554

>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=99.74  E-value=9.9e-18  Score=116.86  Aligned_cols=82  Identities=17%  Similarity=0.191  Sum_probs=73.6

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYF  151 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~  151 (198)
                      |.|++||+|.|+|+++.+++|+|+|        ...+.|+||.++++... ...++++.|++||.|.|+|+++++.+.+.
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i--------~~~~~g~l~~se~s~~~-~~~~~~~~~~vGd~V~~kV~~vd~~~~i~   71 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDI--------YSPYQAFLPVSENPEMK-PNKKPNEVLDIGDAIIAKVLNIDPKMKVT   71 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEC--------SSSSCEEEEGGGCTTCC-TTSCGGGTCCTTCEEEEEEEEECTTCCEE
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEec--------CCCeeEEEecccccccc-cccChhhhcccccEEEEEEEEECCCCCEE
Confidence            7899999999999999999999999        67899999999997432 22378999999999999999998667899


Q ss_pred             EEEecCCCeee
Q 029155          152 LSTAKNDLGVV  162 (198)
Q Consensus       152 LSt~~~~lGvv  162 (198)
                      ||+++..||.+
T Consensus        72 LS~k~~~~~k~   82 (83)
T d2ba0a1          72 LTMKDRICRPI   82 (83)
T ss_dssp             EECCSSSCEEE
T ss_pred             EEecCCCCCCC
Confidence            99999999986

>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=99.52  E-value=6.5e-15  Score=93.51  Aligned_cols=50  Identities=34%  Similarity=0.533  Sum_probs=45.2

Q ss_pred             CcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCC
Q 029155            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA   69 (198)
Q Consensus         8 ~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~   69 (198)
                      +++|+|||.|++ ++|++|+|||.++++  |+|+++|.++..         |+.|+|+|+++
T Consensus         1 r~iV~PGe~i~~-~~~~~G~Gty~~~~~--i~ss~~G~v~~~---------n~~i~V~PL~g   50 (51)
T d2ba0a2           1 RKIVLPGDLLST-NPRAAGYGTYVEGGK--VYAKIIGLFDQT---------ETHVRVIPLKG   50 (51)
T ss_dssp             CCEECTTCEEES-CTTSBCTTEEEETTE--EEECSSEEEEEC---------SSCEEEEECSS
T ss_pred             CCEEcCCcEeec-CCeeCCCCcEEECCE--EEEEEEEEEEEE---------CCEEEEEeCcc
Confidence            479999999987 579999999999999  999999999983         57999999864

>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=99.49  E-value=1e-14  Score=90.60  Aligned_cols=48  Identities=25%  Similarity=0.468  Sum_probs=44.7

Q ss_pred             cEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecC
Q 029155            9 VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (198)
Q Consensus         9 ~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~   67 (198)
                      +||+|||.|...+.|+.|||||.++++  |+||++|.++..         ||+++|+|+
T Consensus         1 ~iv~PGe~It~~~~~mrGHGTy~~~~~--i~aSv~G~verv---------NKLvsV~pL   48 (48)
T d2nn6h2           1 HLVVPGDTITTDTGFMRGHGTYMGEEK--LIASVAGSVERV---------NKLICVKAL   48 (48)
T ss_dssp             CBCCTTCBCCCCTTCCBCTTEEECSSS--EEECSSEEEEEE---------TTEEEEEES
T ss_pred             CEecCCcEeecCCCeEcccccEecCCE--EEEEEeeeEEEe---------ccEEEEEcC
Confidence            479999999998899999999999999  999999999985         689999985

