Psyllid ID: psy800

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200----
Protein Sequence
MTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHTHCGMRPYIQHSMGE
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHHcccEEEEEEcccEEEEEEEEccccEEEEEEEcEEEEcccccEEEEccEEEcccccEEEEEccccccccccccccccccccccccccccccccccccHHHHHHHcccEEEEEEcccEEEEEEEccccccccEEcccEEEEEEccccEEEEEEccEEEEcccEEEEcccccccccHHHHccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHHHHHccccEEEEEEcccEEEEEEEccHHHHHEEHHccEEEccccccEEcccEEEEccccEEEEEEccccEccccccccEEEcEcccccccccccccccccHHHHHHHHcccEEEEEEcccEEEEEEEccHHHHHEEHHccEEEEEcccccEEEcccEEEEcccHHHHHHHHHccccccEEEccccc
Coil and Loop (DISEMBL)
mtapsvatnpstllplelVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEdvtdchdshLLSYFASDLINfiwglpmitpitcaysrshqyRTLTHLLYTmtapsvatnpstllplelVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDvteyestpegrritKLDQILlngnnitmlglhthcgmrpyiqhsmge
Flexible Loop (DISEMBL)
mtapsvatnpstllplELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTeyestpegrriTKLDQILLNGNNITMLGLHTHCGMRPYIQHSMGE
Low Complexity Region (SEG)
MTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHTHCGMRPYIQHSMGE
Disordered region (IsUnstruct)
***********TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHTHCGMRPYI******
Disordered Region (DISOPRED)
*************LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPITCAYSR***************************PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP****ITKLDQILLNGNNITMLGLHTHCGMRPY*Q*S***
Disordered Region (DISEMBL)
********NPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT********RRITKLDQILLNGNNITMLGLHTHCGMRPYIQHSMGE
Disordered Region (DISPRO)
***********TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHTHCGMRPYIQH****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHTHCGMRPYIQHSMGE
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	204	2.2.26 [Sep-21-2011]
Q5R628	91	U6 snRNA-associated Sm-li	yes	N/A	0.397	0.890	0.864	5e-34
P62322	91	U6 snRNA-associated Sm-li	yes	N/A	0.397	0.890	0.864	5e-34
Q9Y4Y9	91	U6 snRNA-associated Sm-li	yes	N/A	0.397	0.890	0.864	5e-34
Q2HJH0	91	U6 snRNA-associated Sm-li	yes	N/A	0.397	0.890	0.864	5e-34
Q55EX5	97	Probable U6 snRNA-associa	yes	N/A	0.357	0.752	0.698	1e-22
O42978	80	U6 snRNA-associated Sm-li	yes	N/A	0.343	0.875	0.541	9e-15
P40089	93	U6 snRNA-associated Sm-li	yes	N/A	0.348	0.763	0.460	2e-10
P40070	187	U6 snRNA-associated Sm-li	no	N/A	0.362	0.395	0.317	0.0006
P62311	102	U6 snRNA-associated Sm-li	no	N/A	0.240	0.480	0.408	0.0009
P62310	102	U6 snRNA-associated Sm-li	no	N/A	0.240	0.480	0.408	0.0009

>sp|Q5R628|LSM5_PONAB U6 snRNA-associated Sm-like protein LSm5 OS=Pongo abelii GN=LSM5 PE=3 SV=3

 Score =  144 bits (362), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 70/81 (86%), Positives = 75/81 (92%)

Query: 106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
           A +  TNPS LLPLELVDKCIGSRIHI+MK+DKEIVGTL GFDDFVNM+LEDVTE+E TP
Sbjct: 2   AANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITP 61

Query: 166 EGRRITKLDQILLNGNNITML 186
           EGRRITKLDQILLNGNNITML
Sbjct: 62  EGRRITKLDQILLNGNNITML 82

Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro.
Pongo abelii (taxid: 9601)

>sp|P62322|LSM5_MOUSE U6 snRNA-associated Sm-like protein LSm5 OS=Mus musculus GN=Lsm5 PE=3 SV=2

 Score =  144 bits (362), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 70/81 (86%), Positives = 75/81 (92%)

Query: 106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
           A +  TNPS LLPLELVDKCIGSRIHI+MK+DKEIVGTL GFDDFVNM+LEDVTE+E TP
Sbjct: 2   AANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITP 61

Query: 166 EGRRITKLDQILLNGNNITML 186
           EGRRITKLDQILLNGNNITML
Sbjct: 62  EGRRITKLDQILLNGNNITML 82

Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro.

Mus musculus (taxid: 10090)

>sp|Q9Y4Y9|LSM5_HUMAN U6 snRNA-associated Sm-like protein LSm5 OS=Homo sapiens GN=LSM5 PE=1 SV=3

 Score =  144 bits (362), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 70/81 (86%), Positives = 75/81 (92%)

Query: 106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
           A +  TNPS LLPLELVDKCIGSRIHI+MK+DKEIVGTL GFDDFVNM+LEDVTE+E TP
Sbjct: 2   AANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITP 61

Query: 166 EGRRITKLDQILLNGNNITML 186
           EGRRITKLDQILLNGNNITML
Sbjct: 62  EGRRITKLDQILLNGNNITML 82

Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro.

Homo sapiens (taxid: 9606)

>sp|Q2HJH0|LSM5_BOVIN U6 snRNA-associated Sm-like protein LSm5 OS=Bos taurus GN=LSM5 PE=3 SV=3

 Score =  144 bits (362), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 70/81 (86%), Positives = 75/81 (92%)

Query: 106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
           A +  TNPS LLPLELVDKCIGSRIHI+MK+DKEIVGTL GFDDFVNM+LEDVTE+E TP
Sbjct: 2   AANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITP 61

Query: 166 EGRRITKLDQILLNGNNITML 186
           EGRRITKLDQILLNGNNITML
Sbjct: 62  EGRRITKLDQILLNGNNITML 82

Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro.

Bos taurus (taxid: 9913)

>sp|Q55EX5|LSM5_DICDI Probable U6 snRNA-associated Sm-like protein LSm5 OS=Dictyostelium discoideum GN=lsm5 PE=3 SV=1

 Score =  106 bits (264), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/73 (69%), Positives = 60/73 (82%)

Query: 114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKL 173
           S LLPLEL++KCIGSRI I MKNDKE VGTL GFD +VN+ L+DVTEYE TPEG +  KL
Sbjct: 14  SQLLPLELIEKCIGSRIWIAMKNDKEFVGTLLGFDAYVNIFLKDVTEYEYTPEGLKTVKL 73

Query: 174 DQILLNGNNITML 186
           D ILLNGN++ +L
Sbjct: 74  DNILLNGNHVCLL 86

Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA.

Dictyostelium discoideum (taxid: 44689)

>sp|O42978|LSM5_SCHPO U6 snRNA-associated Sm-like protein LSm5 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm5 PE=1 SV=2

 Score = 80.1 bits (196), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 39/72 (54%), Positives = 55/72 (76%), Gaps = 2/72 (2%)

Query: 115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLD 174
           T+LPLEL+DKCIGS + +IMK+++E  GTL GFDD+VN++L+DVTEY++        K  
Sbjct: 4   TILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVT--GVTEKHS 61

Query: 175 QILLNGNNITML 186
           ++LLNGN + ML
Sbjct: 62  EMLLNGNGMCML 73

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. LSm5 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

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

>sp|P40089|LSM5_YEAST U6 snRNA-associated Sm-like protein LSm5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM5 PE=1 SV=1

 Score = 65.9 bits (159), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/76 (46%), Positives = 53/76 (69%), Gaps = 5/76 (6%)

Query: 116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGR-RITKLD 174
           +LPLE++DK I  ++ I++++++E  GTL GFDDFVN++LED  E+   PE   R  K+ 
Sbjct: 6   ILPLEVIDKTINQKVLIVLQSNREFEGTLVGFDDFVNVILEDAVEWLIDPEDESRNEKVM 65

Query: 175 Q----ILLNGNNITML 186
           Q    +LL+GNNI +L
Sbjct: 66  QHHGRMLLSGNNIAIL 81

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM5 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM5, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM5 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

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

>sp|P40070|LSM4_YEAST U6 snRNA-associated Sm-like protein LSm4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM4 PE=1 SV=1

 Score = 44.3 bits (103), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 8/82 (9%)

Query: 116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEY--------ESTPEG 167
           +LPL L+    G ++ I +KN + I G L   D+++N+ L +VTEY        E   E 
Sbjct: 1   MLPLYLLTNAKGQQMQIELKNGEIIQGILTNVDNWMNLTLSNVTEYSEESAINSEDNAES 60

Query: 168 RRITKLDQILLNGNNITMLGLH 189
            +  KL++I + G  I  + L 
Sbjct: 61  SKAVKLNEIYIRGTFIKFIKLQ 82

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM4 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM4, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM4 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

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

>sp|P62311|LSM3_MOUSE U6 snRNA-associated Sm-like protein LSm3 OS=Mus musculus GN=Lsm3 PE=3 SV=2

 Score = 43.5 bits (101), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 33/49 (67%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE 166
           PL+L+   +  RI++ M+ND+E+ G L+ +D  +NM+L DV E  +T E
Sbjct: 17  PLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIE 65

Binds specifically to the 3'-terminal U-tract of U6 snRNA.

Mus musculus (taxid: 10090)

>sp|P62310|LSM3_HUMAN U6 snRNA-associated Sm-like protein LSm3 OS=Homo sapiens GN=LSM3 PE=1 SV=2

 Score = 43.5 bits (101), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 33/49 (67%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE 166
           PL+L+   +  RI++ M+ND+E+ G L+ +D  +NM+L DV E  +T E
Sbjct: 17  PLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIE 65

Binds specifically to the 3'-terminal U-tract of U6 snRNA.

Homo sapiens (taxid: 9606)

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	204
242023983	91	conserved hypothetical protein [Pediculu	0.401	0.901	0.975	3e-36
193582383	91	PREDICTED: u6 snRNA-associated Sm-like p	0.397	0.890	0.950	3e-36
156555736	93	PREDICTED: U6 snRNA-associated Sm-like p	0.401	0.881	0.902	7e-35
307178103	91	U6 snRNA-associated Sm-like protein LSm5	0.397	0.890	0.913	9e-35
322791094	83	hypothetical protein SINV_04240 [Solenop	0.397	0.975	0.901	9e-35
332026604	91	U6 snRNA-associated Sm-like protein LSm5	0.401	0.901	0.915	1e-34
307197393	91	U6 snRNA-associated Sm-like protein LSm5	0.387	0.868	0.924	2e-34
170055785	92	Lsm5 protein [Culex quinquefasciatus] gi	0.397	0.880	0.913	8e-34
110760718	91	PREDICTED: u6 snRNA-associated Sm-like p	0.387	0.868	0.924	8e-34
290561451	95	U6 snRNA-associated Sm-like protein LSm5	0.406	0.873	0.867	1e-33

>gi|242023983|ref|XP_002432410.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212517833|gb|EEB19672.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  157 bits (397), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 81/83 (97%), Positives = 81/83 (97%), Gaps = 1/83 (1%)

Query: 104 MTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYES 163
           MTA SVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTL GFDDFVNMLLEDVTEYES
Sbjct: 1   MTA-SVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLLGFDDFVNMLLEDVTEYES 59

Query: 164 TPEGRRITKLDQILLNGNNITML 186
           TPEGRRITKLDQILLNGNNITML
Sbjct: 60  TPEGRRITKLDQILLNGNNITML 82

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193582383|ref|XP_001951255.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm5-like [Acyrthosiphon pisum]

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 77/81 (95%), Positives = 79/81 (97%)

Query: 106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
           A SVATNPSTLLPLELVDKCIGSRIHI+MKNDKEIVGTL GFDDFVNMLLEDVTEYESTP
Sbjct: 2   ATSVATNPSTLLPLELVDKCIGSRIHIVMKNDKEIVGTLLGFDDFVNMLLEDVTEYESTP 61

Query: 166 EGRRITKLDQILLNGNNITML 186
           EGRR+TKLDQILLNGNNITML
Sbjct: 62  EGRRVTKLDQILLNGNNITML 82

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156555736|ref|XP_001602011.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm5-like [Nasonia vitripennis]

 Score =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 74/82 (90%), Positives = 78/82 (95%)

Query: 105 TAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST 164
           +A SV TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTL GFDDFVNMLL+DVTE E+T
Sbjct: 3   SASSVTTNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLKGFDDFVNMLLDDVTESEAT 62

Query: 165 PEGRRITKLDQILLNGNNITML 186
           PEGRR+TKLDQILLNGNNITML
Sbjct: 63  PEGRRVTKLDQILLNGNNITML 84

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307178103|gb|EFN66930.1| U6 snRNA-associated Sm-like protein LSm5 [Camponotus floridanus]

 Score =  152 bits (384), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 74/81 (91%), Positives = 78/81 (96%)

Query: 106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
           A SV+TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTL GFDDFVNMLLEDVTE E+TP
Sbjct: 2   ATSVSTNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLQGFDDFVNMLLEDVTESEATP 61

Query: 166 EGRRITKLDQILLNGNNITML 186
           EGRR+TKLDQILLNG+NITML
Sbjct: 62  EGRRVTKLDQILLNGSNITML 82

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322791094|gb|EFZ15676.1| hypothetical protein SINV_04240 [Solenopsis invicta]

 Score =  152 bits (383), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 73/81 (90%), Positives = 78/81 (96%)

Query: 106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
           A SV+TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTL GFDDFVNMLLEDVTE E+TP
Sbjct: 2   ATSVSTNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLQGFDDFVNMLLEDVTESEATP 61

Query: 166 EGRRITKLDQILLNGNNITML 186
           EGRR+TKLDQILLNG+NITM+
Sbjct: 62  EGRRVTKLDQILLNGSNITMV 82

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332026604|gb|EGI66713.1| U6 snRNA-associated Sm-like protein LSm5 [Acromyrmex echinatior]

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 76/83 (91%), Positives = 80/83 (96%), Gaps = 1/83 (1%)

Query: 104 MTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYES 163
           MTA SV+TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTL GFDDFVNMLLEDVTE E+
Sbjct: 1   MTA-SVSTNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLQGFDDFVNMLLEDVTESEA 59

Query: 164 TPEGRRITKLDQILLNGNNITML 186
           TPEGRR+TKLDQILLNG+NITML
Sbjct: 60  TPEGRRVTKLDQILLNGSNITML 82

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307197393|gb|EFN78665.1| U6 snRNA-associated Sm-like protein LSm5 [Harpegnathos saltator]

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 73/79 (92%), Positives = 77/79 (97%)

Query: 108 SVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG 167
           SV+TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTL GFDDFVNMLLEDVTE E+TPEG
Sbjct: 4   SVSTNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLQGFDDFVNMLLEDVTESEATPEG 63

Query: 168 RRITKLDQILLNGNNITML 186
           RR+TKLDQILLNG+NITML
Sbjct: 64  RRVTKLDQILLNGSNITML 82

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170055785|ref|XP_001863736.1| Lsm5 protein [Culex quinquefasciatus] gi|167875611|gb|EDS38994.1| Lsm5 protein [Culex quinquefasciatus]

 Score =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 74/81 (91%), Positives = 76/81 (93%)

Query: 106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
           A S  +N STLLPLELVDKCIGSRIHIIMKNDKEIVGTL GFDDFVNMLLEDVTEYE+TP
Sbjct: 2   AQSTVSNQSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLLGFDDFVNMLLEDVTEYENTP 61

Query: 166 EGRRITKLDQILLNGNNITML 186
           EGRRITKLDQILLNGNNITML
Sbjct: 62  EGRRITKLDQILLNGNNITML 82

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110760718|ref|XP_001120607.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm5-like [Apis mellifera] gi|340715932|ref|XP_003396461.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm5-like [Bombus terrestris] gi|350396810|ref|XP_003484674.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm5-like [Bombus impatiens] gi|380019757|ref|XP_003693769.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm5-like [Apis florea] gi|383866113|ref|XP_003708516.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm5-like [Megachile rotundata]

 Score =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 73/79 (92%), Positives = 77/79 (97%)

Query: 108 SVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG 167
           SV+TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTL GFDDFVNMLLEDVTE E+TPEG
Sbjct: 4   SVSTNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLLGFDDFVNMLLEDVTESEATPEG 63

Query: 168 RRITKLDQILLNGNNITML 186
           RR+TKLDQILLNG+NITML
Sbjct: 64  RRVTKLDQILLNGSNITML 82

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|290561451|gb|ADD38126.1| U6 snRNA-associated Sm-like protein LSm5 [Lepeophtheirus salmonis]

 Score =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 72/83 (86%), Positives = 79/83 (95%)

Query: 104 MTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYES 163
           M++ SVA NPST+LPLELVDK IGSRIHIIMKNDKEIVGTL GFDDFVNM+LEDVTEYES
Sbjct: 1   MSSISVAPNPSTILPLELVDKAIGSRIHIIMKNDKEIVGTLLGFDDFVNMVLEDVTEYES 60

Query: 164 TPEGRRITKLDQILLNGNNITML 186
           TPEGRR++KLDQILLNGN+ITML
Sbjct: 61  TPEGRRVSKLDQILLNGNHITML 83

Source: Lepeophtheirus salmonis

Species: Lepeophtheirus salmonis

Genus: Lepeophtheirus

Family: Caligidae

Order: Siphonostomatoida

Class: Maxillopoda

Phylum: Arthropoda

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	204
ZFIN|ZDB-GENE-070822-23	91	zgc:171959 "zgc:171959" [Danio	0.397	0.890	0.888	1.5e-33
FB|FBgn0035675	91	CG6610 [Drosophila melanogaste	0.406	0.912	0.855	5.2e-33
UNIPROTKB|Q2HJH0	91	LSM5 "U6 snRNA-associated Sm-l	0.397	0.890	0.864	6.7e-33
UNIPROTKB|Q9Y4Y9	91	LSM5 "U6 snRNA-associated Sm-l	0.397	0.890	0.864	6.7e-33
MGI|MGI:1913623	91	Lsm5 "LSM5 homolog, U6 small n	0.397	0.890	0.864	6.7e-33
WB|WBGene00003079	91	lsm-5 [Caenorhabditis elegans	0.397	0.890	0.765	6.2e-30
UNIPROTKB|O18694	91	lsm-5 "Protein LSM-5" [Caenorh	0.397	0.890	0.765	6.2e-30
TAIR|locus:2156589	88	SAD1 "SUPERSENSITIVE TO ABA AN	0.382	0.886	0.730	1.2e-26
DICTYBASE|DDB_G0268716	97	lsm5 "putative U6 small nuclea	0.357	0.752	0.698	1e-22
ASPGD|ASPL0000026389	129	AN5679 [Emericella nidulans (t	0.406	0.643	0.616	9e-22

ZFIN|ZDB-GENE-070822-23 zgc:171959 "zgc:171959" [Danio rerio (taxid:7955)]

 Score = 365 (133.5 bits), Expect = 1.5e-33, P = 1.5e-33
 Identities = 72/81 (88%), Positives = 75/81 (92%)

Query:   106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
             A   ATNPS LLPLELVDKCIGSRIHI+MKNDKEIVGTL GFDDFVNM+LEDVTE+E TP
Sbjct:     2 AAITATNPSQLLPLELVDKCIGSRIHIVMKNDKEIVGTLLGFDDFVNMVLEDVTEFEITP 61

Query:   166 EGRRITKLDQILLNGNNITML 186
             EGRRITKLDQILLNGNNITML
Sbjct:    62 EGRRITKLDQILLNGNNITML 82

GO:0003674 "molecular_function" evidence=ND

FB|FBgn0035675 CG6610 [Drosophila melanogaster (taxid:7227)]

 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 71/83 (85%), Positives = 77/83 (92%)

Query:   104 MTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYES 163
             MTA    +N STL+PLELVDKCIGSRIHIIMKNDKE+VGTL GFDDFVNMLL+DVTEYE+
Sbjct:     1 MTAVPPPSNISTLMPLELVDKCIGSRIHIIMKNDKEMVGTLLGFDDFVNMLLDDVTEYEN 60

Query:   164 TPEGRRITKLDQILLNGNNITML 186
             TP+GRRITKLDQILLNGNNITML
Sbjct:    61 TPDGRRITKLDQILLNGNNITML 83

GO:0005688 "U6 snRNP" evidence=NAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISS

UNIPROTKB|Q2HJH0 LSM5 "U6 snRNA-associated Sm-like protein LSm5" [Bos taurus (taxid:9913)]

 Score = 359 (131.4 bits), Expect = 6.7e-33, P = 6.7e-33
 Identities = 70/81 (86%), Positives = 75/81 (92%)

Query:   106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
             A +  TNPS LLPLELVDKCIGSRIHI+MK+DKEIVGTL GFDDFVNM+LEDVTE+E TP
Sbjct:     2 AANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITP 61

Query:   166 EGRRITKLDQILLNGNNITML 186
             EGRRITKLDQILLNGNNITML
Sbjct:    62 EGRRITKLDQILLNGNNITML 82

GO:0005634 "nucleus" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q9Y4Y9 LSM5 "U6 snRNA-associated Sm-like protein LSm5" [Homo sapiens (taxid:9606)]

 Score = 359 (131.4 bits), Expect = 6.7e-33, P = 6.7e-33
 Identities = 70/81 (86%), Positives = 75/81 (92%)

Query:   106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
             A +  TNPS LLPLELVDKCIGSRIHI+MK+DKEIVGTL GFDDFVNM+LEDVTE+E TP
Sbjct:     2 AANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITP 61

Query:   166 EGRRITKLDQILLNGNNITML 186
             EGRRITKLDQILLNGNNITML
Sbjct:    62 EGRRITKLDQILLNGNNITML 82

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005634 "nucleus" evidence=TAS

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:0005515 "protein binding" evidence=IPI

MGI|MGI:1913623 Lsm5 "LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 359 (131.4 bits), Expect = 6.7e-33, P = 6.7e-33
 Identities = 70/81 (86%), Positives = 75/81 (92%)

Query:   106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
             A +  TNPS LLPLELVDKCIGSRIHI+MK+DKEIVGTL GFDDFVNM+LEDVTE+E TP
Sbjct:     2 AANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITP 61

Query:   166 EGRRITKLDQILLNGNNITML 186
             EGRRITKLDQILLNGNNITML
Sbjct:    62 EGRRITKLDQILLNGNNITML 82

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0006402 "mRNA catabolic process" evidence=ISO

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=ISO

WB|WBGene00003079 lsm-5 [Caenorhabditis elegans (taxid:6239)]

 Score = 331 (121.6 bits), Expect = 6.2e-30, P = 6.2e-30
 Identities = 62/81 (76%), Positives = 74/81 (91%)

Query:   106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
             A S +TNP+TLLPLEL+DKCIGS+I +IMKNDKEIVGTL GFDD+VNM+LEDV EYE+T 
Sbjct:     2 ATSTSTNPNTLLPLELIDKCIGSKIWVIMKNDKEIVGTLTGFDDYVNMVLEDVVEYENTA 61

Query:   166 EGRRITKLDQILLNGNNITML 186
             +G+R+TKLD ILLNGN+ITML
Sbjct:    62 DGKRMTKLDTILLNGNHITML 82

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0006915 "apoptotic process" evidence=IMP

UNIPROTKB|O18694 lsm-5 "Protein LSM-5" [Caenorhabditis elegans (taxid:6239)]

 Score = 331 (121.6 bits), Expect = 6.2e-30, P = 6.2e-30
 Identities = 62/81 (76%), Positives = 74/81 (91%)

Query:   106 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP 165
             A S +TNP+TLLPLEL+DKCIGS+I +IMKNDKEIVGTL GFDD+VNM+LEDV EYE+T 
Sbjct:     2 ATSTSTNPNTLLPLELIDKCIGSKIWVIMKNDKEIVGTLTGFDDYVNMVLEDVVEYENTA 61

Query:   166 EGRRITKLDQILLNGNNITML 186
             +G+R+TKLD ILLNGN+ITML
Sbjct:    62 DGKRMTKLDTILLNGNHITML 82

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2156589 SAD1 "SUPERSENSITIVE TO ABA AND DROUGHT 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 300 (110.7 bits), Expect = 1.2e-26, P = 1.2e-26
 Identities = 57/78 (73%), Positives = 67/78 (85%)

Query:   109 VATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGR 168
             +A NPS LLP EL+D+CIGS+I +IMK DKE+VG L GFD +VNM+LEDVTEYE T EGR
Sbjct:     1 MANNPSQLLPSELIDRCIGSKIWVIMKGDKELVGILKGFDVYVNMVLEDVTEYEITAEGR 60

Query:   169 RITKLDQILLNGNNITML 186
             R+TKLDQILLNGNNI +L
Sbjct:    61 RVTKLDQILLNGNNIAIL 78

GO:0005634 "nucleus" evidence=ISM;ISS

GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS

GO:0003723 "RNA binding" evidence=ISS

GO:0009414 "response to water deprivation" evidence=IMP

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

DICTYBASE|DDB_G0268716 lsm5 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 263 (97.6 bits), Expect = 1.0e-22, P = 1.0e-22
 Identities = 51/73 (69%), Positives = 60/73 (82%)

Query:   114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKL 173
             S LLPLEL++KCIGSRI I MKNDKE VGTL GFD +VN+ L+DVTEYE TPEG +  KL
Sbjct:    14 SQLLPLELIEKCIGSRIWIAMKNDKEFVGTLLGFDAYVNIFLKDVTEYEYTPEGLKTVKL 73

Query:   174 DQILLNGNNITML 186
             D ILLNGN++ +L
Sbjct:    74 DNILLNGNHVCLL 86

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

GO:0046540 "U4/U6 x U5 tri-snRNP complex" evidence=ISS

GO:0006402 "mRNA catabolic process" evidence=ISS

GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS

GO:0005688 "U6 snRNP" evidence=ISS

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

ASPGD|ASPL0000026389 AN5679 [Emericella nidulans (taxid:162425)]

 Score = 254 (94.5 bits), Expect = 9.0e-22, P = 9.0e-22
 Identities = 53/86 (61%), Positives = 66/86 (76%)

Query:   101 LYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTE 160
             ++   +P+     S LLPLEL+DKC+GSRI IIMKNDKE  GTL GFDD+VNM+LEDVTE
Sbjct:    36 VFCWESPAYPKMASQLLPLELIDKCVGSRIWIIMKNDKEFSGTLLGFDDYVNMVLEDVTE 95

Query:   161 YESTPEGRRITKLDQILLNGNNITML 186
             ++ T  G ++ KL +ILLNGNNI ML
Sbjct:    96 FDYT--GAQV-KLPKILLNGNNICML 118

GO:0005730 "nucleolus" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=IEA

GO:0046540 "U4/U6 x U5 tri-snRNP complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" 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)
Q55EX5	LSM5_DICDI	No assigned EC number	0.6986	0.3578	0.7525	yes	N/A
Q2HJH0	LSM5_BOVIN	No assigned EC number	0.8641	0.3970	0.8901	yes	N/A
Q5R628	LSM5_PONAB	No assigned EC number	0.8641	0.3970	0.8901	yes	N/A
Q9Y4Y9	LSM5_HUMAN	No assigned EC number	0.8641	0.3970	0.8901	yes	N/A
P62322	LSM5_MOUSE	No assigned EC number	0.8641	0.3970	0.8901	yes	N/A
O42978	LSM5_SCHPO	No assigned EC number	0.5416	0.3431	0.875	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	204
cd01732	76	cd01732, LSm5, Like-Sm protein 5	2e-47
cd01732	76	cd01732, LSm5, Like-Sm protein 5	2e-26
smart00651	67	smart00651, Sm, snRNP Sm proteins	2e-17
pfam01423	66	pfam01423, LSM, LSM domain	1e-16
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	2e-14
cd00600	63	cd00600, Sm_like, Sm and related proteins	7e-14
pfam01423	66	pfam01423, LSM, LSM domain	2e-09
smart00651	67	smart00651, Sm, snRNP Sm proteins	3e-09
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	4e-09
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	5e-09
cd00600	63	cd00600, Sm_like, Sm and related proteins	1e-08
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	2e-08
cd01718	79	cd01718, Sm_E, Sm protein E	2e-08
cd01730	82	cd01730, LSm3, Like-Sm protein 3	3e-08
PTZ00138	89	PTZ00138, PTZ00138, small nuclear ribonucleoprotei	1e-06
cd01726	68	cd01726, LSm6, Like-Sm protein 6	1e-06
cd01730	82	cd01730, LSm3, Like-Sm protein 3	3e-06
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	5e-06
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	3e-05
cd01727	91	cd01727, LSm8, Like-Sm protein 8	4e-05
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	1e-04
cd01719	70	cd01719, Sm_G, Sm protein G	2e-04
cd01728	74	cd01728, LSm1, Like-Sm protein 1	3e-04
cd01722	69	cd01722, Sm_F, Sm protein F	4e-04
cd01729	89	cd01729, LSm7, Like-Sm protein 7	8e-04
cd01733	78	cd01733, LSm10, Like-Sm protein 10	0.001
cd06168	73	cd06168, LSMD1, LSM domain containing 1	0.002

>gnl|CDD|212479 cd01732, LSm5, Like-Sm protein 5

 Score =  150 bits (380), Expect = 2e-47
 Identities = 59/72 (81%), Positives = 66/72 (91%)

Query: 115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLD 174
            +LPLEL+DKCIGS+I IIMK+DKE VGTL GFDD+VNM+LEDVTEYE TPEGR+ITKLD
Sbjct: 1   QILPLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLD 60

Query: 175 QILLNGNNITML 186
           QILLNGNNI ML
Sbjct: 61  QILLNGNNIAML 72

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 76

>gnl|CDD|212479 cd01732, LSm5, Like-Sm protein 5

 Score = 96.5 bits (241), Expect = 2e-26
 Identities = 35/45 (77%), Positives = 41/45 (91%)

Query: 12 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
           +LPLEL+DKCIGS+I IIMK+DKE VGTL GFDD+VNM+LEDVT
Sbjct: 1  QILPLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVT 45

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 76

>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins

 Score = 72.5 bits (179), Expect = 2e-17
 Identities = 28/68 (41%), Positives = 41/68 (60%), Gaps = 2/68 (2%)

Query: 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNG 180
            + K IG R+ + +KN +E  GTL GFD F+N++LEDV E     +G +  KL  + + G
Sbjct: 2   FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEET--VKDGEKKRKLGLVFIRG 59

Query: 181 NNITMLGL 188
           NNI  + L
Sbjct: 60  NNIVYIIL 67

small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing. Length = 67

>gnl|CDD|201787 pfam01423, LSM, LSM domain

 Score = 70.7 bits (174), Expect = 1e-16
 Identities = 25/69 (36%), Positives = 42/69 (60%), Gaps = 3/69 (4%)

Query: 120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLN 179
           + + K +G R+ + +KN +E+ GTL GFD F+N++L+DV E     +     KL  +L+ 
Sbjct: 1   KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVN---KLGLVLIR 57

Query: 180 GNNITMLGL 188
           GNNI ++  
Sbjct: 58  GNNIVLISP 66

The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings. Length = 66

>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]

 Score = 65.0 bits (159), Expect = 2e-14
 Identities = 25/78 (32%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 112 NPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRIT 171
           +    LPL  + K +  R+ + +KN +E  GTL GFD ++N++L+DV E  S    + + 
Sbjct: 2   SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVR 61

Query: 172 KL-DQILLNGNNITMLGL 188
           +L  ++L+ G+NI ++  
Sbjct: 62  RLGGEVLIRGDNIVLISP 79

Length = 79

>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins

 Score = 63.4 bits (155), Expect = 7e-14
 Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 3/65 (4%)

Query: 122 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGN 181
           +   IG  + + +K+ + + GTL  FD ++N++L+DV E   T    ++  L  +L+ G+
Sbjct: 1   LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVE---TGRDGKVRVLGLVLIRGS 57

Query: 182 NITML 186
           NI  +
Sbjct: 58  NIVSI 62

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 63

>gnl|CDD|201787 pfam01423, LSM, LSM domain

 Score = 51.8 bits (125), Expect = 2e-09
 Identities = 17/40 (42%), Positives = 29/40 (72%)

Query: 17 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
          + + K +G R+ + +KN +E+ GTL GFD F+N++L+DV 
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVE 40

The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings. Length = 66

>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins

 Score = 51.0 bits (123), Expect = 3e-09
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
           + K IG R+ + +KN +E  GTL GFD F+N++LEDV 
Sbjct: 2  FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVE 40

small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing. Length = 67

>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]

 Score = 51.1 bits (123), Expect = 4e-09
 Identities = 18/48 (37%), Positives = 30/48 (62%)

Query: 9  NPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
          +    LPL  + K +  R+ + +KN +E  GTL GFD ++N++L+DV 
Sbjct: 2  SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVE 49

Length = 79

>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1

 Score = 50.7 bits (122), Expect = 5e-09
 Identities = 21/68 (30%), Positives = 40/68 (58%), Gaps = 3/68 (4%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
           PL+++++ +   + + +K  KE+ G L GFD  +N++LE+  E     EG  + KL  +L
Sbjct: 2   PLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEE---IIEGESVRKLGTVL 58

Query: 178 LNGNNITM 185
           + G+N+  
Sbjct: 59  VRGDNVVF 66

The archaeal Sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Length = 69

>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins

 Score = 49.2 bits (118), Expect = 1e-08
 Identities = 12/43 (27%), Positives = 25/43 (58%)

Query: 19 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
          +   IG  + + +K+ + + GTL  FD ++N++L+DV +    
Sbjct: 1  LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRD 43

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 63

>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein

 Score = 49.0 bits (117), Expect = 2e-08
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 118 PLELVDKCIGSRIHIIMKND-KEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQI 176
           P + V   +GSRI + MK D  ++ G L   DD++N+ L D  E     + R    L  +
Sbjct: 1   PNKKVKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVR---SLGTV 57

Query: 177 LLNGNNI 183
           +L GNNI
Sbjct: 58  VLRGNNI 64

The archaeal Sm-like (LSm): The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 69

>gnl|CDD|212465 cd01718, Sm_E, Sm protein E

 Score = 49.1 bits (118), Expect = 2e-08
 Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 2/58 (3%)

Query: 129 RIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITML 186
           +I +  + D  I G + GFD+++N++L+D  E       R+   L +ILL G+NIT++
Sbjct: 22  QIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRK--PLGRILLKGDNITLI 77

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Length = 79

>gnl|CDD|212477 cd01730, LSm3, Like-Sm protein 3

 Score = 48.8 bits (117), Expect = 3e-08
 Identities = 22/69 (31%), Positives = 38/69 (55%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
           PL+L+   +  R+++ ++ D+E+ G L+ +D  +NM+L DV E  +T E    T  +   
Sbjct: 2   PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYK 61

Query: 178 LNGNNITML 186
               NI ML
Sbjct: 62  TTKRNIPML 70

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 82

>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional

 Score = 44.7 bits (106), Expect = 1e-06
 Identities = 21/62 (33%), Positives = 37/62 (59%), Gaps = 4/62 (6%)

Query: 127 GSRIHIIM--KNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNIT 184
            +R+ I +    +  I G + GFD+++NM+L+D  E  +    R+   L +ILL G+NIT
Sbjct: 26  KTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRK--DLGRILLKGDNIT 83

Query: 185 ML 186
           ++
Sbjct: 84  LI 85

Length = 89

>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6

 Score = 44.0 bits (105), Expect = 1e-06
 Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 3/66 (4%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
           P + + K IG  + + +KN  E  G L   D ++N++LED  EY    +G+ + K     
Sbjct: 2   PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEY---VDGQLVAKYGDAF 58

Query: 178 LNGNNI 183
           + GNN+
Sbjct: 59  IRGNNV 64

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 68

>gnl|CDD|212477 cd01730, LSm3, Like-Sm protein 3

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 14/41 (34%), Positives = 28/41 (68%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV 55
          PL+L+   +  R+++ ++ D+E+ G L+ +D  +NM+L DV
Sbjct: 2  PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDV 42

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 82

>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional

 Score = 42.7 bits (101), Expect = 5e-06
 Identities = 17/66 (25%), Positives = 41/66 (62%), Gaps = 3/66 (4%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
           PL++++  + S + + +K  +E  G L G+D  +N++L++  E +   +G  + KL +++
Sbjct: 5   PLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ---DGEVVRKLGKVV 61

Query: 178 LNGNNI 183
           + G+N+
Sbjct: 62  IRGDNV 67

Length = 72

>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1

 Score = 40.3 bits (95), Expect = 3e-05
 Identities = 13/40 (32%), Positives = 27/40 (67%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 54
          PL+++++ +   + + +K  KE+ G L GFD  +N++LE+
Sbjct: 2  PLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLEN 41

The archaeal Sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Length = 69

>gnl|CDD|212474 cd01727, LSm8, Like-Sm protein 8

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYE-STPEGRRITKLDQ 175
           L  + ++K    R+ +I  + + IVGTL GFD   N++L +  E   S+ EG     L  
Sbjct: 3   LLEDYLNK----RVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEVPLGL 58

Query: 176 ILLNGNNITMLGL 188
            LL G+N+ ++G 
Sbjct: 59  YLLRGDNVAVIGE 71

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 91

>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 15 PLELVDKCIGSRIHIIMKND-KEIVGTLNGFDDFVNMLLEDVTDC 58
          P + V   +GSRI + MK D  ++ G L   DD++N+ L D  +C
Sbjct: 1  PNKKVKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMEC 45

The archaeal Sm-like (LSm): The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 69

>gnl|CDD|212466 cd01719, Sm_G, Sm protein G

 Score = 37.9 bits (89), Expect = 2e-04
 Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 3/48 (6%)

Query: 139 EIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITML 186
           ++ G L GFD F+N++L+D  E     E    T +  +++ GN+I M+
Sbjct: 22  KVSGVLRGFDPFMNLVLDDAVEEVGDGEK---TPIGMVVIRGNSIIMI 66

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Length = 70

>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1

 Score = 37.5 bits (88), Expect = 3e-04
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 14/72 (19%)

Query: 124 KCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTE-------YESTPEGRRITKLDQI 176
           + +  +I +++++ ++++G L  FD F N++LED  E       Y   P G         
Sbjct: 9   EELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRG-------LF 61

Query: 177 LLNGNNITMLGL 188
           ++ G N+ +LG 
Sbjct: 62  IIRGENVVLLGE 73

The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 74

>gnl|CDD|212469 cd01722, Sm_F, Sm protein F

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNI 183
            G  + + +K   E  GTL   D ++N+ L +  EY    +G+    L ++L+  NN+
Sbjct: 10  TGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI---DGKFTGNLGEVLIRCNNV 64

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers. Length = 69

>gnl|CDD|212476 cd01729, LSm7, Like-Sm protein 7

 Score = 36.8 bits (86), Expect = 8e-04
 Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE 166
           L+L  K +  +I +  +  +E+ G L G+D  +N++L+D  EY   PE
Sbjct: 5   LDL-SKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPE 51

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 89

>gnl|CDD|212480 cd01733, LSm10, Like-Sm protein 10

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNG 180
           L+    G    + ++N+  + G ++  D F+N+ L D T       G++    D+  + G
Sbjct: 13  LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFT--DRRGKQ-HHFDEFFVQG 69

Query: 181 NNI 183
            NI
Sbjct: 70  RNI 72

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-membered ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing. Length = 78

>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1

 Score = 35.2 bits (82), Expect = 0.002
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 11/63 (17%)

Query: 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITM 185
           +G  + + + + + +VGT    D   N++L +  EY    +           L       
Sbjct: 8   LGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSD-----------LGAEEPRS 56

Query: 186 LGL 188
           LGL
Sbjct: 57  LGL 59

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSMD1 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes, forming heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 73

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	204
KOG1774|consensus	88		99.93
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.87
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.86
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.86
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.82
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.82
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.82
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.79
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.79
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.79
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.78
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.77
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.76
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.76
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.75
KOG3482|consensus	79		99.73
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.73
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.72
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.71
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.71
KOG1775|consensus	84		99.7
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.7
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.7
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.69
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.69
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.69
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.69
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.68
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.66
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.65
KOG1780|consensus	77		99.64
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.63
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.63
KOG3460|consensus	91		99.62
KOG1780|consensus	77		99.58
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.57
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.55
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.55
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.55
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.53
KOG3482|consensus	79		99.53
KOG1781|consensus	108		99.53
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.53
KOG1775|consensus	84		99.52
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.51
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.5
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.46
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.46
KOG1783|consensus	77		99.46
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.44
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.43
KOG1784|consensus	96		99.4
KOG1783|consensus	77		99.38
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.35
KOG1782|consensus	129		99.34
KOG1774|consensus	88		99.29
KOG3460|consensus	91		99.27
KOG3293|consensus	134		99.23
KOG3448|consensus	96		99.13
KOG3168|consensus	177		99.12
KOG1781|consensus	108		99.09
KOG3172|consensus	119		98.98
KOG3459|consensus	114		98.97
KOG3428|consensus	109		98.7
KOG1784|consensus	96		98.55
KOG3293|consensus	134		98.47
KOG3168|consensus	177		98.31
KOG1782|consensus	129		98.24
KOG3448|consensus	96		98.21
PRK14091	165	RNA-binding protein Hfq; Provisional	97.99
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.94
KOG3459|consensus	114		97.67
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.55
KOG3172|consensus	119		97.45
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	97.16
KOG3428|consensus	109		96.74
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	96.01
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	95.85
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	95.72
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	95.37
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	95.34
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	95.31
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	95.16
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	95.15
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	94.59
COG1923	77	Hfq Uncharacterized host factor I protein [General	94.41
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	93.99
COG1923	77	Hfq Uncharacterized host factor I protein [General	93.65
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	91.46
PRK14091	165	RNA-binding protein Hfq; Provisional	90.61
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	90.57
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	90.38
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	87.82
PRK14638	150	hypothetical protein; Provisional	87.79
PRK02001	152	hypothetical protein; Validated	85.92
PRK14639	140	hypothetical protein; Provisional	85.61
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	85.54
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	84.06
PRK14639	140	hypothetical protein; Provisional	83.79
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	83.65
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	83.43
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	82.48
PRK14638	150	hypothetical protein; Provisional	82.1
PRK14644	136	hypothetical protein; Provisional	80.29

>KOG1774|consensus

Probab=99.93  E-value=1.2e-26  Score=167.96  Aligned_cols=79  Identities=28%  Similarity=0.500  Sum_probs=70.7

Q ss_pred             cceeeccccccceeecccEeEEEeeeccCCcccCCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800           78 LPMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED  157 (204)
Q Consensus        78 ~~~~~PI~~~f~~~~~~~~v~~~l~~~~~~~~~~~~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d  157 (204)
                      -+|++|||+||+|||++.+|++||||+                               -+.+++|.+.|||+|||+||||
T Consensus         8 kvmv~Pin~Ifr~Lq~~t~VqIWl~eq-------------------------------~~~rieG~IvGFDEyMNvVlD~   56 (88)
T KOG1774|consen    8 KVMVQPINLIFRFLQNRTRVQIWLFEQ-------------------------------VGLRIEGRIVGFDEYMNLVLDD   56 (88)
T ss_pred             ceecCcHHHHHHHHhcCCceEEEEEec-------------------------------cCcEEeEEEechHHhhhhhhcc
Confidence            378999999999999999999999997                               4669999999999999999999


Q ss_pred             eEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          158 VTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       158 a~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      |+|...+.  +..+.+|+++++||||.+|...
T Consensus        57 aeev~~k~--~~rk~lGRilLKGDnItli~~~   86 (88)
T KOG1774|consen   57 AEEVHSKT--KSRKELGRILLKGDNITLIQSA   86 (88)
T ss_pred             hhhccccc--cCCCccccEEEcCCcEEEEeec
Confidence            99998653  2356999999999999999654

>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.89  E-value=8.8e-23  Score=148.12  Aligned_cols=74  Identities=81%  Similarity=1.207  Sum_probs=68.3

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      .+|+++|+++++++|+|++++|+++.|+|+|||+|||+||+||+|++..++++..+.+|.++|||+||++|+|.
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~   75 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG   75 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence            57999999999999999999999999999999999999999999998655555678899999999999999975

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.87  E-value=9e-22  Score=141.14  Aligned_cols=70  Identities=24%  Similarity=0.600  Sum_probs=64.8