>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=99.42  E-value=2.2e-13  Score=93.11  Aligned_cols=73  Identities=19%  Similarity=0.229  Sum_probs=66.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS  153 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS  153 (198)
                      +++|++|.|+|+++.+++++|++        .....|+||.++++..+.+  ++++.|++||.|.|+|++++..+.+.||
T Consensus         3 ~kvG~iv~G~V~~v~~~G~fV~l--------~~~~~Glv~~sels~~~~~--~~~~~~~~G~~v~v~Vi~id~~~ri~LS   72 (76)
T d1sroa_           3 IEVGRVYTGKVTRIVDFGAFVAI--------GGGKEGLVHISQIADKRVE--KVTDYLQMGQEVPVKVLEVDRQGRIRLS   72 (76)
T ss_dssp             CCTTSEEEEEEEEEETTEEEEEC--------SSSCCCBCCTTSSCSSCCS--CHHHHCCTTCEEEEEEEECCTTCCCEEE
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEe--------CCCCEEEEEhHHhCccccC--CHHHccCCCCEEEEEEEEECCCCCEEEE
Confidence            58999999999999999999999        5678999999999887766  8899999999999999999866789999


Q ss_pred             Eec
Q 029155          154 TAK  156 (198)
Q Consensus       154 t~~  156 (198)
                      ++.
T Consensus        73 ~k~   75 (76)
T d1sroa_          73 IKE   75 (76)
T ss_dssp             ECC
T ss_pred             EEc
Confidence            985

>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=99.41  E-value=4.9e-13  Score=93.27  Aligned_cols=76  Identities=18%  Similarity=0.210  Sum_probs=56.2

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccE
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY  150 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~  150 (198)
                      ..|++||+|.|+|+++.+++++|+|..      ..+.+|+||.++++..+.+  ++.+.|++||.|.|+|++++. .+.+
T Consensus         9 ~~p~~G~iv~G~V~~i~~~G~fV~l~~------~~~i~G~i~~sels~~~~~--~~~~~~~~Gd~v~~kV~~vd~~~~ki   80 (86)
T d1kl9a2           9 KFPEVEDVVMVNVRSIAEMGAYVSLLE------YNNIEGMILLSELSRRRIR--SINKLIRIGRNECVVVIRVDKEKGYI   80 (86)
T ss_dssp             SSCCTTCEEEEEEEEECSSEEEEEETT------TTTEEEEEEGGGC--------------CTTCEEEEEEEEEETTTTEE
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEEec------CCCEEEEEEeeeccccccc--cceEEeecccEEEEEEEEEECCCCEE
Confidence            468999999999999999999999921      1358999999999876665  889999999999999999974 5789


Q ss_pred             EEEEe
Q 029155          151 FLSTA  155 (198)
Q Consensus       151 ~LSt~  155 (198)
                      .||++
T Consensus        81 ~LS~K   85 (86)
T d1kl9a2          81 DLSKR   85 (86)
T ss_dssp             EEEST
T ss_pred             EEEee
Confidence            99986

>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=99.40  E-value=6.3e-15  Score=94.63  Aligned_cols=39  Identities=31%  Similarity=0.478  Sum_probs=36.8

Q ss_pred             cEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEc
Q 029155            9 VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTL   49 (198)
Q Consensus         9 ~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~   49 (198)
                      ++++|||+|+.++||.||+|||+++|.  ||||++|.+.+.
T Consensus         1 k~~lPGe~L~~~eey~~G~gTy~~~g~--I~as~~G~v~id   39 (55)
T d2nn6i2           1 RYCIPGERLCNLEEGSPGSGTYTRHGY--IFSSLAGCLMKS   39 (55)
T ss_dssp             CCCCTTCEEEETTTCCCSSSCEEETTE--EECCSCSCBCCC
T ss_pred             CcccCCcEEeehheecCCCCeEEcCCE--EEEEeeEEEEEe
Confidence            478999999999999999999999999  999999999984

>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=99.38  E-value=2.1e-13  Score=88.85  Aligned_cols=53  Identities=19%  Similarity=0.251  Sum_probs=47.5