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      ..|+++|+++++++|.|+|+||+.|+|+|.|||+|||++|+||+|.+   +++..+++|.++|||++|++|+|
T Consensus         3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~~V~~i~~   72 (72)
T PRK00737          3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ---DGEVVRKLGKVVIRGDNVVYVSP   72 (72)
T ss_pred             cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEc---CCCeEeEcCcEEEeCCEEEEEcC
Confidence            57999999999999999999999999999999999999999999975   34467899999999999999975

>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences

Probab=99.86  E-value=2.1e-21  Score=137.48  Aligned_cols=68  Identities=24%  Similarity=0.588  Sum_probs=63.1

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      |+++|+++++++|+|+|++|+.|.|+|.|||+|||++|+||+|++.  + ...+.+|.++|||++|++|+|
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~--~-~~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDD--G-EPVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEec--C-CeEeEcCcEEEeCCEEEEEcC
Confidence            8899999999999999999999999999999999999999999863  2 256889999999999999986

They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.86  E-value=1.3e-21  Score=145.90  Aligned_cols=78  Identities=29%  Similarity=0.478  Sum_probs=70.2

Q ss_pred             ceeeccccccceeecccEeEEEeeeccCCcccCCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcce
Q psy800           79 PMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV  158 (204)
Q Consensus        79 ~~~~PI~~~f~~~~~~~~v~~~l~~~~~~~~~~~~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da  158 (204)
                      .|++||+++|+|++.+.+|.+|++++                               ++++++|+|.|||+|||+||+||
T Consensus        11 ~~~~P~~~~~~~~~~~~~V~i~l~~~-------------------------------~~r~~~G~L~gfD~~mNlVL~d~   59 (89)
T PTZ00138         11 IMTQPINQIFRFFTEKTRVQIWLYDH-------------------------------PNLRIEGKILGFDEYMNMVLDDA   59 (89)
T ss_pred             eecCCHHHHHHHhcCCcEEEEEEEeC-------------------------------CCcEEEEEEEEEcccceEEEccE
Confidence            68899999999999999999999885                               68999999999999999999999


Q ss_pred             EEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          159 TEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       159 ~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +|+..  +++..+.+|.++||||||++|++.
T Consensus        60 ~E~~~--~~~~~~~lG~ilIRGnnV~~I~~~   88 (89)
T PTZ00138         60 EEVYT--KKNTRKDLGRILLKGDNITLIMAA   88 (89)
T ss_pred             EEEec--CCceeeEcCeEEEcCCEEEEEEcC
Confidence            99863  234578999999999999999764

>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.85  E-value=3.6e-21  Score=141.24  Aligned_cols=72  Identities=25%  Similarity=0.539  Sum_probs=64.2

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCC-C---------eeeeeeCeEEEeCCcEEEE
Q psy800          117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE-G---------RRITKLDQILLNGNNITML  186 (204)
Q Consensus       117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~-~---------~~~~~lg~ilIRGdnI~~I  186 (204)
                      .|+++|+.+++++|.|+|++||.+.|+|+|||+||||+|+||+|.+.... +         ...+.+|.++||||+|++|
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i   80 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV   80 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence            38999999999999999999999999999999999999999999975311 1         2467899999999999999


Q ss_pred             cc
Q psy800          187 GL  188 (204)
Q Consensus       187 ~~  188 (204)
                      +|
T Consensus        81 ~~   82 (82)
T cd01730          81 SP   82 (82)
T ss_pred             CC
Confidence            85

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.85  E-value=8.5e-21  Score=134.20  Aligned_cols=67  Identities=25%  Similarity=0.515  Sum_probs=62.2

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEc
Q psy800          118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLG  187 (204)
Q Consensus       118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~  187 (204)
                      |+++|+++++++|+|+|++|++|+|+|.|||+|||++|+||+|..   ++.....+|.++|||++|.+|+
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~---~~~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYV---NGQLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEe---CCceeeEeCCEEEECCEEEEEC
Confidence            899999999999999999999999999999999999999999864   3446789999999999999985

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.84  E-value=8.7e-21  Score=140.97  Aligned_cols=74  Identities=24%  Similarity=0.492  Sum_probs=65.1

Q ss_pred             CCcHHHHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCC--C--------eeeeeeCeEEEeCCcE
Q psy800          116 LLPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE--G--------RRITKLDQILLNGNNI  183 (204)
Q Consensus       116 ~~Pl~~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~--~--------~~~~~lg~ilIRGdnI  183 (204)
                      .+|+++|.+++  +++|.|+|++|+.+.|+|.|||+||||+|+||+|.+...+  +        ...+++|.+|||||+|
T Consensus         1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~V   80 (87)
T cd01720           1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSV   80 (87)
T ss_pred             CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEE
Confidence            37999999997  8999999999999999999999999999999999875421  1        2356799999999999


Q ss_pred             EEEccc
Q psy800          184 TMLGLH  189 (204)
Q Consensus       184 ~~I~~~  189 (204)
                      ++|++.
T Consensus        81 v~Is~~   86 (87)
T cd01720          81 ILVLRN   86 (87)
T ss_pred             EEEecC
Confidence            999875

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.84  E-value=6.6e-21  Score=139.23  Aligned_cols=51  Identities=35%  Similarity=0.642  Sum_probs=45.7

Q ss_pred             CCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          136 NDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       136 ~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      +|+.+.|+|.|||+|||+||+||+|+...  ++..+.+|.++||||||++|+|
T Consensus        29 ~g~~~~G~L~gfD~~mNlvL~d~~E~~~~--~~~~~~lG~iliRGnnV~~I~p   79 (79)
T cd01718          29 TDLRIEGVIIGFDEYMNLVLDDAEEVHLK--TKTRKPLGRILLKGDNITLIQN   79 (79)
T ss_pred             CCcEEEEEEEEEccceeEEEcCEEEEecC--CceEeEcCcEEEeCCEEEEEcC
Confidence            89999999999999999999999998632  3456789999999999999985

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.82  E-value=4.2e-20  Score=131.08  Aligned_cols=68  Identities=25%  Similarity=0.469  Sum_probs=62.1

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEc
Q psy800          117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLG  187 (204)
Q Consensus       117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~  187 (204)
                      .|+++|+++++++|+|+|+||+.|+|+|.|||+|||++|+||+|..   ++.....+|.++|||++|.+|+
T Consensus         1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~---~~~~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI---DGKSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEe---CCccccCcCcEEEECCEEEEEC
Confidence            3899999999999999999999999999999999999999999974   3335678999999999999984

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.

>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.82  E-value=8.3e-20  Score=133.92  Aligned_cols=71  Identities=23%  Similarity=0.588  Sum_probs=62.1

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCC-----CeeeeeeCeEEEeCCcEEEEccc
Q psy800          118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE-----GRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~-----~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +++ |.++++++|.|+|++||++.|+|.|||+||||||+||+|+...++     .+..+.+|.++|||+||++|++.
T Consensus         4 ~~~-L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~   79 (81)
T cd01729           4 ILD-LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPV   79 (81)
T ss_pred             hhh-HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecC
Confidence            344 899999999999999999999999999999999999999875321     12568899999999999999875

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.82  E-value=7.8e-20  Score=131.30  Aligned_cols=67  Identities=25%  Similarity=0.585  Sum_probs=61.3

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      ..|+++++|+|.|+|++|+++.|+|.|||+||||+|+||+|+.   ++...+.+|.++|||++|++|++.
T Consensus         3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~---~~~~~~~lg~v~IRG~~I~~i~~~   69 (72)
T cd01719           3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVN---SGGEKNNIGMVVIRGNSIVMLEAL   69 (72)
T ss_pred             hhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEc---cCCceeEeceEEECCCEEEEEEcc
Confidence            4789999999999999999999999999999999999999986   233578999999999999999875

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.81  E-value=2.4e-19  Score=129.55  Aligned_cols=71  Identities=18%  Similarity=0.414  Sum_probs=62.5

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      ++..|+++++++|.|.|++|+++.|+|+|||+|||++|+||.|.....+....+.+|.++|||++|++|+.
T Consensus         3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728           3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence            35578999999999999999999999999999999999999998754333346889999999999999975

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.79  E-value=4.5e-19  Score=127.68  Aligned_cols=70  Identities=29%  Similarity=0.523  Sum_probs=62.6

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecC-CCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP-EGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~-~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      .|+++++++|.|++++|+.+.|+|+|||+|||++|+||.|+.... ++...+.+|.++|||++|++|++.+
T Consensus         3 ~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d   73 (74)
T cd01727           3 TLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID   73 (74)
T ss_pred             hHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence            588999999999999999999999999999999999999986532 3445778999999999999999864

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]

Probab=99.79  E-value=6.2e-19  Score=128.24  Aligned_cols=73  Identities=34%  Similarity=0.638  Sum_probs=63.0

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCee--eeeeCeEEEeCCcEEEEcc
Q psy800          115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRR--ITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       115 ~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~--~~~lg~ilIRGdnI~~I~~  188 (204)
                      ...|+++|+++++++|.|+|++|+++.|+|+|||+|||++|+||+|.... ++..  .+..|.++|||++|.+|++
T Consensus         5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-~~~~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958           5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH-DGEKNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc-CCccccceeccEEEEECCcEEEEeC
Confidence            45789999999999999999999999999999999999999999998741 3333  3344599999999999864

>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.79  E-value=7.9e-19  Score=127.09  Aligned_cols=71  Identities=25%  Similarity=0.446  Sum_probs=63.9

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      .|+++|+++.+++|.|+||+|++++|+|.+||+|||++|+||+|..  .+|+....++.++|||++|.+|+..
T Consensus         1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~--~~g~~~~~~~~v~IRG~~I~~i~~p   71 (76)
T cd01723           1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTS--KDGDKFWKMPECYIRGNTIKYLRVP   71 (76)
T ss_pred             CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEEC--CCCcEeeeCCcEEEeCCEEEEEEcC
Confidence            4999999999999999999999999999999999999999999864  3565556789999999999999743

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.78  E-value=1.4e-18  Score=124.06  Aligned_cols=69  Identities=28%  Similarity=0.484  Sum_probs=62.4

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      |+++|+++.+++|+|+||||..|+|+|.++|+|||++|+||++..  .+| +..++|.++|||++|.+|...
T Consensus         1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~--~~g-~~~~~~~v~IRG~nI~~v~lP   69 (70)
T cd01721           1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTA--RDG-RVSQLEQVYIRGSKIRFFILP   69 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEEC--CCC-cEeEcCcEEEeCCEEEEEEeC
Confidence            889999999999999999999999999999999999999998854  345 357789999999999999654

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.77  E-value=1.9e-18  Score=125.88  Aligned_cols=68  Identities=25%  Similarity=0.501  Sum_probs=60.3

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecC-------CCeeeeeeCeEEEeCCcEEEEcc
Q psy800          121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP-------EGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~-------~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      .|.++++++|.|.|+|||.+.|+|.|||+||||||+||+|++...       .+.+.+.+|.++|||++|++|+.
T Consensus         4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            688999999999999999999999999999999999999987532       12356889999999999999863

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>smart00651 Sm snRNP Sm proteins

Probab=99.76  E-value=4.1e-18  Score=119.24  Aligned_cols=66  Identities=42%  Similarity=0.726  Sum_probs=60.3

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      +|+++++++|+|+|+||+.+.|+|.+||+|||++|+||.|....  +...+++|.++|||++|++|++
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~--~~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD--GEKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecC--CcEEeEeCCEEEcCCEEEEEeC
Confidence            68899999999999999999999999999999999999998732  2468999999999999999864

small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing

>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins

Probab=99.76  E-value=5.2e-18  Score=118.82  Aligned_cols=67  Identities=36%  Similarity=0.640  Sum_probs=60.8

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      .+|+++++++|+|+|+||+.++|+|.+||+|||++|+||.|....  +...+++|.++|||++|++|++
T Consensus         1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~--~~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKN--GPEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETT--ESEEEEEEEEEEEGGGEEEEEE
T ss_pred             ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECC--CCcEeECcEEEEECCEEEEEEC
Confidence            368999999999999999999999999999999999999998732  2268899999999999999975

In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....

>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.75  E-value=5.8e-18  Score=122.84  Aligned_cols=62  Identities=61%  Similarity=0.974  Sum_probs=57.0

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee---cCccccccccEEEee
Q psy800           13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH---DSHLLSYFASDLINF   74 (204)
Q Consensus        13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~---~~~~~~~lG~vlIn~   74 (204)
                      ..|+++|+++++++|+|++++|+++.|+|+|||+|||++|+||+|+.   +++....+|.++|+.
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG   66 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNG   66 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeC
Confidence            47999999999999999999999999999999999999999999998   555667899999954

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG3482|consensus

Probab=99.73  E-value=4.4e-18  Score=121.08  Aligned_cols=67  Identities=21%  Similarity=0.360  Sum_probs=62.7

Q ss_pred             CCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEE---eeec
Q psy800           10 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLI---NFIW   76 (204)
Q Consensus        10 ~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlI---n~~~   76 (204)
                      ..+.+|.+||+.+.+|+|.|+||||.+|+|+|.+.|.||||.|.+|+|++++...+.+|+++|   |++|
T Consensus         4 ~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvly   73 (79)
T KOG3482|consen    4 KQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLY   73 (79)
T ss_pred             cccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEE
Confidence            345699999999999999999999999999999999999999999999999999999999999   5553

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.73  E-value=1.6e-17  Score=119.03  Aligned_cols=62  Identities=21%  Similarity=0.477  Sum_probs=58.1

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ..|+++|+++++++|.|+|+||++|.|+|.|||+|||++|+||.|+.+++..+.+|.++|+.
T Consensus         3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG   64 (72)
T PRK00737          3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRG   64 (72)
T ss_pred             cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeC
Confidence            47999999999999999999999999999999999999999999998877778899999954

>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences

Probab=99.72  E-value=2.6e-17  Score=116.53  Aligned_cols=60  Identities=23%  Similarity=0.504  Sum_probs=56.8

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      |+++|+++++|+|+|+|++|++|.|+|.|||+|||++|+||+|+.++.....+|.++|+.
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG   60 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRG   60 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeC
Confidence            899999999999999999999999999999999999999999998777778899999955

They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.

>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.71  E-value=7.2e-17  Score=120.62  Aligned_cols=69  Identities=29%  Similarity=0.395  Sum_probs=62.4

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      |+++|+++.+++|+|+|++|..|+|+|.++|.|||++|+||+|..   ++.....+|.++|||++|.+|...
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~---~~~~~~~~~~v~IRG~nI~yi~lP   70 (90)
T cd01724           2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTL---KGRNPVPLDTLSIRGNNIRYFILP   70 (90)
T ss_pred             HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEc---CCCceeEcceEEEeCCEEEEEEcC
Confidence            678999999999999999999999999999999999999999875   233567899999999999999644

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.71  E-value=4.2e-17  Score=115.25  Aligned_cols=60  Identities=20%  Similarity=0.405  Sum_probs=56.7

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      |+++|+++++++|.|+|++|++|+|+|.|||.|||++|+||+|..+++....+|.++|+.
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG   60 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRG   60 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEEC
Confidence            899999999999999999999999999999999999999999988777778899999954

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG1775|consensus

Probab=99.70  E-value=1.4e-17  Score=119.60  Aligned_cols=78  Identities=85%  Similarity=1.235  Sum_probs=73.1

Q ss_pred             CCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          112 NPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       112 ~~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      .++..+|++++.++++.+|+|.+|+++++.|+|.|||.|.|+||+|+.|+...++|+...+++++++.|++|.+..|.
T Consensus         2 n~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPG   79 (84)
T KOG1775|consen    2 NPSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPG   79 (84)
T ss_pred             ChhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecC
Confidence            356789999999999999999999999999999999999999999999998878888889999999999999998876

>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.70  E-value=1.2e-16  Score=115.78  Aligned_cols=69  Identities=20%  Similarity=0.415  Sum_probs=61.4

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCC---CeeeeeeCeEEEeCCcEEEEcc
Q psy800          120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE---GRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~---~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      +.|+++++++|.|.|+|||.+.|+|.+||+||||+|+||.|+....+   +...+.+|.++|||++|+.|..
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence            46889999999999999999999999999999999999999975422   2368899999999999999863

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.70  E-value=5.1e-17  Score=119.23  Aligned_cols=61  Identities=23%  Similarity=0.443  Sum_probs=54.1

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc-------------cccccccEEEee
Q psy800           14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH-------------LLSYFASDLINF   74 (204)
Q Consensus        14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~-------------~~~~lG~vlIn~   74 (204)
                      .|+++|+.+++|+|.|+++|||++.|+|+|||+||||+|+||+|++.+.             ..+.+|.++|..
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG   74 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRG   74 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeC
Confidence            4999999999999999999999999999999999999999999998432             355788888843

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.69  E-value=1.3e-16  Score=110.07  Aligned_cols=63  Identities=24%  Similarity=0.553  Sum_probs=57.3

Q ss_pred             HHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEc
Q psy800          122 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLG  187 (204)
Q Consensus       122 L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~  187 (204)
                      |+++++++|+|+|+||+.+.|+|.+||+|||++|+||.|.+..   ....++|.++|||++|.+|.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~---~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE---GKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC---CcEEECCeEEEECCEEEEEC
Confidence            4678999999999999999999999999999999999998732   36789999999999999873

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.69  E-value=1.4e-16  Score=116.81  Aligned_cols=71  Identities=23%  Similarity=0.482  Sum_probs=61.8

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCC-eeeeeeCeEEEeCCcEEEEccc
Q psy800          117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG-RRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~-~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +|+++|+++.|++|+|+||+|..|.|+|.++|.|||++|+||++..  +++ .....++.++|||++|.+|..+
T Consensus         1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~--~~~~~~~~~~~~v~IRG~~I~~I~lp   72 (81)
T cd01725           1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTD--PEKYPHMLSVKNCFIRGSVVRYVQLP   72 (81)
T ss_pred             ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEc--CCCcccccccCeEEEECCEEEEEEeC
Confidence            4889999999999999999999999999999999999999998764  222 1245679999999999999755

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.69  E-value=8.2e-17  Score=115.60  Aligned_cols=60  Identities=18%  Similarity=0.400  Sum_probs=55.8

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      |.+.|+++++|+|+|+|++|++|.|+|.|||+||||+|+||+|+.++...+.+|.++|+.
T Consensus         1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG   60 (72)
T cd01719           1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRG   60 (72)
T ss_pred             CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECC
Confidence            567899999999999999999999999999999999999999998777778899999954

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.69  E-value=1.9e-16  Score=115.41  Aligned_cols=71  Identities=21%  Similarity=0.454  Sum_probs=62.8

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       115 ~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      ...+..+|+.+.|+.|.|+||||..|.|+|.++|.|||++|+||++..  +++ ...++|.++|||++|.+|..
T Consensus         7 ~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~--~~~-~~~~~~~v~IRG~nI~yI~l   77 (78)
T cd01733           7 ENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIID--RNG-KQVQVEEIMVTGRNIRYVHI   77 (78)
T ss_pred             hchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEc--CCC-ceeECCcEEEECCEEEEEEc
Confidence            346788999999999999999999999999999999999999999864  233 45689999999999999864

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.68  E-value=2e-16  Score=112.20  Aligned_cols=61  Identities=21%  Similarity=0.326  Sum_probs=57.1

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      .|+++|+++++++|.|+|++|++|.|+|.|||+|||++|+||+|+.++.....+|.++|+.
T Consensus         1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG   61 (68)
T cd01722           1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRC   61 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEEC
Confidence            5999999999999999999999999999999999999999999998777778899999954

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.