Q ss_pred             ccCCcEEecCCccCCCCCeee-CCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCC
Q 029155            5 EEEMVLVTPGEVLGKATEVKA-GKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK   68 (198)
Q Consensus         5 ~~~~~iV~PGd~l~~~~e~~~-G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~   68 (198)
                      .+++++|+|||.|+....|.+ |+|||.++++  ||||++|++++.         |+.|+|+|++
T Consensus         5 v~~r~iV~PGdvi~~~~~~~~~g~~ty~~~~k--i~asv~G~v~~~---------nkli~ViPL~   58 (59)
T d2je6i2           5 LQPRSIVVPGELLAEGEFQIPWSPYILKINSK--YYSTVVGLFDVK---------DTQFEVIPLE   58 (59)
T ss_dssp             CCSSCEECTTCEEEEECCCCCCCTTEEEETTE--EEECSSEEEEEE---------TTEEEEEESC
T ss_pred             EcCCeEECCCcEeeeCCccccCCCEEEecCCE--EEEEEEEEEEEE---------CCEEEEEECC
Confidence            367899999999998778885 9999999999  999999999995         5799999985

>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=99.38  E-value=4.3e-13  Score=93.02  Aligned_cols=78  Identities=14%  Similarity=0.191  Sum_probs=63.5

Q ss_pred             CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-Ccc
Q 029155           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARA  149 (198)
Q Consensus        71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~  149 (198)
                      .-.|++||+|.|+|+++.+++++|+|..      ..+..|+||.++++..+.+  ++.+.|++||.|.|+|++++. .+.
T Consensus         6 ~~~p~~G~iv~G~V~~v~~~G~fV~l~~------~~gi~Gli~~sels~~~~~--~~~~~~~~G~~v~~kV~~vd~~~~~   77 (84)
T d2ahob2           6 SKLPSEGEILIATVKQVFDYGSYVSLDE------YGGLQAFLPWSEVSSKWVK--NIRDVLKENRKVIVKVIRVDRRKGT   77 (84)
T ss_dssp             SSSCCTTCCCEEEEEEEETTEEEEEETT------TTTEEEEECGGGCC-------CHHHHTCSSCEEECEEEEEETTTTE
T ss_pred             ccCCCCCCEEEEEEEEEECCEEEEEECC------cCCEEEEEEcccccccccc--ccceEeecccEEEEEEEEEECCCCE
Confidence            3578999999999999999999999921      1357999999999876655  889999999999999999974 478


Q ss_pred             EEEEEec
Q 029155          150 YFLSTAK  156 (198)
Q Consensus       150 ~~LSt~~  156 (198)
                      +.||++.
T Consensus        78 i~LS~Kq   84 (84)
T d2ahob2          78 VDVSLKK   84 (84)
T ss_dssp             EEEESSS
T ss_pred             EEEEEcC
Confidence            9999873

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.22  E-value=2.1e-11  Score=86.19  Aligned_cols=75  Identities=25%  Similarity=0.268  Sum_probs=67.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL  152 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L  152 (198)
                      .++|++|.|+|+++.+.+++|++        .....|+||.+++...+.+  ++++.|++||.|.|+|++++. .+.+.|
T Consensus        16 ~k~G~iv~g~V~~v~~~G~~V~l--------~~~i~G~i~~~~ls~~~~~--~~~~~~~vGq~v~~~V~~id~~~~~i~L   85 (94)
T d3bzka4          16 LKPGMVLEGVVTNVTNFGAFVDI--------GVHQDGLVHISALSEKFVK--DPYEVVKAGDIVKVKVMEVDIPRNRVGL   85 (94)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEC--------SSSSCEEEEGGGGCSSCCS--CHHHHCCTTCEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEEECcEEEEEe--------CCCceEEeehhhhhccccc--ChhhhhccCcEEEEEEEEEECCCCEEEE
Confidence            58899999999999999999999        6788999999999876665  889999999999999999974 578999


Q ss_pred             EEecCC
Q 029155          153 STAKND  158 (198)
Q Consensus       153 St~~~~  158 (198)
                      |++..+
T Consensus        86 S~K~~e   91 (94)
T d3bzka4          86 SMRMSD   91 (94)
T ss_dssp             ESCTTC
T ss_pred             EEeccC
Confidence            998654