>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.66  E-value=5.7e-16  Score=113.23  Aligned_cols=65  Identities=25%  Similarity=0.466  Sum_probs=57.6

Q ss_pred             CCCCCcHHHHHhhcCC--EEEEEEe--CCeEEEEEEEeecCeeeeEecceEEeec-CccccccccEEEee
Q psy800           10 PSTLLPLELVDKCIGS--RIHIIMK--NDKEIVGTLNGFDDFVNMLLEDVTDCHD-SHLLSYFASDLINF   74 (204)
Q Consensus        10 ~~~~~P~~~L~~~~~k--~V~V~l~--~g~~~~G~L~gfD~~mNlvL~~~~E~~~-~~~~~~lG~vlIn~   74 (204)
                      +....|++.+.+++++  +|.|+++  +|+++.|+|.|||+||||+|+||+|+.+ ++....+|.++|+.
T Consensus         2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRG   71 (79)
T cd01718           2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKG   71 (79)
T ss_pred             ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeC
Confidence            4678999999999998  7888777  8999999999999999999999999985 55677899999944

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.65  E-value=6.7e-16  Score=114.78  Aligned_cols=61  Identities=23%  Similarity=0.449  Sum_probs=54.2

Q ss_pred             CcHHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc-------------cccccccEEEee
Q psy800           14 LPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH-------------LLSYFASDLINF   74 (204)
Q Consensus        14 ~P~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~-------------~~~~lG~vlIn~   74 (204)
                      .|+++|++++  +++|+|+|++|+++.|+|.|||+||||+|+||+|+..+.             ..+++|.+||..
T Consensus         2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRG   77 (87)
T cd01720           2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRG   77 (87)
T ss_pred             ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeC
Confidence            6999999998  899999999999999999999999999999999987543             244689999943

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG1780|consensus

Probab=99.64  E-value=3.4e-16  Score=111.81  Aligned_cols=66  Identities=23%  Similarity=0.561  Sum_probs=59.7

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      -|++|++|++.++|..||.+.|+|+|||.|||+||+|+.|...  ++ ....+|.++|||++|+.+.+.
T Consensus         8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~--~~-~~~~ig~~vIrgnsiv~~eaL   73 (77)
T KOG1780|consen    8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNG--DG-DKNNIGMVVIRGNSIVMVEAL   73 (77)
T ss_pred             hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecC--cC-CcceeeeEEEeccEEEEEeec
Confidence            7999999999999999999999999999999999999999752  22 468899999999999998654

>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.63  E-value=9.1e-16  Score=112.51  Aligned_cols=59  Identities=19%  Similarity=0.421  Sum_probs=51.9

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC--------ccccccccEEEee
Q psy800           15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS--------HLLSYFASDLINF   74 (204)
Q Consensus        15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~--------~~~~~lG~vlIn~   74 (204)
                      +++ |+++++|+|.|+|+|||+|+|+|.|||+||||+|++|+|+..+        ...+.+|.++|+.
T Consensus         4 ~~~-L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG   70 (81)
T cd01729           4 ILD-LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRG   70 (81)
T ss_pred             hhh-HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcC
Confidence            455 7899999999999999999999999999999999999999854        2457789999943

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]

Probab=99.63  E-value=1.6e-15  Score=110.32  Aligned_cols=65  Identities=32%  Similarity=0.529  Sum_probs=56.4

Q ss_pred             CCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee--cCcc-ccccc-cEEEee
Q psy800           10 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH--DSHL-LSYFA-SDLINF   74 (204)
Q Consensus        10 ~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~--~~~~-~~~lG-~vlIn~   74 (204)
                      .....|+++|+++++++|.|+|++|++|.|+|+|||+|||++|+||+|+.  ++.. ...+| +++|+.
T Consensus         3 ~~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG   71 (79)
T COG1958           3 MLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRG   71 (79)
T ss_pred             cccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEEC
Confidence            44567999999999999999999999999999999999999999999998  5554 34445 888854

>KOG3460|consensus

Probab=99.62  E-value=1.3e-16  Score=116.21  Aligned_cols=76  Identities=26%  Similarity=0.505  Sum_probs=67.1

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCC----------eeeeeeCeEEEeCCcE
Q psy800          114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG----------RRITKLDQILLNGNNI  183 (204)
Q Consensus       114 ~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~----------~~~~~lg~ilIRGdnI  183 (204)
                      +..-|+++|+-+++++|.|++|++|++.|+|.|||+|+|++|.||+|....-++          ..++.+..+|+|||+|
T Consensus         2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~V   81 (91)
T KOG3460|consen    2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGV   81 (91)
T ss_pred             cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeE
Confidence            346799999999999999999999999999999999999999999998764111          1467889999999999


Q ss_pred             EEEccc
Q psy800          184 TMLGLH  189 (204)
Q Consensus       184 ~~I~~~  189 (204)
                      ++|+|.
T Consensus        82 ilvspp   87 (91)
T KOG3460|consen   82 ILVSPP   87 (91)
T ss_pred             EEEcCc
Confidence            999986

>KOG1780|consensus

Probab=99.58  E-value=1.8e-15  Score=108.16  Aligned_cols=66  Identities=17%  Similarity=0.375  Sum_probs=58.1

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEeeecccceeecc
Q psy800           18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPI   84 (204)
Q Consensus        18 ~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~~~g~~~~~PI   84 (204)
                      =|++|++|++.++|++||.+.|+|+|||.|||+||+||.|...++....+|.++|... +++++.+.
T Consensus         8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgn-siv~~eaL   73 (77)
T KOG1780|consen    8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGN-SIVMVEAL   73 (77)
T ss_pred             hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEecc-EEEEEeec
Confidence            5889999999999999999999999999999999999999998888899999999553 33555544

>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.57  E-value=8.9e-15  Score=104.38  Aligned_cols=60  Identities=23%  Similarity=0.269  Sum_probs=54.1

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      |+++|+++.+++|.|+||||.+|+|+|.+||.|||++|+||+|...++....+|+++|+.
T Consensus         1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG   60 (70)
T cd01721           1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRG   60 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeC
Confidence            899999999999999999999999999999999999999998876554456789999944

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.55  E-value=1.5e-14  Score=104.43  Aligned_cols=60  Identities=15%  Similarity=0.243  Sum_probs=52.2

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc---cccccccEEEee
Q psy800           15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH---LLSYFASDLINF   74 (204)
Q Consensus        15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~---~~~~lG~vlIn~   74 (204)
                      +...|+++++|+|.|++++|++|.|+|+|||+|||++|+||.|+...+   .+..+|.++|+.
T Consensus         3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG   65 (74)
T cd01728           3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRG   65 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEEC
Confidence            467799999999999999999999999999999999999999987322   356789998844

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.55  E-value=1.3e-14  Score=104.95  Aligned_cols=61  Identities=23%  Similarity=0.315  Sum_probs=54.1

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee-cCccccccccEEEee
Q psy800           14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH-DSHLLSYFASDLINF   74 (204)
Q Consensus        14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~-~~~~~~~lG~vlIn~   74 (204)
                      .|++||+++.+++|.|+||||+++.|+|.+||.|||++|+||.|.. +++....+|+++|+.
T Consensus         1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG   62 (76)
T cd01723           1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRG   62 (76)
T ss_pred             CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeC
Confidence            4999999999999999999999999999999999999999999985 444445678999954

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.55  E-value=1.5e-14  Score=104.07  Aligned_cols=67  Identities=21%  Similarity=0.344  Sum_probs=54.8

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec----CccccccccEEEeeecccceeecc
Q psy800           17 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD----SHLLSYFASDLINFIWGLPMITPI   84 (204)
Q Consensus        17 ~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~----~~~~~~lG~vlIn~~~g~~~~~PI   84 (204)
                      +-|+++++++|+|++++|+.+.|+|+|||+|||++|++|+|+..    +.....+|.++|+.- +.++..|+
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~-~I~~i~~~   72 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGD-NIAVVGEI   72 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCC-EEEEEEcc
Confidence            35789999999999999999999999999999999999999863    224667899999552 33444454

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.53  E-value=2.7e-14  Score=103.96  Aligned_cols=56  Identities=18%  Similarity=0.364  Sum_probs=49.1

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC----------ccccccccEEEe
Q psy800           18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS----------HLLSYFASDLIN   73 (204)
Q Consensus        18 ~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~----------~~~~~lG~vlIn   73 (204)
                      -|.++++++|.|+++|||++.|+|.|||+||||+|+||+|+...          ...+.+|.++|.
T Consensus         4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iR   69 (79)
T cd01717           4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLR   69 (79)
T ss_pred             hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEc
Confidence            46789999999999999999999999999999999999998742          234678999883

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG3482|consensus

Probab=99.53  E-value=2.4e-14  Score=102.06  Aligned_cols=73  Identities=25%  Similarity=0.422  Sum_probs=67.0

Q ss_pred             CCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          113 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       113 ~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      ..+..|--+|+.+.+|+|.|+||-|.+|+|+|.+.|.|||+.|.+|+|+.   +|.....+|.++||.+||.+|..
T Consensus         4 ~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~i---dG~~~g~lGEilIRCNNvlyi~g   76 (79)
T KOG3482|consen    4 KQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYI---DGVSTGNLGEILIRCNNVLYIRG   76 (79)
T ss_pred             cccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhh---cccccccceeEEEEeccEEEEec
Confidence            34458889999999999999999999999999999999999999999986   67778899999999999999964

>KOG1781|consensus

Probab=99.53  E-value=1.2e-15  Score=114.40  Aligned_cols=81  Identities=22%  Similarity=0.522  Sum_probs=67.4

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCC-----eeeeeeCeEEEeCCcEEEEccccCCC
Q psy800          119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG-----RRITKLDQILLNGNNITMLGLHTHCG  193 (204)
Q Consensus       119 l~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~-----~~~~~lg~ilIRGdnI~~I~~~~~~~  193 (204)
                      +=-|.+|++++|+|++.+||...|+|+|||+.|||||+|+.|+-..++.     ...|++|.+++||..+++|+|.+..-
T Consensus        19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e   98 (108)
T KOG1781|consen   19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE   98 (108)
T ss_pred             HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence            3358899999999999999999999999999999999999998654322     24699999999999999999985331


Q ss_pred             --CCcccc
Q psy800          194 --MRPYIQ  199 (204)
Q Consensus       194 --~~~~~~  199 (204)
                        .+|.+|
T Consensus        99 ~I~npf~~  106 (108)
T KOG1781|consen   99 EIANPFVQ  106 (108)
T ss_pred             hhccchhc
Confidence              156555

>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins

Probab=99.53  E-value=4.6e-14  Score=98.72  Aligned_cols=58  Identities=31%  Similarity=0.483  Sum_probs=54.1

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc-cccccccEEEee
Q psy800           17 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH-LLSYFASDLINF   74 (204)
Q Consensus        17 ~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~-~~~~lG~vlIn~   74 (204)
                      .+|+++++++|+|.+++|++++|+|.+||+|||++|+||.|..... ...++|.++|+.
T Consensus         1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG   59 (67)
T PF01423_consen    1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRG   59 (67)
T ss_dssp             HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEG
T ss_pred             ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEEC
Confidence            4799999999999999999999999999999999999999999776 888899999965

In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....

>KOG1775|consensus

Probab=99.52  E-value=4.1e-15  Score=106.82  Aligned_cols=76  Identities=61%  Similarity=0.930  Sum_probs=67.3

Q ss_pred             CCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee---cCccccccccEEEeeecccceeecc
Q psy800            8 TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH---DSHLLSYFASDLINFIWGLPMITPI   84 (204)
Q Consensus         8 ~~~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~---~~~~~~~lG~vlIn~~~g~~~~~PI   84 (204)
                      ++++...|++++.++++.+|||.+|+++++.|+|.|||.|.|++|+|+.||-   ++....+++++++|.. ++.|+.|-
T Consensus         1 ~n~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGN-ni~mLvPG   79 (84)
T KOG1775|consen    1 TNPSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGN-NITMLVPG   79 (84)
T ss_pred             CChhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCC-cEEEEecC
Confidence            3567889999999999999999999999999999999999999999999987   4456778899999884 66777664

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.51  E-value=7.4e-14  Score=104.22  Aligned_cols=68  Identities=19%  Similarity=0.355  Sum_probs=58.2

Q ss_pred             CCCCCCCCcHHHHHhhcCC--EEEEEEeC--CeEEEEEEEeecCeeeeEecceEEeec-CccccccccEEEee
Q psy800            7 ATNPSTLLPLELVDKCIGS--RIHIIMKN--DKEIVGTLNGFDDFVNMLLEDVTDCHD-SHLLSYFASDLINF   74 (204)
Q Consensus         7 ~~~~~~~~P~~~L~~~~~k--~V~V~l~~--g~~~~G~L~gfD~~mNlvL~~~~E~~~-~~~~~~lG~vlIn~   74 (204)
                      ...+....|++++.+++.+  +|.|.+.+  +++++|+|.|||+|||++|+||+|+.. ++..+.+|.++|+.
T Consensus         7 ~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRG   79 (89)
T PTZ00138          7 KLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKG   79 (89)
T ss_pred             ccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcC
Confidence            5667788999999999975  67777766  589999999999999999999999975 44667899999943

>smart00651 Sm snRNP Sm proteins

Probab=99.50  E-value=7.2e-14  Score=97.66  Aligned_cols=58  Identities=34%  Similarity=0.559  Sum_probs=53.0

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC-ccccccccEEEee
Q psy800           17 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS-HLLSYFASDLINF   74 (204)
Q Consensus        17 ~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~-~~~~~lG~vlIn~   74 (204)
                      .+|+++++++|+|.|++|+++.|+|.|||+|||++|+||.|+..+ .....+|.++|+.
T Consensus         1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG   59 (67)
T smart00651        1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRG   59 (67)
T ss_pred             ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcC
Confidence            378999999999999999999999999999999999999999866 6778889999954

small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing

>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.46  E-value=2.1e-13  Score=101.96  Aligned_cols=60  Identities=20%  Similarity=0.172  Sum_probs=56.1

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      |..||+++.|++|.|+|+||.+|.|+|.++|.|||++|+||+|..+++....+|+++|+.
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG   61 (90)
T cd01724           2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRG   61 (90)
T ss_pred             HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeC
Confidence            678999999999999999999999999999999999999999998887778899999944

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.46  E-value=2e-13  Score=98.84  Aligned_cols=58  Identities=16%  Similarity=0.216  Sum_probs=51.4

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC------ccccccccEEEee
Q psy800           17 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS------HLLSYFASDLINF   74 (204)
Q Consensus        17 ~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~------~~~~~lG~vlIn~   74 (204)
                      +-|+++++++|.|+++|||.|.|+|.|||+||||+|+||.|+...      ...+.+|.++|..
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG   66 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPG   66 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeC
Confidence            468899999999999999999999999999999999999999843      4567889888844

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG1783|consensus

Probab=99.46  E-value=1.4e-14  Score=103.29  Aligned_cols=73  Identities=25%  Similarity=0.468  Sum_probs=67.9

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       114 ~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      ....|-++|++.++++|.|+|.+|-.|+|+|...|.|||+.|+.++|..   +|+..+++|..||||++|.+|+..
T Consensus         3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~---ngql~n~ygdaFirGnnVlyIs~~   75 (77)
T KOG1783|consen    3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV---NGQLKNKYGDAFIRGNNVLYISTQ   75 (77)
T ss_pred             cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh---cCcccccccceeeccccEEEEEec
Confidence            3467899999999999999999999999999999999999999999985   677889999999999999999865

>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.44  E-value=5.1e-13  Score=97.36  Aligned_cols=64  Identities=16%  Similarity=0.207  Sum_probs=56.9

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        11 ~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      .-..+..||+.+.|++|.|+||||.+|.|+|.++|.|||++|+||++...++....+|+++|..
T Consensus         6 ~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG   69 (78)
T cd01733           6 LENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTG   69 (78)
T ss_pred             hhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEEC
Confidence            3456789999999999999999999999999999999999999999887666666789999943

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.43  E-value=4.2e-13  Score=92.46  Aligned_cols=56  Identities=21%  Similarity=0.420  Sum_probs=51.4

Q ss_pred             HHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           19 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        19 L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      |+++++++|+|++++|+.|.|+|.+||+|||++|+||.|...+.....+|.++|+.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG   56 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRG   56 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEEC
Confidence            46789999999999999999999999999999999999998777778889999854

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG1784|consensus

Probab=99.40  E-value=2.2e-13  Score=100.92  Aligned_cols=70  Identities=24%  Similarity=0.519  Sum_probs=64.1

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeec-CCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST-PEGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~-~~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      -|+.|++++|.|.+.|||.+.|.|+|||+..||+|+|+.|+.++ ..+..+..+|..+|||+||..|.+.+
T Consensus         4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iD   74 (96)
T KOG1784|consen    4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEID   74 (96)
T ss_pred             hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecc
Confidence            48899999999999999999999999999999999999998875 34567889999999999999998875

>KOG1783|consensus

Probab=99.38  E-value=7.8e-14  Score=99.45  Aligned_cols=64  Identities=20%  Similarity=0.375  Sum_probs=61.1

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        11 ~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ....|.+||++.++|+|.|||.+|..|+|+|...|.|||+.||.++|+.+++..+++|+.||+.
T Consensus         3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirG   66 (77)
T KOG1783|consen    3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRG   66 (77)
T ss_pred             cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeecc
Confidence            5678999999999999999999999999999999999999999999999999999999999954

>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.35  E-value=2.9e-12  Score=93.92  Aligned_cols=61  Identities=21%  Similarity=0.364  Sum_probs=52.4

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc--cccccccEEEee
Q psy800           14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH--LLSYFASDLINF   74 (204)
Q Consensus        14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~--~~~~lG~vlIn~   74 (204)
                      .|+.||+++.|++|.|+||+|..|+|+|.++|.|||++|+||++...+.  ....+++++|+.
T Consensus         1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG   63 (81)
T cd01725           1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRG   63 (81)
T ss_pred             ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEEC
Confidence            4789999999999999999999999999999999999999998775332  234568899844

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG1782|consensus

Probab=99.34  E-value=1.5e-13  Score=106.88  Aligned_cols=72  Identities=18%  Similarity=0.381  Sum_probs=64.7

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccccCC
Q psy800          121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHTHC  192 (204)
Q Consensus       121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~~~  192 (204)
                      -|-+++++++.|.|+|||.+.|.|++||||-|++|++|.|+.+..+.......|.++|||+||++++..+..
T Consensus        13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~d   84 (129)
T KOG1782|consen   13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLD   84 (129)
T ss_pred             HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcc
Confidence            378899999999999999999999999999999999999988765555678889999999999999877655

>KOG1774|consensus

Probab=99.29  E-value=2.5e-12  Score=93.57  Aligned_cols=68  Identities=19%  Similarity=0.408  Sum_probs=57.1

Q ss_pred             CCCCCCCCcHHHHHhhcCC----EEEEEEeCCeEEEEEEEeecCeeeeEecceEEee-cCccccccccEEEee
Q psy800            7 ATNPSTLLPLELVDKCIGS----RIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH-DSHLLSYFASDLINF   74 (204)
Q Consensus         7 ~~~~~~~~P~~~L~~~~~k----~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~-~~~~~~~lG~vlIn~   74 (204)
                      -.++....|.+++.+|+..    +||..-+-|..++|.+.|||+|||+||+||+|.. +.+..+.+|+++++.
T Consensus         5 kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKG   77 (88)
T KOG1774|consen    5 KVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKG   77 (88)
T ss_pred             cccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcC
Confidence            3456678999999998864    5777777799999999999999999999999987 455666999999954

>KOG3460|consensus

Probab=99.27  E-value=9.6e-13  Score=96.11  Aligned_cols=49  Identities=33%  Similarity=0.637  Sum_probs=46.9

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee
Q psy800           11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH   59 (204)
Q Consensus        11 ~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~   59 (204)
                      .+..|+++|+-+++.+|.||++++|++.|+|.|||+|+|++|.||+|.+
T Consensus         2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eeti   50 (91)
T KOG3460|consen    2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETI   50 (91)
T ss_pred             cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheE
Confidence            4678999999999999999999999999999999999999999999987

>KOG3293|consensus

Probab=99.23  E-value=1.9e-11  Score=95.21  Aligned_cols=72  Identities=22%  Similarity=0.447  Sum_probs=66.3

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      ++||.+|+.+-++++.|+||||..|.|.|..+|.+|||.|.++.+..  +||.+--.+..++|||.+|.|+...
T Consensus         1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts--~Dgdkf~r~pEcYirGttIkylri~   72 (134)
T KOG3293|consen    1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTS--EDGDKFFRMPECYIRGTTIKYLRIP   72 (134)
T ss_pred             CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEec--cCCCceeecceeEEecceeEEEecc
Confidence            47999999999999999999999999999999999999999999975  5777778889999999999999654

>KOG3448|consensus

Probab=99.13  E-value=3e-10  Score=84.01  Aligned_cols=72  Identities=21%  Similarity=0.421  Sum_probs=60.8

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +-+++++.++|++|.|+|||+-.+.|+|.|.|+|+|+-|+|......++- ..-..+..++|||+.|.||..+
T Consensus         2 LFysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~ky-Phm~Sv~ncfIRGSvvrYv~l~   73 (96)
T KOG3448|consen    2 LFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKY-PHMLSVKNCFIRGSVVRYVQLP   73 (96)
T ss_pred             chHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccC-CCeeeeeeEEEeccEEEEEEeC
Confidence            34678999999999999999999999999999999999999998653211 1356678999999999999654

>KOG3168|consensus

Probab=99.12  E-value=1.1e-11  Score=101.33  Aligned_cols=69  Identities=23%  Similarity=0.526  Sum_probs=60.7

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeec-------CCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST-------PEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~-------~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      .|-+.+|.+..|.++|||.+.|.+++||.|||+||.||+|....       .++++.+-+|.+++||++|++.+..
T Consensus         8 kml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVe   83 (177)
T KOG3168|consen    8 KMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVE   83 (177)
T ss_pred             HHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEecc
Confidence            46678999999999999999999999999999999999996532       3456789999999999999998654

>KOG1781|consensus

Probab=99.09  E-value=8e-12  Score=93.85  Aligned_cols=65  Identities=20%  Similarity=0.395  Sum_probs=53.1

Q ss_pred             HHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC--------ccccccccEEEeeecccceeecc
Q psy800           19 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS--------HLLSYFASDLINFIWGLPMITPI   84 (204)
Q Consensus        19 L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~--------~~~~~lG~vlIn~~~g~~~~~PI   84 (204)
                      |.+|++|+|+|++.+||+..|+|+|||+.|||||+||+|+..+        ...+.+|-+++.. .+++.+.|-
T Consensus        22 Lsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RG-Talvlisp~   94 (108)
T KOG1781|consen   22 LSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRG-TALVLISPA   94 (108)
T ss_pred             HHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcc-cEEEEEcCC
Confidence            5689999999999999999999999999999999999999732        1347788888766 344555443

>KOG3172|consensus

Probab=98.98  E-value=1.5e-09  Score=82.85  Aligned_cols=71  Identities=27%  Similarity=0.471  Sum_probs=64.2

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       115 ~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      ...|+++|++.-++.|++++..|..|+|+|.-.|++||+.|+|+....  .|| ...++.+++|||+.|.++..
T Consensus         3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~--~dg-~vs~le~V~IRGS~IRFlvl   73 (119)
T KOG3172|consen    3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTA--RDG-RVSQLEQVFIRGSKIRFLVL   73 (119)
T ss_pred             cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEc--cCC-cceeeeeEEEecCeEEEEEC
Confidence            467999999999999999999999999999999999999999999875  455 57789999999999998743

>KOG3459|consensus

Probab=98.97  E-value=7.9e-11  Score=90.12  Aligned_cols=74  Identities=22%  Similarity=0.460  Sum_probs=64.2

Q ss_pred             CCcHHHHHhhcC--CEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeec----CCCe------eeeeeCeEEEeCCcE
Q psy800          116 LLPLELVDKCIG--SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST----PEGR------RITKLDQILLNGNNI  183 (204)
Q Consensus       116 ~~Pl~~L~~~i~--k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~----~~~~------~~~~lg~ilIRGdnI  183 (204)
                      .+|++++...+.  .+|.|.+||++.+.|+++|||.|.|++|+++.|.|..    .+|+      ..+.+|+++||||+|
T Consensus        23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv  102 (114)
T KOG3459|consen   23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV  102 (114)
T ss_pred             cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence            479999999885  5799999999999999999999999999999999875    1333      268899999999999


Q ss_pred             EEEccc
Q psy800          184 TMLGLH  189 (204)
Q Consensus       184 ~~I~~~  189 (204)
                      +++...
T Consensus       103 I~v~r~  108 (114)
T KOG3459|consen  103 ILVLRN  108 (114)
T ss_pred             EEEEec
Confidence            998644

>KOG3428|consensus

Probab=98.70  E-value=1.1e-07  Score=72.88  Aligned_cols=71  Identities=25%  Similarity=0.351  Sum_probs=62.0