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.02  E-value=8.4e-10  Score=79.48  Aligned_cols=79  Identities=19%  Similarity=0.245  Sum_probs=63.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccc---------cccccCCCCCCEEEEEEEEe
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDK---------VDMHLSFRPGDIVRASVLSL  144 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~---------~~~~~~~~~GDiV~AkV~s~  144 (198)
                      |++||++-|+|++|.+.+++|+|        . +.+|++|.+++...+...         .+..+.|++||.|.++|+++
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            78999999999999999999999        4 489999999997543210         14468999999999999999


Q ss_pred             CC-Cc-----cEEEEEecCCCee
Q 029155          145 GD-AR-----AYFLSTAKNDLGV  161 (198)
Q Consensus       145 ~~-~~-----~~~LSt~~~~lGv  161 (198)
                      +. .+     .+.||.+...+|.
T Consensus        72 d~~~~~~~~~~i~ls~K~~~~~~   94 (106)
T d1go3e1          72 SLKAERKRGSKIALTMRQPYLGK   94 (106)
T ss_dssp             ECCC-----CEEEEECCSTTCEE
T ss_pred             chhhccccCceeecccccCCCCc
Confidence            63 22     2788888887764

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

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

Probab=99.01  E-value=4.2e-10  Score=82.66  Aligned_cols=80  Identities=11%  Similarity=0.141  Sum_probs=66.5

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeecccccc-CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF  151 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~-~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~  151 (198)
                      +++|++|.|+|++|.+++++|+|        . ..+.|+||.+++...... .+..+.|++||.|.|+|++++. .+.+.
T Consensus        19 l~~G~iv~G~V~~i~~~G~~V~l--------g~~~~~G~l~~~els~~~~~-~~~~~~~~vGq~v~~~V~~vd~~~~~i~   89 (119)
T d1wi5a_          19 LKPGMLLTGTVSSLEDHGYLVDI--------GVDGTRAFLPLLKAQEYIRQ-KNKGAKLKVGQYLNCIVEKVKGNGGVVS   89 (119)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEC--------CCSSCEEEEEHHHHHHHHHH-HSSSCCCCTTCEEEEEEEECCTTSCEEE
T ss_pred             cCCCCEEEEEEEEEeccEEEEEE--------eccccceEEeHHHhcccccc-CCHHHhcccceEEEEEEEEEeCCCCEEE
Confidence            68999999999999999999999        4 468999999998754322 1567899999999999999985 46799


Q ss_pred             EEEecCCCeee
Q 029155          152 LSTAKNDLGVV  162 (198)
Q Consensus       152 LSt~~~~lGvv  162 (198)
                      ||++...+-.-
T Consensus        90 LS~k~~~~~~~  100 (119)
T d1wi5a_          90 LSVGHSEVSTA  100 (119)
T ss_dssp             EECCCCCSCCC
T ss_pred             EEecHHHhhhh
Confidence            99997765433

>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=98.79  E-value=1.9e-08  Score=70.01  Aligned_cols=80  Identities=11%  Similarity=0.039  Sum_probs=62.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccc-c-------cccccCCCCCCEEEEEEEEeC
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-K-------VDMHLSFRPGDIVRASVLSLG  145 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d-~-------~~~~~~~~~GDiV~AkV~s~~  145 (198)
                      |-+|+++.|+|++++..+++|+|        . +++|++|.+++...+.- .       .+-.+.|++||.|++||++++
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--------G-PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCI   71 (91)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE--------T-TEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEE--------c-CeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEe
Confidence            67899999999999999999999        3 57999999988643321 0       123457999999999999986


Q ss_pred             -CCcc--EEEEEecCCCeee
Q 029155          146 -DARA--YFLSTAKNDLGVV  162 (198)
Q Consensus       146 -~~~~--~~LSt~~~~lGvv  162 (198)
                       +.++  ...|++++.||.|
T Consensus        72 ~~~~~i~~ig~~~~d~LG~i   91 (91)
T d1y14b1          72 SQVSSIHAIGSIKEDYLGAI   91 (91)
T ss_dssp             EETTEEEEEEECCSTTCEEC
T ss_pred             cccCccEEEEEccCCCCCcC
Confidence             2333  4558888999975