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEE-ccccCCC
Q psy800          119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITML-GLHTHCG  193 (204)
Q Consensus       119 l~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I-~~~~~~~  193 (204)
                      +.+|+++.+++|+|+|++|..+.|++.+.|-+||..|.++.-..   .| +..++..+.+||++|.|+ -|++.++
T Consensus         4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~---~~-~pv~l~~lsirgnniRy~~lpD~l~l   75 (109)
T KOG3428|consen    4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTV---KG-EPVRLDTLSIRGNNIRYYILPDSLNL   75 (109)
T ss_pred             HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEec---CC-CceeEEEEEeecceEEEEEccCCcCc
Confidence            56899999999999999999999999999999999999988764   24 567899999999999997 5666553

>KOG1784|consensus

Probab=98.55  E-value=8.5e-08  Score=71.37  Aligned_cols=55  Identities=22%  Similarity=0.419  Sum_probs=46.4

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC----ccccccccEEE
Q psy800           18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS----HLLSYFASDLI   72 (204)
Q Consensus        18 ~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~----~~~~~lG~vlI   72 (204)
                      -|+.|+|++|.|...|||.+.|.|+|||+-.||+|+++-|++-+    .....+|--+|
T Consensus         4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyii   62 (96)
T KOG1784|consen    4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYII   62 (96)
T ss_pred             hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEE
Confidence            47899999999999999999999999999999999999998733    34445564444

>KOG3293|consensus

Probab=98.47  E-value=2.2e-07  Score=72.62  Aligned_cols=49  Identities=24%  Similarity=0.419  Sum_probs=46.4

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc
Q psy800           14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH   62 (204)
Q Consensus        14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~   62 (204)
                      .|+.+|+.+-+.++.|.||+|.+|.|.|..+|.+|||.|.++.++.++.
T Consensus         2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dg   50 (134)
T KOG3293|consen    2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDG   50 (134)
T ss_pred             cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCC
Confidence            6999999999999999999999999999999999999999999988543

>KOG3168|consensus

Probab=98.31  E-value=7.1e-08  Score=79.08  Aligned_cols=58  Identities=16%  Similarity=0.407  Sum_probs=46.9

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec----------CccccccccEEE
Q psy800           14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD----------SHLLSYFASDLI   72 (204)
Q Consensus        14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~----------~~~~~~lG~vlI   72 (204)
                      .+.++| +.+|.++.|.++|||.|.|.+.+||.||||+|.||+|+..          .++++.+|-+++
T Consensus         5 ~sskml-~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvll   72 (177)
T KOG3168|consen    5 KSSKML-QHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLL   72 (177)
T ss_pred             chhHHH-HhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEe
Confidence            344555 5789999999999999999999999999999999999752          234555666665

>KOG1782|consensus

Probab=98.24  E-value=6.8e-08  Score=75.44  Aligned_cols=41  Identities=20%  Similarity=0.618  Sum_probs=39.4

Q ss_pred             HHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee
Q psy800           19 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH   59 (204)
Q Consensus        19 L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~   59 (204)
                      +-++++|++.|-|+|||.+.|.|++||+|-|++|++|.|++
T Consensus        14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi   54 (129)
T KOG1782|consen   14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERI   54 (129)
T ss_pred             HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhhe
Confidence            66899999999999999999999999999999999999987

>KOG3448|consensus

Probab=98.21  E-value=2.3e-06  Score=63.51  Aligned_cols=43  Identities=28%  Similarity=0.553  Sum_probs=40.3

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEe
Q psy800           16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDC   58 (204)
Q Consensus        16 ~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~   58 (204)
                      .+|.+.++++.|.|.||++..+.|+|.|.|+|+|+-|+|..-.
T Consensus         4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~   46 (96)
T KOG3448|consen    4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVT   46 (96)
T ss_pred             HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEee
Confidence            5789999999999999999999999999999999999997654

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=97.99  E-value=0.00013  Score=60.11  Aligned_cols=111  Identities=19%  Similarity=0.292  Sum_probs=66.9

Q ss_pred             HHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEec-ceEEeecCccccccccEEE--eeecccceeeccccccce
Q psy800           16 LELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLE-DVTDCHDSHLLSYFASDLI--NFIWGLPMITPITCAYSR   90 (204)
Q Consensus        16 ~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~-~~~E~~~~~~~~~lG~vlI--n~~~g~~~~~PI~~~f~~   90 (204)
                      -.||+.+-  +.+|.|.|.+|-.++|.+.|||.|. +.|+ +..            ..+|  .-+.-+....|++..+ .
T Consensus        14 D~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ft-VlL~~~gk------------qqLIYKHAISTI~p~~~i~~~~-~   79 (165)
T PRK14091         14 DIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFS-ILLRRDGQ------------SQLVYKHAISTIMPAHPLDLSR-F   79 (165)
T ss_pred             HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceE-EEEEeCCc------------eEEEEeeeeeeecccCCcchhh-h
Confidence            45665554  3589999999999999999999999 4443 221            2222  2222223334444211 1


Q ss_pred             eecccEeEEEeeeccCCcccCCCCCCCcHHHHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceE
Q psy800           91 SHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNML  154 (204)
Q Consensus        91 ~~~~~~v~~~l~~~~~~~~~~~~~~~~Pl~~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlV  154 (204)
                       + +      .|..      +.++..+-=.+|..+.  ..+|+|.|.||-.+.|.+.|||.|.=|.
T Consensus        80 -~-~------~~~~------~~~~~nlQd~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL  131 (165)
T PRK14091         80 -S-K------SLDA------NKKSRLLQDVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLL  131 (165)
T ss_pred             -c-c------hhhh------cccccccHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEE
Confidence             1 1      1111      1111122223555554  3569999999999999999999998444

>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=97.94  E-value=7.3e-06  Score=57.75  Aligned_cols=25  Identities=44%  Similarity=0.470  Sum_probs=23.4

Q ss_pred             EEEEEEEEEcCccceEEcceEEEee
Q psy800          139 EIVGTLNGFDDFVNMLLEDVTEYES  163 (204)
Q Consensus       139 ~i~G~L~gfD~~mNlVL~da~E~~~  163 (204)
                      .++|.|.+||.|+||+|.|+.|.+.
T Consensus        24 ~~~G~lvAFDK~wNm~L~DV~E~y~   48 (66)
T cd01739          24 VCSGFLVAFDKFWNMALVDVDETYR   48 (66)
T ss_pred             EEEEEEEeeeeehhheehhhhhhhc
Confidence            7899999999999999999999874

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

>KOG3459|consensus

Probab=97.67  E-value=5.6e-06  Score=63.66  Aligned_cols=49  Identities=24%  Similarity=0.478  Sum_probs=44.6

Q ss_pred             CCCCcHHHHHhhcC--CEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee
Q psy800           11 STLLPLELVDKCIG--SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH   59 (204)
Q Consensus        11 ~~~~P~~~L~~~~~--k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~   59 (204)
                      -...|++++...+.  .+|+|.+++++.+.|++.|||.|.|++|+++.|..
T Consensus        21 f~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelw   71 (114)
T KOG3459|consen   21 FNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELW   71 (114)
T ss_pred             cCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHC
Confidence            34589999998884  69999999999999999999999999999999976

>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=97.55  E-value=7.8e-05  Score=52.57  Aligned_cols=37  Identities=30%  Similarity=0.437  Sum_probs=30.2

Q ss_pred             CEEEEEEeC--C--eEEEEEEEeecCeeeeEecceEEeecC
Q psy800           25 SRIHIIMKN--D--KEIVGTLNGFDDFVNMLLEDVTDCHDS   61 (204)
Q Consensus        25 k~V~V~l~~--g--~~~~G~L~gfD~~mNlvL~~~~E~~~~   61 (204)
                      ++|.|.++.  |  -.+.|.|.+||.|+||+|.|+.|....
T Consensus         9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~   49 (66)
T cd01739           9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK   49 (66)
T ss_pred             cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence            566666664  3  378999999999999999999997644

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

>KOG3172|consensus

Probab=97.45  E-value=0.00025  Score=54.53  Aligned_cols=63  Identities=21%  Similarity=0.233  Sum_probs=55.9

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           12 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        12 ~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ...|.++|.+.-+.-|.+.+..|..|.|+|.-.|.+||.+|+|..-...+.....+-.++|..
T Consensus         3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRG   65 (119)
T KOG3172|consen    3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRG   65 (119)
T ss_pred             cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEec
Confidence            457999999999999999999999999999999999999999998887766666777788843

>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1

Probab=97.16  E-value=0.0011  Score=47.43  Aligned_cols=65  Identities=9%  Similarity=0.238  Sum_probs=40.9

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEEEcC---ccceEEcceEEEeecCC--C--eeeeeeCeEEEeCCcEE
Q psy800          120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDD---FVNMLLEDVTEYESTPE--G--RRITKLDQILLNGNNIT  184 (204)
Q Consensus       120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~---~mNlVL~da~E~~~~~~--~--~~~~~lg~ilIRGdnI~  184 (204)
                      -++..++|++|.|.++||..|+|.|.+++.   -+-++|+-|........  .  .......+++|.++.|+
T Consensus         5 ~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    5 YLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred             HHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence            356778999999999999999999999997   89999999988643211  1  12334566677766654

>KOG3428|consensus

Probab=96.74  E-value=0.0032  Score=48.51  Aligned_cols=46  Identities=24%  Similarity=0.364  Sum_probs=41.5

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC
Q psy800           16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS   61 (204)
Q Consensus        16 ~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~   61 (204)
                      ..||+++.+.+|.|.|++|....|++.+.|.+||..|.++.=...+
T Consensus         4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~   49 (109)
T KOG3428|consen    4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG   49 (109)
T ss_pred             HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC
Confidence            4689999999999999999999999999999999999988755543

>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others

Probab=96.01  E-value=0.014  Score=40.75  Aligned_cols=28  Identities=25%  Similarity=0.532  Sum_probs=24.8

Q ss_pred             CCEEEEEEeCCeEEEEEEEEEcCccceE
Q psy800          127 GSRIHIIMKNDKEIVGTLNGFDDFVNML  154 (204)
Q Consensus       127 ~k~V~V~Lk~gr~i~G~L~gfD~~mNlV  154 (204)
                      ..+|+|.|.||-.+.|.+.|||+|+=++
T Consensus        11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll   38 (61)
T cd01716          11 KIPVTIYLVNGVQLKGQIESFDNFTVLL   38 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEcceEEEE
Confidence            4569999999999999999999998444

Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.

>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1

Probab=95.85  E-value=0.025  Score=40.39  Aligned_cols=44  Identities=16%  Similarity=0.274  Sum_probs=34.6

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEeecC---eeeeEecceEEeecC
Q psy800           18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDD---FVNMLLEDVTDCHDS   61 (204)
Q Consensus        18 ~L~~~~~k~V~V~l~~g~~~~G~L~gfD~---~mNlvL~~~~E~~~~   61 (204)
                      ++..++|++|.|.++||..|+|.|.+++.   =+.++|.-|....++
T Consensus         6 l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~   52 (77)
T PF14438_consen    6 LLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKS   52 (77)
T ss_dssp             HHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-
T ss_pred             HHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccc
Confidence            56678899999999999999999999999   789999988876543

>TIGR02383 Hfq RNA chaperone Hfq

Probab=95.72  E-value=0.021  Score=39.90  Aligned_cols=29  Identities=21%  Similarity=0.492  Sum_probs=25.3

Q ss_pred             CCEEEEEEeCCeEEEEEEEEEcCccceEE
Q psy800          127 GSRIHIIMKNDKEIVGTLNGFDDFVNMLL  155 (204)
Q Consensus       127 ~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL  155 (204)
                      ..+|+|.|.||-.+.|.+.|||+|+=++-
T Consensus        15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~   43 (61)
T TIGR02383        15 RIPVTVFLVNGVQLKGVIESFDNFTVLLE   43 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence            45799999999999999999999985543

This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.

>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown

Probab=95.37  E-value=0.1  Score=34.16  Aligned_cols=33  Identities=27%  Similarity=0.455  Sum_probs=29.0

Q ss_pred             cCCEEEEEEeCCeEEEEEEEEEcCccceEEcceE
Q psy800          126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT  159 (204)
Q Consensus       126 i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~  159 (204)
                      ++++|+|.+ ++..++|+..|+|+.-.|+++...
T Consensus         2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~   34 (48)
T PF02237_consen    2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTED   34 (48)
T ss_dssp             TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETT
T ss_pred             CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECC
Confidence            689999999 677889999999999999997644

It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....

>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others

Probab=95.34  E-value=0.056  Score=37.76  Aligned_cols=33  Identities=18%  Similarity=0.448  Sum_probs=27.1

Q ss_pred             HHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeee
Q psy800           18 LVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNM   50 (204)
Q Consensus        18 ~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNl   50 (204)
                      ||+.+-  +.+|.|.|.||-.++|.+.|||.|+=+
T Consensus         3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVl   37 (61)
T cd01716           3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVL   37 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEE
Confidence            444443  458999999999999999999999933

Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.

>TIGR02383 Hfq RNA chaperone Hfq

Probab=95.31  E-value=0.06  Score=37.63  Aligned_cols=35  Identities=17%  Similarity=0.471  Sum_probs=28.2

Q ss_pred             HHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeE
Q psy800           17 ELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNML   51 (204)
Q Consensus        17 ~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlv   51 (204)
                      .||+.+-  +.+|.|.|.+|-.++|.+.|||.|+=|.
T Consensus         6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll   42 (61)
T TIGR02383         6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLL   42 (61)
T ss_pred             HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEE
Confidence            3555444  4689999999999999999999999333

This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.

>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A

Probab=95.16  E-value=0.12  Score=39.13  Aligned_cols=63  Identities=30%  Similarity=0.464  Sum_probs=51.1

Q ss_pred             hhcCCEEEEEEeCCeEEEEEEEEEcC-ccceEEcceEEEeecCCCe--------eeeeeCeEEEeCCcEEEEcc
Q psy800          124 KCIGSRIHIIMKNDKEIVGTLNGFDD-FVNMLLEDVTEYESTPEGR--------RITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       124 ~~i~k~V~V~Lk~gr~i~G~L~gfD~-~mNlVL~da~E~~~~~~~~--------~~~~lg~ilIRGdnI~~I~~  188 (204)
                      .|+|++|.+..+++-+|+|+|...|. --.|.|.++.-.-++  +.        ...-+..++.||..|.-+..
T Consensus         5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE--~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v   76 (96)
T PF12701_consen    5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTE--GRPTDREIPPSDEVYDYIVFRGSDIKDLKV   76 (96)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTET--TSS-SS---C-CSSSSEEEEETTTEEEEEE
T ss_pred             cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcC--CCCcCcccCCCCceeeEEEEEccccceEEE
Confidence            58999999999999999999999994 788999998875432  21        13457899999999987644

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=95.15  E-value=0.039  Score=40.47  Aligned_cols=31  Identities=26%  Similarity=0.505  Sum_probs=26.2

Q ss_pred             CCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800          127 GSRIHIIMKNDKEIVGTLNGFDDFVNMLLED  157 (204)
Q Consensus       127 ~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d  157 (204)
                      ..+|+|.|.||-.+.|.+.|||+|+=++-.+
T Consensus        19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~   49 (79)
T PRK00395         19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNT   49 (79)
T ss_pred             CCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence            4569999999999999999999998555333

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=94.59  E-value=0.11  Score=38.13  Aligned_cols=35  Identities=23%  Similarity=0.471  Sum_probs=28.3

Q ss_pred             HHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeE
Q psy800           17 ELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNML   51 (204)
Q Consensus        17 ~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlv   51 (204)
                      .||+.+-  +.+|.|.|.+|-.++|.+.|||.|+=|.
T Consensus        10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll   46 (79)
T PRK00395         10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLL   46 (79)
T ss_pred             HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEE
Confidence            4555444  4689999999999999999999999443

>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]

Probab=94.41  E-value=0.09  Score=38.28  Aligned_cols=30  Identities=30%  Similarity=0.614  Sum_probs=25.5

Q ss_pred             CCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800          127 GSRIHIIMKNDKEIVGTLNGFDDFVNMLLED  157 (204)
Q Consensus       127 ~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d  157 (204)
                      ..+|+|.|.||-.+.|.+.|||+|. +.|++
T Consensus        19 ~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~   48 (77)
T COG1923          19 KIPVTIFLVNGFKLQGQVESFDNFV-VLLKN   48 (77)
T ss_pred             CCeEEEEEEcCEEEEEEEEeeeeEE-EEEEc
Confidence            4679999999999999999999998 44443

>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=93.99  E-value=0.29  Score=35.50  Aligned_cols=62  Identities=26%  Similarity=0.416  Sum_probs=46.5

Q ss_pred             hhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecC---CCe----eeeeeCeEEEeCCcEEE
Q psy800          124 KCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTP---EGR----RITKLDQILLNGNNITM  185 (204)
Q Consensus       124 ~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~---~~~----~~~~lg~ilIRGdnI~~  185 (204)
                      +++++++.+..+.+-+|+|+|.++| +---+.|.|+...-++.   ++.    ...-+..++.||+.|.-
T Consensus         3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD   72 (74)
T cd01736           3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD   72 (74)
T ss_pred             cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence            5899999999999999999999999 44668899987654321   111    23446788899987753

Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.

>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]

Probab=93.65  E-value=0.32  Score=35.43  Aligned_cols=30  Identities=30%  Similarity=0.614  Sum_probs=26.0

Q ss_pred             CCEEEEEEeCCeEEEEEEEeecCeeeeEecc
Q psy800           24 GSRIHIIMKNDKEIVGTLNGFDDFVNMLLED   54 (204)
Q Consensus        24 ~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~   54 (204)
                      +.+|.|.|.||-.+.|.+.|||+|. +.|++
T Consensus        19 ~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~   48 (77)
T COG1923          19 KIPVTIFLVNGFKLQGQVESFDNFV-VLLKN   48 (77)
T ss_pred             CCeEEEEEEcCEEEEEEEEeeeeEE-EEEEc
Confidence            5689999999999999999999998 44443

>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins

Probab=91.46  E-value=1.1  Score=32.85  Aligned_cols=63  Identities=14%  Similarity=0.324  Sum_probs=46.2

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      -|..|....|++|.+.|.++.++.|++.|+| .-.|+..+|-.-    +=|    ....-+||..-|+.++-
T Consensus        15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~T----PlG----v~~eAlLR~~DVi~~~f   78 (80)
T PF11095_consen   15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQT----PLG----VQPEALLRCSDVISISF   78 (80)
T ss_dssp             HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEET----TTT----EEEEEEEEGGGEEEEEE
T ss_pred             HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCC----Ccc----cChhheeecCCEEEEEe
Confidence            3566777889999999999999999999999 556766655431    223    24688999999998864

Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=90.61  E-value=0.84  Score=37.82  Aligned_cols=35  Identities=17%  Similarity=0.337  Sum_probs=28.7

Q ss_pred             HHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeee
Q psy800           16 LELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNM   50 (204)
Q Consensus        16 ~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNl   50 (204)
                      -.||+.+-  +.+|.|.|.+|-.++|.+.|||.|+=|
T Consensus        94 d~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvl  130 (165)
T PRK14091         94 DVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCML  130 (165)
T ss_pred             HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEE
Confidence            45665554  358999999999999999999999933

>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella

Probab=90.57  E-value=2  Score=35.33  Aligned_cols=110  Identities=16%  Similarity=0.191  Sum_probs=66.0

Q ss_pred             CCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEe--eecccceeeccccccceeecccEeE-EE
Q psy800           24 GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLIN--FIWGLPMITPITCAYSRSHQYRTLT-HL  100 (204)
Q Consensus        24 ~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn--~~~g~~~~~PI~~~f~~~~~~~~v~-~~  100 (204)
                      +-+|.|.+.||+.+.|.+.||+.-=|.+|.-+.  .++..     ++-+.  .+..+... |.+-.+..+    .|. ..
T Consensus        29 ~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~--~~~~n-----Ri~~plE~I~t~Ee~-~~~d~~g~~----ti~~d~   96 (165)
T PF03614_consen   29 DIPVRVVSENGQVFCMYVSGFMSKENKILAPDP--FKKEN-----RIRLPLERISTIEEL-IVSDFKGRL----TIHPDY   96 (165)
T ss_pred             CCceEEEecCCcEEEEEEeccCcccCEEeccCC--CCCCc-----eEEEEhHHhhhHhhh-ccccccccE----Eechhh
Confidence            568999999999999999999999999987554  12211     12111  11111111 111111111    110 11


Q ss_pred             eeeccCCcccCCCCCCCcHHHHHhhc--CCEEEEEEeCCeEEEEEEEEEcCc
Q psy800          101 LYTMTAPSVATNPSTLLPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDF  150 (204)
Q Consensus       101 l~~~~~~~~~~~~~~~~Pl~~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~  150 (204)
                      +-.+     ...|+...-+++-+++.  ++-|.|.+.|||.++|+-.|.|..
T Consensus        97 ~~~q-----~~~psrrDFF~Icrka~qqg~sIrVyM~DgR~ieG~stGvnac  143 (165)
T PF03614_consen   97 FNNQ-----PYKPSRRDFFSICRKAHQQGKSIRVYMADGREIEGKSTGVNAC  143 (165)
T ss_pred             cccc-----cCCCccchHHHHHHHHHHCCCeEEEEEcCCcEEEeeecccceE
Confidence            1111     13344455567777765  778999999999999999998753

The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent

>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=90.38  E-value=0.71  Score=32.21  Aligned_cols=36  Identities=19%  Similarity=0.306  Sum_probs=30.6

Q ss_pred             hcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEE
Q psy800          125 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTE  160 (204)
Q Consensus       125 ~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E  160 (204)
                      .+|..|.+++..|.+++|.+.+||.-.++++-.+.+
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s   39 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS   39 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence            478999999999999999999999888877655443

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.

>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown

Probab=87.82  E-value=1.4  Score=28.70  Aligned_cols=32  Identities=28%  Similarity=0.469  Sum_probs=28.3

Q ss_pred             cCCEEEEEEeCCeEEEEEEEeecCeeeeEecce
Q psy800           23 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV   55 (204)
Q Consensus        23 ~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~   55 (204)
                      +|++|.+.. ++..+.|+..|.|..=.|+++..
T Consensus         2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~   33 (48)
T PF02237_consen    2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTE   33 (48)
T ss_dssp             TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEET
T ss_pred             CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEEC
Confidence            689999999 77778999999999999998653

It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....