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.69  E-value=4.7e-08  Score=68.39  Aligned_cols=80  Identities=24%  Similarity=0.268  Sum_probs=63.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc---cc-------cccccCCCCCCEEEEEEEE
Q 029155           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI---DK-------VDMHLSFRPGDIVRASVLS  143 (198)
Q Consensus        74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~---d~-------~~~~~~~~~GDiV~AkV~s  143 (198)
                      |-+|+++.|+|++++..+++|++        . +++|++|.+++.....   ++       .+-...|+.||.|++||++
T Consensus         2 Pf~Gev~~g~V~~v~~~G~fv~l--------g-~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~   72 (94)
T d2c35b1           2 PFKGEVVDAVVTQVNKVGLFTEI--------G-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVG   72 (94)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE--------T-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEe--------c-CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEE
Confidence            67899999999999999999999        3 5799999999875431   11       1224568999999999999


Q ss_pred             eC-CCcc--EEEEEecCCCeee
Q 029155          144 LG-DARA--YFLSTAKNDLGVV  162 (198)
Q Consensus       144 ~~-~~~~--~~LSt~~~~lGvv  162 (198)
                      ++ +.+.  ...|++++-||.|
T Consensus        73 v~~~~~~I~~igt~~~d~LG~i   94 (94)
T d2c35b1          73 TRVDKNDIFAIGSLMDDYLGLV   94 (94)
T ss_dssp             EEEETTEEEEEEECCSTTCEEC
T ss_pred             EecCcCcceEEEEccCCCcccC
Confidence            76 3334  3488999999975

>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=98.47  E-value=2.4e-09  Score=69.91  Aligned_cols=58  Identities=14%  Similarity=0.143  Sum_probs=34.4

Q ss_pred             EEEEEEecceEEEEEeeeccccccCcceeEEecccccccc--ccccccccCCCCCCEEEEEEEEeCCC
Q 029155           82 ARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE--IDKVDMHLSFRPGDIVRASVLSLGDA  147 (198)
Q Consensus        82 G~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~--~d~~~~~~~~~~GDiV~AkV~s~~~~  147 (198)
                      |+|++|.+++++|+|        ....+|+||+|+++...  ..-.++++.|++||.|.++|++++..
T Consensus         1 G~V~~i~~fG~FV~l--------~~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~   60 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSL--------LPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSR   60 (62)
T ss_dssp             CBEEECC-CSCEECC--------C---CCCCC-------------------CCSSCBCCCCCCCCCSS
T ss_pred             CEEEEEEeceEEEEe--------cCCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCC
Confidence            789999999999999        66899999999997532  11227899999999999999999753

>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=98.38  E-value=1.4e-06  Score=58.00  Aligned_cols=57  Identities=21%  Similarity=0.279  Sum_probs=49.6

Q ss_pred             CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC
Q 029155           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG  145 (198)
Q Consensus        72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~  145 (198)
                      |.-++|++|.|.|.++..+.+.|+|        . ..+|+|+.++.-        ..+.|++||-|+|-|..+.
T Consensus         4 f~~~~geiv~G~V~r~~~~~~~Vdl--------g-~~eaiLp~~eqi--------p~E~~~~Gdrik~~i~~V~   60 (72)
T d1hh2p1           4 YSELKGTVTTAEVIRVMGEWADIRI--------G-KLETRLPKKEWI--------PGEEIKAGDLVKVYIIDVV   60 (72)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEEE--------T-TEEEEEEGGGSC--------TTCCCCTTCEEEEEEEEEE
T ss_pred             HhhccCcEEEEEEEEEcCCCEEEEE--------C-CcEEECCHHHcC--------CCCCCCCCCEEEEEEEEEE
Confidence            5678999999999999999999999        3 589999987742        3688999999999999885

>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=97.72  E-value=5.1e-05  Score=50.72  Aligned_cols=59  Identities=15%  Similarity=0.214  Sum_probs=45.6

Q ss_pred             CCCCEEEEEEEEEecc----eEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC
Q 029155           75 EPGSVVIARVTKVMTR----MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD  146 (198)
Q Consensus        75 ~vGDiViG~V~~v~~~----~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~  146 (198)
                      ++|++|.|.|.++..+    .+.|+|..-     ....+|+|+.++-        -..+.|++||-|+|-|..+..
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~-----~~~~EaiLp~~eq--------ip~E~y~~Gdrik~~i~~V~~   65 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTE-----TKASEGVIPAAEQ--------VPGESYEHGNRLRCYVVGVTR   65 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSS-----SSCEEEEECGGGS--------CTTCCCCTTCEEEEEEEEEEC
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCC-----CCCEEEECCHHHc--------CCCcccCCCCEEEEEEEEEEe
Confidence            6899999999999654    478998310     1357899987763        236889999999999999863

>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=97.14  E-value=0.0015  Score=44.38  Aligned_cols=70  Identities=13%  Similarity=0.189  Sum_probs=53.1

Q ss_pred             CEEEEEEEEEec--ceEEEEEeeeccccccCcceeEEeccccccccc-------cccccccCCCCCCEEEEEEEEeC-CC
Q 029155           78 SVVIARVTKVMT--RMASADIMCVGAKSVREKFSGIIRQQDVRATEI-------DKVDMHLSFRPGDIVRASVLSLG-DA  147 (198)
Q Consensus        78 DiViG~V~~v~~--~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~-------d~~~~~~~~~~GDiV~AkV~s~~-~~  147 (198)
                      +|-.|+|++|.+  +.|||||        ...-.|.||.+|+...+.       .+..+.+.+++||.|...|..=. ..
T Consensus         2 NIY~G~V~~V~pgl~AAFVDi--------G~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~   73 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGN   73 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEES--------SSSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTT
T ss_pred             CcEEEEEEEecCCceEEEEEe--------CCCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccCC
Confidence            577899999977  5799999        677789999998764321       23467889999999999999843 12


Q ss_pred             ccEEEEEe
Q 029155          148 RAYFLSTA  155 (198)
Q Consensus       148 ~~~~LSt~  155 (198)
                      ....||+.
T Consensus        74 KGprlT~~   81 (87)
T d1smxa_          74 KGAALTTF   81 (87)
T ss_dssp             BCCEEESC
T ss_pred             CCceEEEE
Confidence            44666664

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=97.13  E-value=0.0011  Score=45.05  Aligned_cols=67  Identities=7%  Similarity=0.093  Sum_probs=49.8

Q ss_pred             CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc--c--ccc------cccCCCCCCEEEEEEEEeCC
Q 029155           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--D--KVD------MHLSFRPGDIVRASVLSLGD  146 (198)
Q Consensus        77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~--d--~~~------~~~~~~~GDiV~AkV~s~~~  146 (198)
                      |..-.|.|++|+..+.+|+|.       ....+|++|.+++...+.  +  ...      -...|++||.|.++|++++.
T Consensus         4 ~~~F~g~Is~v~~~GifV~L~-------e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~   76 (87)
T d2ix0a3           4 DTRFAAEIVDISRGGMRVRLV-------DNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRM   76 (87)
T ss_dssp             CCCEEEEEEEEETTEEEEEET-------TTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEET
T ss_pred             CCEEEEEEEEEEcCeEEEEEe-------cCCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEec
Confidence            455679999999999999992       235799999999975321  1  011      13579999999999999974


Q ss_pred             -CccE
Q 029155          147 -ARAY  150 (198)
Q Consensus       147 -~~~~  150 (198)
                       .+.+
T Consensus        77 ~~r~I   81 (87)
T d2ix0a3          77 ETRSI   81 (87)
T ss_dssp             TTTEE
T ss_pred             ccCeE
Confidence             3444

>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=96.52  E-value=0.0017  Score=41.78  Aligned_cols=59  Identities=24%  Similarity=0.281  Sum_probs=46.0