>PRK14638 hypothetical protein; Provisional

Probab=87.79  E-value=1.1  Score=36.34  Aligned_cols=40  Identities=23%  Similarity=0.334  Sum_probs=31.4

Q ss_pred             CCCcHH---HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEE
Q psy800          115 TLLPLE---LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL  155 (204)
Q Consensus       115 ~~~Pl~---~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL  155 (204)
                      ...||.   -+.+++|++|.|++++++.++|+|.++|+- ++.|
T Consensus        85 ldRpL~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l  127 (150)
T PRK14638         85 LDRPLRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITI  127 (150)
T ss_pred             CCCCCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            345544   466778999999999999999999999964 3444

>PRK02001 hypothetical protein; Validated

Probab=85.92  E-value=1.6  Score=35.59  Aligned_cols=40  Identities=33%  Similarity=0.512  Sum_probs=31.6

Q ss_pred             CCCcHH---HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEE
Q psy800          115 TLLPLE---LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL  155 (204)
Q Consensus       115 ~~~Pl~---~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL  155 (204)
                      ...||.   -+.+++|+.|.|.+.+++.++|+|.++|+- +++|
T Consensus        75 ldRpL~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l  117 (152)
T PRK02001         75 LTSPLKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL  117 (152)
T ss_pred             CCCcCCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence            345544   466778999999999999999999999874 3444

>PRK14639 hypothetical protein; Provisional

Probab=85.61  E-value=1.7  Score=34.82  Aligned_cols=35  Identities=29%  Similarity=0.438  Sum_probs=29.4

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEE
Q psy800          120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL  155 (204)
Q Consensus       120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL  155 (204)
                      +-+.+++|+.|.|++++++.+.|+|.++|+- ++.|
T Consensus        81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l  115 (140)
T PRK14639         81 EHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL  115 (140)
T ss_pred             HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            3566788999999999999999999999883 4544

>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function

Probab=85.54  E-value=5.2  Score=28.34  Aligned_cols=53  Identities=19%  Similarity=0.342  Sum_probs=40.3

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       119 l~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      ++.|++++|++|.|.+..| .++|+|.+.. +|.  +|+..        +      ..++||=..|+.|.|
T Consensus        13 yq~lq~liG~~vvV~T~~g-~v~G~L~~V~pDhI--vl~~~--------~------~~~~IR~~~IV~v~p   66 (66)
T PF10842_consen   13 YQTLQSLIGQRVVVQTTRG-SVRGILVDVKPDHI--VLEEN--------G------TPFFIRIAQIVWVMP   66 (66)
T ss_pred             HHHHHHhcCCEEEEEEcCC-cEEEEEEeecCCEE--EEEeC--------C------cEEEEEeeeEEEEcC
Confidence            5689999999999999776 5599999985 554  44432        1      368888888888754

>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins

Probab=84.06  E-value=1.8  Score=35.99  Aligned_cols=59  Identities=20%  Similarity=0.431  Sum_probs=39.7

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEc
Q psy800          118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLG  187 (204)
Q Consensus       118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~  187 (204)
                      |++ +.+|++|.|.|.+.| +++.|.|..+| ..-|+||-+..|     +++  ..  --+|=|-.|..|.
T Consensus         9 p~~-~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e-----~~~--~s--v~~I~ghaVk~ve   68 (166)
T PF06372_consen    9 PLE-WQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE-----DGK--RS--VKVIMGHAVKSVE   68 (166)
T ss_dssp             HHH-HHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T-----TS---EE--EEEE-GGGEEEEE
T ss_pred             HHH-HHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc-----CCc--ee--EEEEEccceEEEE
Confidence            444 678999999999999 99999999999 567899986664     332  22  3566777777664

The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.

>PRK14639 hypothetical protein; Provisional

Probab=83.79  E-value=1.9  Score=34.52  Aligned_cols=33  Identities=30%  Similarity=0.483  Sum_probs=27.8

Q ss_pred             HhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEec
Q psy800           20 DKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLE   53 (204)
Q Consensus        20 ~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~   53 (204)
                      ++++|+.|.|++++++.+.|+|.++|.- ++.|+
T Consensus        84 ~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~  116 (140)
T PRK14639         84 AKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE  116 (140)
T ss_pred             HHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            3688999999999999999999999983 45543

>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A

Probab=83.65  E-value=2.4  Score=32.11  Aligned_cols=38  Identities=32%  Similarity=0.433  Sum_probs=34.3

Q ss_pred             hhcCCEEEEEEeCCeEEEEEEEeecC-eeeeEecceEEe
Q psy800           21 KCIGSRIHIIMKNDKEIVGTLNGFDD-FVNMLLEDVTDC   58 (204)
Q Consensus        21 ~~~~k~V~V~l~~g~~~~G~L~gfD~-~mNlvL~~~~E~   58 (204)
                      .|+|++|.+..+.+-.|+|+|...|. --.+.|.++.-+
T Consensus         5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~   43 (96)
T PF12701_consen    5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSF   43 (96)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEET
T ss_pred             cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeec
Confidence            68999999999999999999999998 567999998764

>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=83.43  E-value=2.7  Score=29.28  Aligned_cols=34  Identities=21%  Similarity=0.321  Sum_probs=29.6

Q ss_pred             hcCCEEEEEEeCCeEEEEEEEeecCeeeeEecce
Q psy800           22 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV   55 (204)
Q Consensus        22 ~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~   55 (204)
                      ++|..|.++.-.|.+++|.+.+||.-.++..=.+
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~   37 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKC   37 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEEC
Confidence            4689999999999999999999999998764443

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.

>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins

Probab=82.48  E-value=2  Score=35.68  Aligned_cols=43  Identities=21%  Similarity=0.416  Sum_probs=32.6

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCee-eeEecceEE
Q psy800           13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFV-NMLLEDVTD   57 (204)
Q Consensus        13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~m-NlvL~~~~E   57 (204)
                      ..|+.+. .|++|+|.|.+.+ +++.|.|-.+|.-- |+||-+-.|
T Consensus         7 ~~p~~~~-~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e   50 (166)
T PF06372_consen    7 KSPLEWQ-DYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE   50 (166)
T ss_dssp             S-HHHHH-CTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred             CCHHHHH-HhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence            5688777 6999999999999 99999999999865 788875543

The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.

>PRK14638 hypothetical protein; Provisional

Probab=82.10  E-value=2.2  Score=34.63  Aligned_cols=36  Identities=25%  Similarity=0.510  Sum_probs=28.6

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEe
Q psy800           15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL   52 (204)
Q Consensus        15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL   52 (204)
                      |.+|. ++.|+.|.|++++++.+.|+|.++|.- ++.|
T Consensus        92 ~~~f~-r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l  127 (150)
T PRK14638         92 PKDYV-RFTGKLAKIVTKDGKTFIGRIESFVDG-TITI  127 (150)
T ss_pred             HHHHH-HhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            33444 678999999999999999999999963 3444

>PRK14644 hypothetical protein; Provisional

Probab=80.29  E-value=3.9  Score=32.68  Aligned_cols=35  Identities=20%  Similarity=0.298  Sum_probs=29.4

Q ss_pred             HHHhhcCCEEEEEEeCC----eEEEEEEEEEcCccceEEc
Q psy800          121 LVDKCIGSRIHIIMKND----KEIVGTLNGFDDFVNMLLE  156 (204)
Q Consensus       121 ~L~~~i~k~V~V~Lk~g----r~i~G~L~gfD~~mNlVL~  156 (204)
                      -+.+++|+.|.|+|++.    +.++|+|.++|+- ++.|+
T Consensus        79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            57888999999999887    8999999999974 35554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	204
2fwk_A	121	Crystal Structure Of Cryptosporidium Parvum U6 Snrn		2e-16
3swn_A	82	Structure Of The Lsm657 Complex: An Assembly Interm		7e-16
4emk_A	94	Crystal Structure Of Splsm567 Length = 94		6e-14
1ljo_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm2) Fr		7e-05
3cw1_E	92	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		6e-04

>pdb|2FWK|A Chain A, Crystal Structure Of Cryptosporidium Parvum U6 Snrna- Associated Sm-Like Protein Lsm5 Length = 121

Iteration: 1
 Score = 82.0 bits (201), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 56/83 (67%), Gaps = 12/83 (14%)
Query: 116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEY------ESTPEGRR 169
           +LPL L+DKCIG+RI+++MK DKE  G L GFD++VNM+L+DV EY      E    G +
Sbjct: 27  ILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNK 86
Query: 170 ------ITKLDQILLNGNNITML 186
                 + +L+ ILL+GNN+ ML
Sbjct: 87  KLKRVMVNRLETILLSGNNVAML 109

>pdb|3SWN|A Chain A, Structure Of The Lsm657 Complex: An Assembly Intermediate Of The Lsm1 7 And Lsm2 8 Rings Length = 82

Iteration: 1
 Score = 80.1 bits (196), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 39/72 (54%), Positives = 55/72 (76%), Gaps = 2/72 (2%)
Query: 115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLD 174
           T+LPLEL+DKCIGS + +IMK+++E  GTL GFDD+VN++L+DVTEY++        K  
Sbjct: 6   TILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVT--GVTEKHS 63
Query: 175 QILLNGNNITML 186
           ++LLNGN + ML
Sbjct: 64  EMLLNGNGMCML 75

>pdb|4EMK|A Chain A, Crystal Structure Of Splsm567 Length = 94

Iteration: 1
 Score = 73.9 bits (180), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 37/72 (51%), Positives = 51/72 (70%), Gaps = 2/72 (2%)
Query: 115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLD 174
           T+LPLEL+DKCIGS + +I K+++E  GTL GFDD+VN++L+DVTEY++        K  
Sbjct: 18  TILPLELIDKCIGSNLWVIXKSEREFAGTLVGFDDYVNIVLKDVTEYDTVT--GVTEKHS 75
Query: 175 QILLNGNNITML 186
           + LLNGN    L
Sbjct: 76  EXLLNGNGXCXL 87

>pdb|1LJO|A Chain A, Crystal Structure Of An Sm-Like Protein (Af-Sm2) From Archaeoglobus Fulgidus At 1.95a Resolution Length = 77

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 44/74 (59%), Gaps = 4/74 (5%)
Query: 114 STLLPLELVDKCIGSRIHIIMKNDK-EIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITK 172
           + +LP ++V   +G  I + MK ++ ++VG L G DD++N+ L +  E +      ++  
Sbjct: 2   AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE---EKVRS 58
Query: 173 LDQILLNGNNITML 186
           L +I+L GNN+ ++
Sbjct: 59  LGEIVLRGNNVVLI 72

>pdb|3CW1|E Chain E, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 92

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 47/84 (55%), Gaps = 7/84 (8%)
Query: 105 TAPSVATNPSTLLPLELVDKCIGSRIHIIM--KNDKEIVGTLNGFDDFVNMLLEDVTEYE 162
               V   P  L+   L ++   SRI + +  + +  I G + GFD+++N++L+D  E  
Sbjct: 9   KVQKVMVQPINLIFRYLQNR---SRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIH 65
Query: 163 STPEGRRITKLDQILLNGNNITML 186
           S  + R+  +L +I+L G+NIT+L
Sbjct: 66  SKTKSRK--QLGRIMLKGDNITLL 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	204
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	2e-28
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	3e-16
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	4e-25
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	6e-12
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	2e-24
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	5e-17
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	2e-24
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	3e-14
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	5e-22
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	2e-13
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	2e-21
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	1e-12
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	2e-21
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	8e-13
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	6e-19
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	5e-11
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	8e-19
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	2e-11
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	5e-18
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	1e-12
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	6e-17
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	5e-10
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	2e-15
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	5e-08
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	1e-14
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	7e-08
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	3e-14
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	1e-07
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	8e-14
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	2e-08
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	3e-13
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	1e-06
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	6e-12
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	5e-07
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	2e-11
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	2e-05
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	4e-11
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	1e-06
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	6e-11
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	6e-06
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	2e-08
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	5e-04
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	2e-08
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	6e-06

>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A Length = 94

 Score =  101 bits (252), Expect = 2e-28
 Identities = 40/85 (47%), Positives = 57/85 (67%), Gaps = 2/85 (2%)

Query: 102 YTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEY 161
           +     S      T+LPLEL+DKCIGS + +IMK+++E  GTL GFDD+VN++L+DVTEY
Sbjct: 5   HHHHHHSQDPMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEY 64

Query: 162 ESTPEGRRITKLDQILLNGNNITML 186
           ++        K  ++LLNGN + ML
Sbjct: 65  DTVTGVTE--KHSEMLLNGNGMCML 87

>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A Length = 94

 Score = 69.9 bits (171), Expect = 3e-16
 Identities = 30/57 (52%), Positives = 42/57 (73%)

Query: 3  APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH 59
            S      T+LPLEL+DKCIGS + +IMK+++E  GTL GFDD+VN++L+DVT+  
Sbjct: 9  HHSQDPMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYD 65

>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E Length = 92

 Score = 92.9 bits (231), Expect = 4e-25
 Identities = 22/75 (29%), Positives = 46/75 (61%), Gaps = 6/75 (8%)

Query: 116 LLPLELVDKCIGSR----IHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRIT 171
           + P+ L+ + + +R    + +  + +  I G + GFD+++N++L+D  E  S  + R+  
Sbjct: 15  VQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRK-- 72

Query: 172 KLDQILLNGNNITML 186
           +L +I+L G+NIT+L
Sbjct: 73  QLGRIMLKGDNITLL 87

>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E Length = 92

 Score = 58.7 bits (142), Expect = 6e-12
 Identities = 12/53 (22%), Positives = 30/53 (56%), Gaps = 4/53 (7%)

Query: 13 LLPLELVDKCIGSR----IHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
          + P+ L+ + + +R    + +  + +  I G + GFD+++N++L+D  + H  
Sbjct: 15 VQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSK 67

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121

 Score = 92.4 bits (229), Expect = 2e-24
 Identities = 39/94 (41%), Positives = 56/94 (59%), Gaps = 12/94 (12%)

Query: 105 TAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST 164
              S     + +LPL L+DKCIG+RI+++MK DKE  G L GFD++VNM+L+DV EY   
Sbjct: 16  QGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFK 75

Query: 165 PEGR------------RITKLDQILLNGNNITML 186
            +               + +L+ ILL+GNN+ ML
Sbjct: 76  ADEEDISGGNKKLKRVMVNRLETILLSGNNVAML 109

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121

 Score = 72.7 bits (178), Expect = 5e-17
 Identities = 28/59 (47%), Positives = 40/59 (67%)

Query: 2  TAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
             S     + +LPL L+DKCIG+RI+++MK DKE  G L GFD++VNM+L+DV +   
Sbjct: 16 QGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGF 74

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Length = 77

 Score = 90.8 bits (226), Expect = 2e-24
 Identities = 22/74 (29%), Positives = 44/74 (59%), Gaps = 4/74 (5%)

Query: 114 STLLPLELVDKCIGSRIHIIMKNDK-EIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITK 172
           + +LP ++V   +G  I + MK ++ ++VG L G DD++N+ L +  E +      ++  
Sbjct: 2   AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECK---GEEKVRS 58

Query: 173 LDQILLNGNNITML 186
           L +I+L GNN+ ++
Sbjct: 59  LGEIVLRGNNVVLI 72

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Length = 77

 Score = 64.3 bits (157), Expect = 3e-14
 Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 11 STLLPLELVDKCIGSRIHIIMKNDK-EIVGTLNGFDDFVNMLLEDVTDCHD 60
          + +LP ++V   +G  I + MK ++ ++VG L G DD++N+ L +  +C  
Sbjct: 2  AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKG 52

>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Length = 83

 Score = 84.7 bits (210), Expect = 5e-22
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 110 ATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRR 169
           +   +   PL+ +   + S + I +K D+E  G L  FD  +N++L D  E E   +G  
Sbjct: 8   SQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEV 64

Query: 170 ITKLDQILLNGNNITML 186
             +L  +L+ G+NI  +
Sbjct: 65  TRRLGTVLIRGDNIVYI 81

>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Length = 83

 Score = 62.4 bits (152), Expect = 2e-13
 Identities = 15/54 (27%), Positives = 27/54 (50%)

Query: 7  ATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
          +   +   PL+ +   + S + I +K D+E  G L  FD  +N++L D  +  D
Sbjct: 8  SQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED 61

>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Length = 75

 Score = 82.7 bits (205), Expect = 2e-21
 Identities = 16/69 (23%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
           PL+++ + +   + +I+K   E  G L G+D  +N++L D    +   +G  + +  +I+
Sbjct: 5   PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQ---DGEVVKRYGKIV 61

Query: 178 LNGNNITML 186
           + G+N+  +
Sbjct: 62  IRGDNVLAI 70

>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Length = 75

 Score = 60.0 bits (146), Expect = 1e-12
 Identities = 13/46 (28%), Positives = 25/46 (54%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
          PL+++ + +   + +I+K   E  G L G+D  +N++L D     D
Sbjct: 5  PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQD 50

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Length = 77

 Score = 82.7 bits (205), Expect = 2e-21
 Identities = 17/69 (24%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
           PL+++++ + S + + +K  +E  GTL+G+D  +N++L D  E +    G  + K+  ++
Sbjct: 5   PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQ---NGEVVRKVGSVV 61

Query: 178 LNGNNITML 186
           + G+ +  +
Sbjct: 62  IRGDTVVFV 70

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Length = 77

 Score = 60.4 bits (147), Expect = 8e-13
 Identities = 13/47 (27%), Positives = 30/47 (63%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
          PL+++++ + S + + +K  +E  GTL+G+D  +N++L D  +  + 
Sbjct: 5  PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG 51

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Length = 105

 Score = 77.1 bits (190), Expect = 6e-19
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 105 TAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST 164
           +      +   +LPL L++   G  I + +KN +   G L   D+++N+ L +V      
Sbjct: 4   SHHHHHHSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRT--M 61

Query: 165 PEGRRITKLDQILLNGNNI 183
           P+G +  +L +  + GNNI
Sbjct: 62  PDGDKFFRLPECYIRGNNI 80

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Length = 105

 Score = 56.7 bits (137), Expect = 5e-11
 Identities = 14/55 (25%), Positives = 27/55 (49%)

Query: 2  TAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
          +      +   +LPL L++   G  I + +KN +   G L   D+++N+ L +V 
Sbjct: 4  SHHHHHHSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVI 58

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96

 Score = 76.7 bits (189), Expect = 8e-19
 Identities = 17/74 (22%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRIT----KL 173
           PL+L+   +  R++I ++  + +VGTL  FD   N++L D  E         ++    + 
Sbjct: 11  PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRC 70

Query: 174 DQILLNGNNITMLG 187
           + + + G+ +T++ 
Sbjct: 71  EMVFIRGDTVTLIS 84

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96

 Score = 57.4 bits (139), Expect = 2e-11
 Identities = 14/42 (33%), Positives = 25/42 (59%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
          PL+L+   +  R++I ++  + +VGTL  FD   N++L D  
Sbjct: 11 PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAV 52

>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Length = 93

 Score = 74.5 bits (183), Expect = 5e-18
 Identities = 17/78 (21%), Positives = 38/78 (48%)

Query: 109 VATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGR 168
           + +  +   PL+LV   +   +++ ++ D+E+ G L+ +D+ +NM+L D  E  +  +  
Sbjct: 1   MESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDE 60

Query: 169 RITKLDQILLNGNNITML 186
              K   +     +  ML
Sbjct: 61  ETDKDKALKTIRKHYEML 78

>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Length = 93

 Score = 60.6 bits (147), Expect = 1e-12
 Identities = 13/51 (25%), Positives = 30/51 (58%)

Query: 6  VATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
          + +  +   PL+LV   +   +++ ++ D+E+ G L+ +D+ +NM+L D  
Sbjct: 1  MESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAE 51

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Length = 81

 Score = 71.2 bits (175), Expect = 6e-17
 Identities = 17/69 (24%), Positives = 40/69 (57%), Gaps = 3/69 (4%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
             +++ + + + + + +K +KE+ G L  +D  +N++L D  E +S   G+   KL  I+
Sbjct: 10  AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGK---KLGTIV 66

Query: 178 LNGNNITML 186
           + G+N+ ++
Sbjct: 67  IRGDNVILI 75

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Length = 81

 Score = 53.1 bits (128), Expect = 5e-10
 Identities = 9/47 (19%), Positives = 25/47 (53%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
            +++ + + + + + +K +KE+ G L  +D  +N++L D  +    
Sbjct: 10 AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD 56

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Length = 86

 Score = 67.5 bits (165), Expect = 2e-15
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKL 173
             L P   ++   G  + + +K   E  G L   D ++NM L +  EY    +G     L
Sbjct: 3   LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYI---DGALSGHL 59

Query: 174 DQILLNGNNITMLGL 188
            ++L+  NN+  +  
Sbjct: 60  GEVLIRCNNVLYIRG 74

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Length = 86

 Score = 47.8 bits (114), Expect = 5e-08
 Identities = 12/50 (24%), Positives = 21/50 (42%)

Query: 11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
            L P   ++   G  + + +K   E  G L   D ++NM L +  +  D
Sbjct: 3  LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYID 52

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Length = 75

 Score = 65.0 bits (159), Expect = 1e-14
 Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 3/69 (4%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
           P E ++K IG ++ I + +  +  G L+  D ++N+ LE   EY     G++        
Sbjct: 5   PNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYV---NGKKTNVYGDAF 61

Query: 178 LNGNNITML 186
           + GNN+  +
Sbjct: 62  IRGNNVLYV 70

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Length = 75

 Score = 46.9 bits (112), Expect = 7e-08
 Identities = 12/46 (26%), Positives = 25/46 (54%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
          P E ++K IG ++ I + +  +  G L+  D ++N+ LE   +  +
Sbjct: 5  PNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVN 50

>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C Length = 113

 Score = 65.4 bits (159), Expect = 3e-14
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 5/81 (6%)

Query: 111 TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRI 170
             P     L+L  +    RI       ++I G L GFD  +N++L+DV E    PE  ++
Sbjct: 18  ERPRKESILDL-SRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKL 76

Query: 171 T----KLDQILLNGNNITMLG 187
           T    KL  +++ G  + ++ 
Sbjct: 77  TGAIRKLGLVVVRGTTLVLIA 97

>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C Length = 113

 Score = 47.6 bits (113), Expect = 1e-07
 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 8  TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH 62
            P     L+L  +    RI       ++I G L GFD  +N++L+DV +   + 
Sbjct: 18 ERPRKESILDL-SRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNP 71