Q ss_pred             eeccCCcEEecCCccCCC--CCeeeCCCEEEe-CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecC
Q 029155            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~-~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~   67 (198)
                      +|...+++|.||..|..-  ..|.||.|+..- |..  |||.+.|.|+....    ..+++.|+|.|.
T Consensus         4 vK~~~Gq~V~~G~IivRQRGtk~~pG~nVg~GkD~T--LfAl~~G~V~F~~~----~~~~~~VsV~P~   65 (66)
T d1v8qa_           4 VKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFT--LFALVDGVVEFQDR----GRLGRYVHVRPL   65 (66)
T ss_dssp             ECSCTTCEECTTCEEEECSSCSSEECTTEEECTTCC--EEESSSEEEEEEEC----GGGCEEEEEEEC
T ss_pred             cEEeCCEEEeCCeEEEEeccCeEeCCCCeeecCCCc--EEEeeeeEEEEEEe----CCCCeEEEEEEC
Confidence            467788999999998743  469999999877 545  99999999988531    123568899985

>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=96.52  E-value=0.0011  Score=44.99  Aligned_cols=56  Identities=23%  Similarity=0.191  Sum_probs=30.8

Q ss_pred             CCcEEecCCccCCCC-------------------------CeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCe
Q 029155            7 EMVLVTPGEVLGKAT-------------------------EVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPT   61 (198)
Q Consensus         7 ~~~iV~PGd~l~~~~-------------------------e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~   61 (198)
                      -.++|+|||.|...+                         ..+.|+|...+++.  |.++.+|.++..++..  ...-..
T Consensus         8 ~~qvVlPGD~l~lp~~~~~~g~~~~~~~~l~L~~~~~~~~~v~lGPGLRq~~d~--v~atKaG~LR~k~P~~--~~~~~~   83 (91)
T d2nn6g2           8 LGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDR--LLVTKCGRLRHKEPGS--GSGGGV   83 (91)
T ss_dssp             GSSBCCSSEEECCSCSCCEECSSEEECC-----------------------CCC--EEECSCCEEEEECCTT--TSSCCE
T ss_pred             cCCEEeCCcEEEecccccccccCcCcccccccccccCCCceEEeCCccceeCCE--EEEeecceeeecCCCC--CCCcce
Confidence            357999999994211                         25679999999988  9999999999864210  001236


Q ss_pred             EEEec
Q 029155           62 VEVTG   66 (198)
Q Consensus        62 i~V~p   66 (198)
                      .||..
T Consensus        84 yWVDs   88 (91)
T d2nn6g2          84 YWVDS   88 (91)
T ss_dssp             EEEEC
T ss_pred             EEeec
Confidence            78875

>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=95.93  E-value=0.0035  Score=42.11  Aligned_cols=60  Identities=20%  Similarity=0.285  Sum_probs=45.3

Q ss_pred             eeccCCcEEecCCccCCC--CCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecC
Q 029155            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~   67 (198)
                      +|....++|.||+.|..-  ..|.||.+++.-.+ .+|||.+-|.|....    ...+++.|+|.|.
T Consensus        22 vK~~~Gq~V~~G~IivRQRGtk~hpG~nVg~GkD-~TLfA~~~G~V~F~k----~~~~rk~V~V~p~   83 (84)
T d2zjrt1          22 VKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRD-HTLFALSDGKVVFIN----KGKGARFISIEAA   83 (84)
T ss_dssp             CSSCTTCEECSSCEEECCSSSSSEECTTEECCTT-SCEEESSCEEEEEEE----ETTTEEEEEECCC
T ss_pred             EEECCCEEEeCCcEEEEecCceEcCCCCccccCC-CcEEEeeceEEEEEE----cCCCCEEEEEEeC
Confidence            466788999999998753  36999999987632 349999999999853    1123467888874

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=84.30  E-value=0.25  Score=27.80  Aligned_cols=24  Identities=8%  Similarity=0.110  Sum_probs=19.0