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Length = 126

 Score = 64.3 bits (156), Expect = 8e-14
 Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKL 173
           S  +P++++ +  G  +       +   G L   +D +N  + ++T    T    R+ +L
Sbjct: 2   SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITV---TYRDGRVAQL 58

Query: 174 DQILLNGNNITMLGL 188
           +Q+ + G+ I  L L
Sbjct: 59  EQVYIRGSKIRFLIL 73

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Length = 126

 Score = 49.7 bits (118), Expect = 2e-08
 Identities = 8/46 (17%), Positives = 21/46 (45%)

Query: 11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
          S  +P++++ +  G  +       +   G L   +D +N  + ++T
Sbjct: 2  SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNIT 47

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Length = 76

 Score = 61.2 bits (149), Expect = 3e-13
 Identities = 17/70 (24%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
           P EL  K +  ++ + +   + + G L GFD F+N+++++  E  ++ +      +  ++
Sbjct: 6   PPEL-KKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQN---NIGMVV 61

Query: 178 LNGNNITMLG 187
           + GN+I ML 
Sbjct: 62  IRGNSIIMLE 71

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Length = 76

 Score = 43.9 bits (104), Expect = 1e-06
 Identities = 12/47 (25%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
          P EL  K +  ++ + +   + + G L GFD F+N+++++  +   S
Sbjct: 6  PPEL-KKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATS 51

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Length = 81

 Score = 58.2 bits (141), Expect = 6e-12
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 108 SVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG 167
           +   +         +   IG ++ + +++  EI G L  FD  VN+LLED  E       
Sbjct: 2   ASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG--- 58

Query: 168 RRITKLDQILLNGNNITMLG 187
             + K   +++ G N+  + 
Sbjct: 59  -NVYKRGTMVVRGENVLFIS 77

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Length = 81

 Score = 45.1 bits (107), Expect = 5e-07
 Identities = 15/57 (26%), Positives = 26/57 (45%)

Query: 5  SVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
          +   +         +   IG ++ + +++  EI G L  FD  VN+LLED  +  D 
Sbjct: 2  ASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG 58

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Length = 93

 Score = 57.2 bits (138), Expect = 2e-11
 Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 4/89 (4%)

Query: 99  HLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMK-NDKEIVGTLNGFDDFVNMLLED 157
           H  + M+  S  +    + P   +   +  R+ + +K N  E  GTL   D++ N+ L +
Sbjct: 3   HHHHHMSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNE 62

Query: 158 VTEYESTPEGRRITKLDQILLNGNNITML 186
             E+     G     L +I +  NN+  +
Sbjct: 63  AEEFV---AGVSHGTLGEIFIRCNNVLYI 88

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Length = 93

 Score = 40.6 bits (95), Expect = 2e-05
 Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 1  MTAPSVATNPSTLLPLELVDKCIGSRIHIIMK-NDKEIVGTLNGFDDFVNMLLEDVTDCH 59
          M+  S  +    + P   +   +  R+ + +K N  E  GTL   D++ N+ L +  +  
Sbjct: 8  MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV 67

Query: 60 D 60
           
Sbjct: 68 A 68

>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A Length = 119

 Score = 57.3 bits (138), Expect = 4e-11
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQI 176
             +  + K     + I +KN  ++ GT+ G D  +N  L+ V     T + R   +L+ +
Sbjct: 2   KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKM---TLKNREPVQLETL 58

Query: 177 LLNGNNI 183
            + GNNI
Sbjct: 59  SIRGNNI 65

>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A Length = 119

 Score = 45.0 bits (106), Expect = 1e-06
 Identities = 11/43 (25%), Positives = 20/43 (46%)

Query: 14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
            +  + K     + I +KN  ++ GT+ G D  +N  L+ V 
Sbjct: 2  KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVK 44

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Length = 75

 Score = 55.5 bits (134), Expect = 6e-11
 Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKL 173
           S  +P++++ +  G  +       +   G L   +D +N  + ++T    T    R+ +L
Sbjct: 2   SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITV---TYRDGRVAQL 58

Query: 174 DQILLNGNNI 183
           +Q+ + G  I
Sbjct: 59  EQVYIRGCKI 68

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Length = 75

 Score = 42.0 bits (99), Expect = 6e-06
 Identities = 8/46 (17%), Positives = 21/46 (45%)

Query: 11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
          S  +P++++ +  G  +       +   G L   +D +N  + ++T
Sbjct: 2  SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNIT 47

>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Length = 91

 Score = 49.1 bits (117), Expect = 2e-08
 Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 7/70 (10%)

Query: 124 KCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEY-------ESTPEGRRITKLDQI 176
           + I  R+  I+++ +  +GT   FD  +N++L D  E+           E      L  +
Sbjct: 11  QHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLV 70

Query: 177 LLNGNNITML 186
           LL G N+  +
Sbjct: 71  LLRGENLVSM 80

>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Length = 91

 Score = 37.1 bits (86), Expect = 5e-04
 Identities = 10/37 (27%), Positives = 21/37 (56%)

Query: 21 KCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
          + I  R+  I+++ +  +GT   FD  +N++L D  +
Sbjct: 11 QHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDE 47

>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B Length = 118

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 17/81 (20%), Positives = 43/81 (53%), Gaps = 13/81 (16%)

Query: 118 PLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEY--------ESTPEG 167
           PL ++ + +   +++ I  +N+K+++G +  FD   NM+LE+V E         +   + 
Sbjct: 28  PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKS 87

Query: 168 RRITK---LDQILLNGNNITM 185
           + + K   + ++ L G+++ +
Sbjct: 88  KPVNKDRYISKMFLRGDSVIV 108

>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B Length = 118

 Score = 43.0 bits (101), Expect = 6e-06
 Identities = 13/44 (29%), Positives = 28/44 (63%), Gaps = 2/44 (4%)

Query: 15 PLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
          PL ++ + +   +++ I  +N+K+++G +  FD   NM+LE+V 
Sbjct: 28 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVK 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	204
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.87
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.87
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.86
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.86
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.86
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.86
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.85
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.85
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.85
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.85
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.85
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.84
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.84
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.84
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.84
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.83
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.81
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.81
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.8
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.8
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.79
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.77
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.76
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.75
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.75
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.74
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.73
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.72
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.72
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.71
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.71
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.71
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.7
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.69
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.69
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.69
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.68
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.68
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.67
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.67
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.64
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.61
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.61
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.61
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.58
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.57
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.55
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.37
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	98.27
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	97.98
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	96.58
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	96.55
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.29
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	96.27
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	96.27
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	96.26
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	96.23
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	96.06
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.05
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.04
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	95.96
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	95.93
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	95.92
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	95.91
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	94.73
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	94.38
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	94.1
1ycy_A	71	Conserved hypothetical protein; structural genomic	92.06
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	91.6
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	91.5
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	90.55
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	90.53
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	89.51
1ycy_A	71	Conserved hypothetical protein; structural genomic	89.35
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	83.62

>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A

Probab=99.87  E-value=3.5e-22  Score=149.33  Aligned_cols=75  Identities=52%  Similarity=0.873  Sum_probs=66.5

Q ss_pred             CCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          113 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       113 ~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      .....|+++|.++++++|+|+|++|++|+|+|+|||+||||||+||+|+..  +++..+.+|.++|||+||++|++.
T Consensus        16 ~~~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~--~~~~~~~lg~v~IRG~nI~~i~p~   90 (94)
T 4emk_A           16 SMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDT--VTGVTEKHSEMLLNGNGMCMLIPG   90 (94)
T ss_dssp             ----CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEET--TTCCEEEEEEEEECSTTEEEEEEC
T ss_pred             cccccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEec--CCCcEeEcCEEEEcCCEEEEEEeC
Confidence            346789999999999999999999999999999999999999999999973  334688999999999999999876

>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A

Probab=99.87  E-value=5.8e-22  Score=144.47  Aligned_cols=77  Identities=29%  Similarity=0.532  Sum_probs=68.6

Q ss_pred             ccCCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          109 VATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       109 ~~~~~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      |+.......|+++|.++++++|+|+|+||+++.|+|.|||+|||++|+||+|++   .+...+.+|.++|||++|++|+|
T Consensus         7 s~~~~~~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A            7 SSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             ---CCCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEC
T ss_pred             ccccccCcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEe---cCCcccCCCEEEECCCEEEEEEC
Confidence            344556789999999999999999999999999999999999999999999997   34578899999999999999975

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1

Probab=99.86  E-value=1.5e-21  Score=140.08  Aligned_cols=73  Identities=30%  Similarity=0.645  Sum_probs=67.1

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCC-eEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          115 TLLPLELVDKCIGSRIHIIMKND-KEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       115 ~~~Pl~~L~~~i~k~V~V~Lk~g-r~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      ...|+++|.++++++|+|+|++| ++++|+|.|||+|||++|+||+|++   .++..+.+|.++|||++|++|++.+
T Consensus         3 m~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~nI~~i~~~d   76 (77)
T 1ljo_A            3 MVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECK---GEEKVRSLGEIVLRGNNVVLIQPQE   76 (77)
T ss_dssp             CCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEEC-
T ss_pred             ccchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEe---cCCcEeECCeEEEeCCeEEEEEeCC
Confidence            35899999999999999999999 9999999999999999999999987   3457899999999999999998753

>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A*

Probab=99.86  E-value=1.6e-21  Score=139.21  Aligned_cols=71  Identities=23%  Similarity=0.516  Sum_probs=66.4

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      ..|+++|+++++++|+|+|+||+.++|+|.|||+|||++|+||+|++   .+...+.+|.++|||++|++|++.
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~~I~~i~~~   73 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQ---DGEVVKRYGKIVIRGDNVLAISPT   73 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEEC
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEe---eCCceeECCEEEECCCEEEEEEeC
Confidence            47999999999999999999999999999999999999999999987   245789999999999999999875

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1

Probab=99.86  E-value=1.1e-21  Score=142.30  Aligned_cols=76  Identities=22%  Similarity=0.408  Sum_probs=68.3

Q ss_pred             CCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          112 NPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       112 ~~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      ...+..|+++|+++++++|+|+|+||+++.|+|.|||+|||++|+||+|++.   +...+.+|.++|||++|++|++.+
T Consensus         4 ~~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~---~~~~~~lg~v~iRG~~I~~i~~~~   79 (81)
T 1th7_A            4 NFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQS---DGSGKKLGTIVIRGDNVILISPLQ   79 (81)
T ss_dssp             CTTCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECS---SSCEEEEEEEEECGGGEEEEEEC-
T ss_pred             cccccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEec---CCceeECCEEEECCCEEEEEEecC
Confidence            3445789999999999999999999999999999999999999999999873   346789999999999999998763

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A*

Probab=99.86  E-value=2.2e-21  Score=139.04  Aligned_cols=72  Identities=24%  Similarity=0.549  Sum_probs=66.9

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      ..|+++|+++++++|+|+|+||+.+.|+|.|||+|||++|+||+|++.   +...+++|.++|||++|++|++.+
T Consensus         3 ~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~---~~~~~~lg~v~iRG~~I~~i~~~d   74 (77)
T 1i4k_A            3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQN---GEVVRKVGSVVIRGDTVVFVSPAP   74 (77)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEET---TEEEEEEEEEEECGGGEEEEEECC
T ss_pred             ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEec---CCcEeECCEEEECCCEEEEEEeCC
Confidence            479999999999999999999999999999999999999999999872   356889999999999999998764

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F

Probab=99.85  E-value=2.8e-21  Score=142.02  Aligned_cols=75  Identities=24%  Similarity=0.356  Sum_probs=67.9

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccccCC
Q psy800          115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHTHC  192 (204)
Q Consensus       115 ~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~~~  192 (204)
                      +..|+++|+++++++|+|+|++|+.|.|+|.|||+|||++|+||+|+.   +++..+++|.++|||++|++|++.+..
T Consensus         4 ~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~---~g~~~~~lg~v~IRG~nI~~i~~~d~~   78 (86)
T 3s6n_F            4 PLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYI---DGALSGHLGEVLIRCNNVLYIRGVEEE   78 (86)
T ss_dssp             CCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEESSEEECGGGEEEEEECC--
T ss_pred             CcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEc---CCceeeEccEEEEeCCeEEEEEeCCcc
Confidence            467999999999999999999999999999999999999999999975   455678999999999999999887543

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B

Probab=99.85  E-value=1.1e-21  Score=140.38  Aligned_cols=71  Identities=25%  Similarity=0.506  Sum_probs=66.5

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      ..|+++|+++++++|+|+|+||++|.|+|.|||+|||++|+||+|+.   +++..+++|.++|||++|++|++.
T Consensus         3 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~~I~~i~~~   73 (75)
T 4emk_B            3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYV---NGKKTNVYGDAFIRGNNVLYVSAL   73 (75)
T ss_dssp             SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEE---TTEEEEEEEEEEEEGGGSSEEEEC
T ss_pred             CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEe---cCCcccEecEEEEcCCeEEEEEec
Confidence            57999999999999999999999999999999999999999999986   455688999999999999999875

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A*

Probab=99.85  E-value=1.9e-21  Score=141.01  Aligned_cols=75  Identities=24%  Similarity=0.407  Sum_probs=66.3

Q ss_pred             CCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          112 NPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       112 ~~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      .+....|+++|.++++++|+|+|+||++|.|+|.|||+|||++|+||+|+    ++...+.+|.++|||++|++|++.+
T Consensus         6 ~~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~----~~~~~~~lg~v~iRG~~I~~i~~~d   80 (81)
T 1i8f_A            6 SKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI----IDGNVYKRGTMVVRGENVLFISPVP   80 (81)
T ss_dssp             ----CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE----ETTEEEEEEEEEECGGGEEEEEECC
T ss_pred             CccccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE----cCCcccCCCEEEECCCEEEEEEeCC
Confidence            44568899999999999999999999999999999999999999999998    2346899999999999999998763

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A

Probab=99.85  E-value=1.9e-21  Score=144.94  Aligned_cols=76  Identities=21%  Similarity=0.363  Sum_probs=61.3

Q ss_pred             CCCCCCCcHHHHHhhcCCEEEEEEeCC-eEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          111 TNPSTLLPLELVDKCIGSRIHIIMKND-KEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       111 ~~~~~~~Pl~~L~~~i~k~V~V~Lk~g-r~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +..+...|+++|.++++++|+|+|++| ++|+|+|.|||+|||++|+||+|++   +++..+.+|.++|||++|++|.+.
T Consensus        15 ~~~~~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~---~~~~~~~lg~v~IRG~nI~~I~~~   91 (93)
T 1n9r_A           15 SAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV---AGVSHGTLGEIFIRCNNVLYIREL   91 (93)
T ss_dssp             -----------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEE---TTEEEEECCSEEECGGGEEEEEEC
T ss_pred             cccccCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEc---CCCeEeEcCEEEEcCCeEEEEEeC
Confidence            455678899999999999999999999 9999999999999999999999986   455788999999999999999865

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae}

Probab=99.85  E-value=4.4e-21  Score=143.53  Aligned_cols=76  Identities=22%  Similarity=0.461  Sum_probs=68.6

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCC----CeeeeeeCeEEEeCCcEEEEcccc
Q psy800          115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE----GRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       115 ~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~----~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      .+.|+.+|.++++++|+|+|++||++.|+|+|||+||||||+||+|++...+    +...+.+|.++|||++|++|++.+
T Consensus         8 ~~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d   87 (96)
T 3bw1_A            8 METPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPS   87 (96)
T ss_dssp             CCCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC
T ss_pred             hhhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecC
Confidence            4679999999999999999999999999999999999999999999986421    346789999999999999998764

>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe}

Probab=99.84  E-value=5.1e-21  Score=142.54  Aligned_cols=76  Identities=21%  Similarity=0.443  Sum_probs=65.5

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecC--CC--------eeeeeeCeEEEeCCcE
Q psy800          114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP--EG--------RRITKLDQILLNGNNI  183 (204)
Q Consensus       114 ~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~--~~--------~~~~~lg~ilIRGdnI  183 (204)
                      +...|+++|+.+++++|+|+|++|+.|.|+|+|||+||||+|+||+|++...  ++        ...+.+|.++|||++|
T Consensus         6 ~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nV   85 (93)
T 4emg_A            6 AVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSV   85 (93)
T ss_dssp             ---CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGE
T ss_pred             ccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeE
Confidence            4578999999999999999999999999999999999999999999998531  12        2478999999999999


Q ss_pred             EEEccc
Q psy800          184 TMLGLH  189 (204)
Q Consensus       184 ~~I~~~  189 (204)
                      ++|+|.
T Consensus        86 v~I~p~   91 (93)
T 4emg_A           86 ILIAPP   91 (93)
T ss_dssp             EEEECC
T ss_pred             EEEEec
Confidence            999985

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1

Probab=99.84  E-value=7.8e-21  Score=136.17  Aligned_cols=71  Identities=21%  Similarity=0.358  Sum_probs=65.7

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      ..|+++|+++++++|+|+|++|++|+|+|.|||+|||++|+||+|+.  .++ ..+++|.++|||++|.+|+..
T Consensus         4 ~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~--~~~-~~~~lg~v~IRG~nI~~i~lP   74 (75)
T 1d3b_A            4 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY--RDG-RVAQLEQVYIRGCKIRFLILP   74 (75)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC--TTS-CEEEEEEEEECGGGEEEEEEC
T ss_pred             cCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEEC--CCC-cEEEcCeEEEeCCEEEEEEcC
Confidence            57999999999999999999999999999999999999999999986  344 578999999999999999764

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A

Probab=99.84  E-value=2e-21  Score=151.12  Aligned_cols=79  Identities=48%  Similarity=0.882  Sum_probs=67.4

Q ss_pred             CCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeec-------CCCee-----eeeeCeEEE
Q psy800          111 TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST-------PEGRR-----ITKLDQILL  178 (204)
Q Consensus       111 ~~~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~-------~~~~~-----~~~lg~ilI  178 (204)
                      +.+....|+++|.++++++|+|+|++|++|.|+|+|||+||||||+||+|++..       .+++.     .+.+|.++|
T Consensus        22 ~~~~~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~I  101 (121)
T 2fwk_A           22 KGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILL  101 (121)
T ss_dssp             --CCCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEE
T ss_pred             ccccccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEE
Confidence            445678999999999999999999999999999999999999999999999853       02333     688999999


Q ss_pred             eCCcEEEEccc
Q psy800          179 NGNNITMLGLH  189 (204)
Q Consensus       179 RGdnI~~I~~~  189 (204)
                      ||++|++|++.
T Consensus       102 RG~nVv~I~~~  112 (121)
T 2fwk_A          102 SGNNVAMLVPG  112 (121)
T ss_dssp             CGGGEEEEESS
T ss_pred             CCCEEEEEEec
Confidence            99999999876

>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E

Probab=99.84  E-value=3.5e-21  Score=143.34  Aligned_cols=75  Identities=29%  Similarity=0.558  Sum_probs=64.6

Q ss_pred             CCCCCcHHHHHhhcCCEEEEEE----eCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          113 PSTLLPLELVDKCIGSRIHIIM----KNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       113 ~~~~~Pl~~L~~~i~k~V~V~L----k~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      +....|+++|.++++++|.|++    ++|++|+|+|+|||+||||||+||+|+..  +++..+.+|.++|||+||++|++
T Consensus        12 ~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~--~~~~~~~lg~v~iRG~nV~~i~~   89 (92)
T 3s6n_E           12 KVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHS--KTKSRKQLGRIMLKGDNITLLQS   89 (92)
T ss_dssp             --CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECS--SSCCEEEEEEEEECGGGEEEEEE
T ss_pred             eeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEec--CCCceeEcCeEEEeCCEEEEEEe
Confidence            3456788888888888888777    89999999999999999999999999874  33467899999999999999987


Q ss_pred             c
Q psy800          189 H  189 (204)
Q Consensus       189 ~  189 (204)
                      .
T Consensus        90 ~   90 (92)
T 3s6n_E           90 V   90 (92)
T ss_dssp             C
T ss_pred             C
Confidence            6

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe}

Probab=99.83  E-value=1.3e-20  Score=143.45  Aligned_cols=74  Identities=30%  Similarity=0.588  Sum_probs=56.2

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       115 ~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      +..|+++|+++++++|+|+|++|++|+|+|.|||+||||+|+||+|..  .+|+..+.+|.++|||++|++|++.+
T Consensus        14 ~~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~--~dg~~~~~lg~v~IRG~nI~~I~~pd   87 (105)
T 4emh_A           14 PMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTM--PDGDKFFRLPECYIRGNNIKYLRIQD   87 (105)
T ss_dssp             ------------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC--TTSCEEEEEEEEEECGGGEEEEEC--
T ss_pred             CCcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEc--cCCceeeEcCeEEEeCCeEEEEecCH
Confidence            468999999999999999999999999999999999999999999986  35656789999999999999998764

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G

Probab=99.81  E-value=3e-20  Score=133.27  Aligned_cols=70  Identities=20%  Similarity=0.489  Sum_probs=52.5

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      |-.+|+++++++|+|+|+||+.|+|+|.|||+|||++|+||+|+..  + ...+.+|.++|||++|++|++.+
T Consensus         5 ~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~--~-~~~~~lg~v~iRG~~I~~i~~~d   74 (76)
T 3s6n_G            5 HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMAT--S-GQQNNIGMVVIRGNSIIMLEALE   74 (76)
T ss_dssp             ---------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCC--C-----CBSSEEECSSSEEEEEC--
T ss_pred             chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEcc--C-CcEeEcCEEEECCCeEEEEEecc
Confidence            4568999999999999999999999999999999999999999863  2 35789999999999999998753

>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C

Probab=99.81  E-value=4.7e-20  Score=141.96  Aligned_cols=79  Identities=24%  Similarity=0.455  Sum_probs=57.3

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCC----eeeeeeCeEEEeCCcEEEEccc
Q psy800          114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG----RRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       114 ~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~----~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +..-|+..|.++++++|+|+|+|||.|.|+|+|||+||||||+||+|++...++    ...+.+|.++|||++|++|++.
T Consensus        20 ~kke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~   99 (113)
T 4emk_C           20 PRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPM   99 (113)
T ss_dssp             ------------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEEC
T ss_pred             CccchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEec
Confidence            334577889999999999999999999999999999999999999999854322    3578999999999999999987