Q ss_pred             ec-CCCceeEEccCCeEEeCCCCCE
Q 029155          165 ES-TAGGTMVPISWTEMQCPLTGQT  188 (198)
Q Consensus       165 ~~-~~g~~m~~~~~~~~~c~~cg~~  188 (198)
                      .| +|+....--+...|.||+||..
T Consensus         5 ~CP~C~seytYedg~l~vCPeC~hE   29 (38)
T d2akla2           5 PCPQCNSEYTYEDGALLVCPECAHE   29 (38)
T ss_dssp             CCTTTCCCCCEECSSSEEETTTTEE
T ss_pred             cCCCCCCcceEcCCCEEECCcccCc
Confidence            47 7888776667789999999964

>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=81.60  E-value=0.033  Score=37.16  Aligned_cols=45  Identities=22%  Similarity=0.285  Sum_probs=36.2

Q ss_pred             eeccCCcEEecCCccCCC--CCeeeCCCEEEe-CCceEEEEeEeeeEEEc
Q 029155            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTL   49 (198)
Q Consensus         3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~-~g~~~i~asv~G~v~~~   49 (198)
                      +|....++|.||+.|..-  ..|.||.++..- |..  |||.+.|.|+..
T Consensus        22 vK~~~Gq~V~~G~IivRQRGtk~hPG~nVg~GkD~T--LfAl~~G~V~F~   69 (84)
T d2gycu1          22 VKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHT--LFAKADGKVKFE   69 (84)
T ss_dssp             CSSSCCCSSCCSBSSCCCCCCSSCCCCCSSSCCCCC--CCCCSCCCCSSS
T ss_pred             eEEcCCEEEcCCcEEEEeccceEcCCCCeeecCCCe--EEEeccEEEEEE
Confidence            467788999999999753  368999998765 544  999999999874

>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=81.56  E-value=2.1  Score=30.37  Aligned_cols=55  Identities=15%  Similarity=0.181  Sum_probs=35.6

Q ss_pred             EEEEEEEEEe--cceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEE
Q 029155           79 VVIARVTKVM--TRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRAS  140 (198)
Q Consensus        79 iViG~V~~v~--~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~Ak  140 (198)
                      .|-|||+.++  .+.++++|..-     ...++-+++...+.....+  .....+++||+|-++
T Consensus        58 ~vaGRI~~~R~~Gk~~F~~i~D~-----~g~iQi~~~~~~~~~~~~~--~~~k~ld~GDiIgv~  114 (143)
T d1e1oa1          58 SVAGRMMTRRIMGKASFVTLQDV-----GGRIQLYVARDSLPEGVYN--DQFKKWDLGDIIGAR  114 (143)
T ss_dssp             EEEEEEEEEEEETTEEEEEEEET-----TEEEEEEEETTTSSTTHHH--HTGGGCCTTCEEEEE
T ss_pred             EEEEEEEEEcccCCeeEEEEEeC-----CceEEEEEccccchhhhHH--HHHhcCCcccEEEee
Confidence            3789999886  57788888432     2245666665555432222  345779999998653

>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=80.87  E-value=1.3  Score=30.93  Aligned_cols=35  Identities=23%  Similarity=0.313  Sum_probs=24.6

Q ss_pred             CCCCEE---------EEEEEEEecceEEEEEeeeccccccCcceeEEe
Q 029155           75 EPGSVV---------IARVTKVMTRMASADIMCVGAKSVREKFSGIIR  113 (198)
Q Consensus        75 ~vGDiV---------iG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~  113 (198)
                      ++||+|         +|.|++.+++.+.|.|.+|-    ..+-+|-||
T Consensus         3 ~~g~~V~~~yKTG~Yigei~e~~~~~~lVkVlaVl----KHP~QGDLH   46 (124)
T d1y71a1           3 EIGEIVTGIYKTGKYIGEVTNSRPGSYVVKVLAVL----KHPVQGDLH   46 (124)
T ss_dssp             CTTCEEEEEETTEEEEEEEEEEETTEEEEEEEEEE----ECCCC----
T ss_pred             ccCcEEEEEEecceeEEEEEeecCCeEEEEEEEEe----cCCCccCcC
Confidence            567777         78999999999999998763    334555555