Q ss_pred             cCC
Q psy800          190 THC  192 (204)
Q Consensus       190 ~~~  192 (204)
                      +..
T Consensus       100 d~~  102 (113)
T 4emk_C          100 DGS  102 (113)
T ss_dssp             C--
T ss_pred             Ccc
Confidence            543

>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A

Probab=99.80  E-value=5.6e-20  Score=135.69  Aligned_cols=73  Identities=23%  Similarity=0.419  Sum_probs=62.8

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeec--C-----CCeeeeeeCeEEEeCCcEEEEccc
Q psy800          117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST--P-----EGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~--~-----~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      .|...|.++++++|+|+|+||+.+.|+|.|||+||||||+||+|++..  .     ++...+.+|.++|||++|++|++.
T Consensus         4 ~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~~~   83 (91)
T 1d3b_B            4 GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   83 (91)
T ss_dssp             ---CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             ChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEEcC
Confidence            355689999999999999999999999999999999999999997531  1     234688999999999999999876

>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A

Probab=99.80  E-value=1.1e-19  Score=141.01  Aligned_cols=72  Identities=25%  Similarity=0.337  Sum_probs=65.2

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      +.|+++|+++++++|+|+|++|++|.|+|.|||+||||+|+||+|+.  .+ .....+|.++|||+||++|++.+
T Consensus         1 M~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~--~~-~~~~~lg~v~IRG~nI~~I~~pd   72 (119)
T 1b34_A            1 MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTL--KN-REPVQLETLSIRGNNIRYFILPD   72 (119)
T ss_dssp             -CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEEC--TT-SCCEEEEEEEECGGGEEEEECCT
T ss_pred             CChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEec--CC-CceeEcceEEEcCCeEEEEEecc
Confidence            37999999999999999999999999999999999999999999985  23 35689999999999999998764

>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B

Probab=99.79  E-value=1.3e-19  Score=140.27  Aligned_cols=77  Identities=22%  Similarity=0.456  Sum_probs=63.3

Q ss_pred             CCCCcHHHHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecC--C--C-------eeeeeeCeEEEeC
Q psy800          114 STLLPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP--E--G-------RRITKLDQILLNG  180 (204)
Q Consensus       114 ~~~~Pl~~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~--~--~-------~~~~~lg~ilIRG  180 (204)
                      ....|+++|.+++  +++|+|+|++|+.|.|+|+|||+||||||+||+|++...  +  +       +..+.+|.++|||
T Consensus        24 ~~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG  103 (118)
T 1b34_B           24 FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRG  103 (118)
T ss_dssp             --CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECG
T ss_pred             cccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcC
Confidence            3568999999999  599999999999999999999999999999999987431  1  1       1256799999999


Q ss_pred             CcEEEEcccc
Q psy800          181 NNITMLGLHT  190 (204)
Q Consensus       181 dnI~~I~~~~  190 (204)
                      ++|++|++.+
T Consensus       104 ~nVv~I~~~~  113 (118)
T 1b34_B          104 DSVIVVLRNP  113 (118)
T ss_dssp             GGEEEEEECC
T ss_pred             CEEEEEEeCc
Confidence            9999998764

>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A

Probab=99.77  E-value=8.4e-19  Score=127.69  Aligned_cols=71  Identities=24%  Similarity=0.388  Sum_probs=63.0

Q ss_pred             CCCCCCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800            4 PSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus         4 ~~~~~~~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      +|+.+.++...|+++|+++++++|.|+|+||++|.|+|.|||+|||++|+||+|+..++....+|.++|+.
T Consensus         5 ~ms~~~~~~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~IRG   75 (83)
T 1mgq_A            5 DVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRG   75 (83)
T ss_dssp             -----CCCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECG
T ss_pred             EcccccccCcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEEECC
Confidence            35567888899999999999999999999999999999999999999999999999888888999999955

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D

Probab=99.76  E-value=1.9e-18  Score=135.36  Aligned_cols=72  Identities=21%  Similarity=0.366  Sum_probs=65.8

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      ..|+++|+++++++|+|+|++|++|.|+|.+||+|||++|+||+|+.  .++ +...++.++|||++|.+|...+
T Consensus         4 ~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~--~~g-~~~~l~~v~IRGnnI~~I~lpd   75 (126)
T 2y9a_D            4 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY--RDG-RVAQLEQVYIRGSKIRFLILPD   75 (126)
T ss_dssp             CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEEC--TTS-CCEEEEEEEECGGGEEEEECCS
T ss_pred             ccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEc--CCC-cEeecccEEEeCCEEEEEEccc
Confidence            57999999999999999999999999999999999999999999985  344 4789999999999999997543

>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A

Probab=99.75  E-value=2.6e-18  Score=128.33  Aligned_cols=66  Identities=47%  Similarity=0.792  Sum_probs=58.2

Q ss_pred             CCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee-cCccccccccEEEee
Q psy800            9 NPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH-DSHLLSYFASDLINF   74 (204)
Q Consensus         9 ~~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~-~~~~~~~lG~vlIn~   74 (204)
                      ......|+++|+++++++|+|+|++|++|.|+|+|||+||||+|+||+|+. +++..+.+|.++|+.
T Consensus        15 ~~~~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG   81 (94)
T 4emk_A           15 MSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNG   81 (94)
T ss_dssp             -----CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECS
T ss_pred             ccccccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcC
Confidence            356789999999999999999999999999999999999999999999999 777788999999965

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A

Probab=99.75  E-value=3.7e-18  Score=145.26  Aligned_cols=73  Identities=23%  Similarity=0.422  Sum_probs=64.5

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEee-c-C-----CCeeeeeeCeEEEeCCcEEEEccc
Q psy800          117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYES-T-P-----EGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~-~-~-----~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      .+-..|.+++||+|+|+|+|||+|+|+|+|||+||||||+||+|++. + +     ++++.+++|.++||||||++|+..
T Consensus         4 ~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isve   83 (231)
T 3pgw_B            4 GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   83 (231)
T ss_pred             CchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEec
Confidence            45568999999999999999999999999999999999999999874 1 1     234689999999999999999855

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A

Probab=99.74  E-value=1.8e-18  Score=128.82  Aligned_cols=74  Identities=18%  Similarity=0.257  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCCCCCcHHHHHhhcCCEEEEEEeCC-eEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800            1 MTAPSVATNPSTLLPLELVDKCIGSRIHIIMKND-KEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus         1 ~~~~~~~~~~~~~~P~~~L~~~~~k~V~V~l~~g-~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ||....++..+...|+++|+++++++|.|+|+|| ++|.|+|.|||+|||++|+||+|+.+++....+|.++|+.
T Consensus         8 ~~~~~~~~~~~~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~IRG   82 (93)
T 1n9r_A            8 MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRC   82 (93)
T ss_dssp             ------------------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECG
T ss_pred             cccCccccccccCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEEEcC
Confidence            5666777788889999999999999999999999 9999999999999999999999999888888999999955

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B

Probab=99.73  E-value=7.3e-18  Score=120.45  Aligned_cols=71  Identities=18%  Similarity=0.368  Sum_probs=62.9

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEeeecccceeecc
Q psy800           13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPI   84 (204)
Q Consensus        13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~~~g~~~~~PI   84 (204)
                      ..|+++|+++++|+|.|+|+||++|.|+|.|||+|||++|+||+|+.+++....+|.++|+.- .+..+.|+
T Consensus         3 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~-~I~~i~~~   73 (75)
T 4emk_B            3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGN-NVLYVSAL   73 (75)
T ss_dssp             SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEEEEGG-GSSEEEEC
T ss_pred             CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEEEcCC-eEEEEEec
Confidence            579999999999999999999999999999999999999999999998888889999999763 33444443

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1

Probab=99.72  E-value=8.8e-18  Score=121.57  Aligned_cols=68  Identities=18%  Similarity=0.272  Sum_probs=62.7

Q ss_pred             CCCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800            7 ATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus         7 ~~~~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      +++.....|+++|+++++++|+|+|+||++|.|+|.|||+|||++|+||+|+..++....+|.++|+.
T Consensus         2 ~m~~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG   69 (81)
T 1th7_A            2 AMNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRG   69 (81)
T ss_dssp             CCCTTCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECG
T ss_pred             cccccccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEEECC
Confidence            44566689999999999999999999999999999999999999999999999888888999999955

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A*

Probab=99.72  E-value=7e-18  Score=122.18  Aligned_cols=68  Identities=21%  Similarity=0.271  Sum_probs=58.2

Q ss_pred             CCCCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800            6 VATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus         6 ~~~~~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      +.+++....|+++|.++++++|.|+|+||++|.|+|.|||+|||++|+||+|+ +++..+.+|.++|+.
T Consensus         3 ~~~~~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~~~~lg~v~iRG   70 (81)
T 1i8f_A            3 SDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTMVVRG   70 (81)
T ss_dssp             -------CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETTEEEEEEEEEECG
T ss_pred             cccCccccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCCcccCCCEEEECC
Confidence            45567788999999999999999999999999999999999999999999999 777788999999955

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F

Probab=99.71  E-value=1.9e-17  Score=121.46  Aligned_cols=63  Identities=24%  Similarity=0.333  Sum_probs=59.4

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           12 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        12 ~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ...|+++|+++++++|.|+|+||++|.|+|.|||+|||++|+||+|+.+++....+|.++|+.
T Consensus         4 ~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~IRG   66 (86)
T 3s6n_F            4 PLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRC   66 (86)
T ss_dssp             CCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEEECG
T ss_pred             CcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEEEeC
Confidence            568999999999999999999999999999999999999999999999887778899999955

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1

Probab=99.71  E-value=2.7e-17  Score=117.85  Aligned_cols=63  Identities=25%  Similarity=0.569  Sum_probs=59.5

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCC-eEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           12 TLLPLELVDKCIGSRIHIIMKND-KEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        12 ~~~P~~~L~~~~~k~V~V~l~~g-~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      +..|+++|.++++++|+|+|++| ++|.|+|.|||+|||++|+||+|+.+++....+|.++|+.
T Consensus         3 m~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG   66 (77)
T 1ljo_A            3 MVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRG   66 (77)
T ss_dssp             CCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECG
T ss_pred             ccchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEEEeC
Confidence            35899999999999999999999 9999999999999999999999999888888999999955

>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A*

Probab=99.71  E-value=2.5e-17  Score=117.40  Aligned_cols=62  Identities=23%  Similarity=0.430  Sum_probs=58.9

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ..|+++|+++++++|+|+|+||++|.|+|.|||+|||++|+||+|+..+.....+|.++|+.
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG   64 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRG   64 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECG
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEEECC
Confidence            47999999999999999999999999999999999999999999999888888999999955

>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E

Probab=99.70  E-value=8.8e-18  Score=124.93  Aligned_cols=75  Identities=17%  Similarity=0.403  Sum_probs=62.0

Q ss_pred             CCCCCCCcHHHHHhhcCCEEEEEE----eCCeEEEEEEEeecCeeeeEecceEEee-cCccccccccEEEeeecccceee
Q psy800            8 TNPSTLLPLELVDKCIGSRIHIIM----KNDKEIVGTLNGFDDFVNMLLEDVTDCH-DSHLLSYFASDLINFIWGLPMIT   82 (204)
Q Consensus         8 ~~~~~~~P~~~L~~~~~k~V~V~l----~~g~~~~G~L~gfD~~mNlvL~~~~E~~-~~~~~~~lG~vlIn~~~g~~~~~   82 (204)
                      .++.+..|+++|.++++++|.|++    ++|++|+|+|+|||+||||+|+||+|+. +++....+|.++|+.- .+..+.
T Consensus        10 ~~~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~-nV~~i~   88 (92)
T 3s6n_E           10 VQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGD-NITLLQ   88 (92)
T ss_dssp             ----CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGG-GEEEEE
T ss_pred             cceeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCC-EEEEEE
Confidence            345689999999999999999999    9999999999999999999999999998 5667788999999653 334444


Q ss_pred             c
Q psy800           83 P   83 (204)
Q Consensus        83 P   83 (204)
                      |
T Consensus        89 ~   89 (92)
T 3s6n_E           89 S   89 (92)
T ss_dssp             E
T ss_pred             e
Confidence            4

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1

Probab=99.69  E-value=3.3e-17  Score=117.20  Aligned_cols=63  Identities=13%  Similarity=0.135  Sum_probs=58.0

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           12 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        12 ~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ...|+++|+++++++|.|+|++|++|+|+|.|||+|||++|+||+|+..++....+|+++|+.
T Consensus         3 ~~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~IRG   65 (75)
T 1d3b_A            3 IGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRG   65 (75)
T ss_dssp             -CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECG
T ss_pred             ccCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEEEeC
Confidence            357999999999999999999999999999999999999999999998666688999999954

>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe}

Probab=99.69  E-value=3.5e-17  Score=121.78  Aligned_cols=65  Identities=20%  Similarity=0.403  Sum_probs=55.7

Q ss_pred             CCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec-----C--------ccccccccEEEee
Q psy800           10 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD-----S--------HLLSYFASDLINF   74 (204)
Q Consensus        10 ~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~-----~--------~~~~~lG~vlIn~   74 (204)
                      .....|+++|+.+++++|+|+|++|++|.|+|.|||+||||+|+||+|+..     +        ...+.+|.++|+.
T Consensus         5 ~~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG   82 (93)
T 4emg_A            5 QAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRG   82 (93)
T ss_dssp             ----CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECG
T ss_pred             cccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECC
Confidence            456799999999999999999999999999999999999999999999984     2        2467899999955

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A*

Probab=99.69  E-value=4.5e-17  Score=116.52  Aligned_cols=62  Identities=24%  Similarity=0.465  Sum_probs=58.9

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ..|+++|+++++++|.|+|+||++|.|+|.|||+|||++|+||+|+..++..+.+|.++|+.
T Consensus         3 ~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG   64 (77)
T 1i4k_A            3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRG   64 (77)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECG
T ss_pred             ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCcEeECCEEEECC
Confidence            47999999999999999999999999999999999999999999999888888999999955

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G

Probab=99.68  E-value=4.9e-17  Score=116.46  Aligned_cols=71  Identities=15%  Similarity=0.337  Sum_probs=48.9

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEeeecccceeeccc
Q psy800           14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPIT   85 (204)
Q Consensus        14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~~~g~~~~~PI~   85 (204)
                      .|.++|+++++++|+|+|+||++|.|+|.|||+|||++|+||+|+..++....+|.++|+.- .+....|+.
T Consensus         4 ~~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~iRG~-~I~~i~~~d   74 (76)
T 3s6n_G            4 AHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGN-SIIMLEALE   74 (76)
T ss_dssp             ----------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEEECSS-SEEEEEC--
T ss_pred             cchHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEEECCC-eEEEEEecc
Confidence            36789999999999999999999999999999999999999999987777889999999652 334454543

>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1

Probab=99.68  E-value=5.4e-17  Score=127.68  Aligned_cols=65  Identities=15%  Similarity=0.403  Sum_probs=59.4

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       119 l~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      ..+|++++|++|+|+|++|+.|.|+|.|||+|||++|+||+|..    +   +.+|.++|||+||++|++.+
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~----~---~~lg~v~IRG~nI~~I~~~d   66 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA----G---EKFNRVFIMYRYIVHIDSTE   66 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT----C---CEEEEEEECGGGEEEEEECC
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc----C---CEeceEEEeCCeEEEEEcCC
Confidence            35899999999999999999999999999999999999999962    2   68999999999999998764

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A

Probab=99.67  E-value=4.2e-17  Score=126.62  Aligned_cols=67  Identities=42%  Similarity=0.754  Sum_probs=57.7

Q ss_pred             CCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec----------Ccc-----ccccccEEE
Q psy800            8 TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD----------SHL-----LSYFASDLI   72 (204)
Q Consensus         8 ~~~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~----------~~~-----~~~lG~vlI   72 (204)
                      +.+....|+++|.++++++|+|+|++|++|.|+|+|||+||||||+||+|+..          +..     .+.+|.++|
T Consensus        22 ~~~~~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~I  101 (121)
T 2fwk_A           22 KGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILL  101 (121)
T ss_dssp             --CCCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEE
T ss_pred             ccccccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEE
Confidence            45577899999999999999999999999999999999999999999999883          223     678999999


Q ss_pred             ee
Q psy800           73 NF   74 (204)
Q Consensus        73 n~   74 (204)
                      +.
T Consensus       102 RG  103 (121)
T 2fwk_A          102 SG  103 (121)
T ss_dssp             CG
T ss_pred             CC
Confidence            54

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae}

Probab=99.67  E-value=9.1e-17  Score=120.04  Aligned_cols=64  Identities=25%  Similarity=0.362  Sum_probs=57.5

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec-------CccccccccEEEee
Q psy800           11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD-------SHLLSYFASDLINF   74 (204)
Q Consensus        11 ~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~-------~~~~~~lG~vlIn~   74 (204)
                      -...|+++|+++++|+|+|+|+|||+|.|+|+|||+||||+|+||+|+..       +...+.+|.++|+.
T Consensus         7 ~~~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG   77 (96)
T 3bw1_A            7 HMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRG   77 (96)
T ss_dssp             CCCCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECG
T ss_pred             hhhhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECC
Confidence            35789999999999999999999999999999999999999999999974       24467799999955

>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C

Probab=99.64  E-value=2.3e-16  Score=121.36  Aligned_cols=77  Identities=21%  Similarity=0.371  Sum_probs=50.9

Q ss_pred             CCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC-------ccccccccEEEeeecccce
Q psy800            8 TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS-------HLLSYFASDLINFIWGLPM   80 (204)
Q Consensus         8 ~~~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~-------~~~~~lG~vlIn~~~g~~~   80 (204)
                      +..+...|...|.++++++|+|+|+|||+|.|+|.|||+||||||+||+|+..+       ...+.+|.++|+.- .++.
T Consensus        17 ~~~~kke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~-nIv~   95 (113)
T 4emk_C           17 TERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGT-TLVL   95 (113)
T ss_dssp             ---------------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTT-TEEE
T ss_pred             ccCCccchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCC-eEEE
Confidence            344556788889999999999999999999999999999999999999999853       35788999999552 3344


Q ss_pred             eeccc
Q psy800           81 ITPIT   85 (204)
Q Consensus        81 ~~PI~   85 (204)
                      +.|+.
T Consensus        96 I~~~d  100 (113)
T 4emk_C           96 IAPMD  100 (113)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            44443

>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A

Probab=99.61  E-value=2.5e-16  Score=116.00  Aligned_cols=62  Identities=18%  Similarity=0.292  Sum_probs=52.2

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee----------cCccccccccEEEee
Q psy800           13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH----------DSHLLSYFASDLINF   74 (204)
Q Consensus        13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~----------~~~~~~~lG~vlIn~   74 (204)
                      ..|..+|.++++++|+|+|+||++|.|+|.|||+||||+|+||+|+.          ++...+.+|.++|+.
T Consensus         3 ~~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG   74 (91)
T 1d3b_B            3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRG   74 (91)
T ss_dssp             ----CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECG
T ss_pred             CChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECC
Confidence            46788999999999999999999999999999999999999999975          234577889999844

>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A

Probab=99.61  E-value=9.1e-16  Score=118.82  Aligned_cols=61  Identities=20%  Similarity=0.159  Sum_probs=57.4

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      .|+++|+++++++|+|+|+||++|.|+|.|||+|||++|+||+|+..++....+|.++|+.
T Consensus         2 ~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~~lg~v~IRG   62 (119)
T 1b34_A            2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRG   62 (119)
T ss_dssp             CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECG
T ss_pred             ChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEEEcC
Confidence            6999999999999999999999999999999999999999999998777778999999943

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe}

Probab=99.61  E-value=6.1e-16  Score=117.55  Aligned_cols=65  Identities=25%  Similarity=0.403  Sum_probs=46.7

Q ss_pred             CCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee-cCccccccccEEEee
Q psy800           10 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH-DSHLLSYFASDLINF   74 (204)
Q Consensus        10 ~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~-~~~~~~~lG~vlIn~   74 (204)
                      ..+..|++||+++++++|.|+|+||++|.|+|.|||+||||+|+||+|.. +++....+|.++|+.
T Consensus        12 ~~~~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG   77 (105)
T 4emh_A           12 QDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRG   77 (105)
T ss_dssp             --------------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECG
T ss_pred             CCCCcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeC
Confidence            34568999999999999999999999999999999999999999999986 454677899999954

>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B

Probab=99.58  E-value=2.8e-15  Score=115.80  Aligned_cols=67  Identities=21%  Similarity=0.393  Sum_probs=53.1

Q ss_pred             CCCCCCCcHHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc--------------cccccccEE
Q psy800            8 TNPSTLLPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH--------------LLSYFASDL   71 (204)
Q Consensus         8 ~~~~~~~P~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~--------------~~~~lG~vl   71 (204)
                      .......|+++|.+++  +++|+|+|+||++|.|+|+|||+||||+|+||+|+....              ..+.+|.++
T Consensus        21 ~~~~~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~  100 (118)
T 1b34_B           21 EEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMF  100 (118)
T ss_dssp             -----CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEE
T ss_pred             hhhcccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEE
Confidence            4445779999999999  599999999999999999999999999999999987321              134689999


Q ss_pred             Eee
Q psy800           72 INF   74 (204)
Q Consensus        72 In~   74 (204)
                      |+.
T Consensus       101 IRG  103 (118)
T 1b34_B          101 LRG  103 (118)
T ss_dssp             ECG
T ss_pred             EcC
Confidence            955

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D

Probab=99.57  E-value=3.7e-15  Score=116.61  Aligned_cols=62  Identities=13%  Similarity=0.165  Sum_probs=56.9

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEe
Q psy800           12 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLIN   73 (204)
Q Consensus        12 ~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn   73 (204)
                      ...|++||+++++++|+|+|+||++|.|+|.+||.|||++|+||+|+..+.....+|+++|+
T Consensus         3 ~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IR   64 (126)
T 2y9a_D            3 IGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIR   64 (126)
T ss_dssp             -CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEEC
T ss_pred             cccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEe
Confidence            35799999999999999999999999999999999999999999999855557889999994

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A

Probab=99.55  E-value=7.7e-15  Score=124.83  Aligned_cols=60  Identities=18%  Similarity=0.316  Sum_probs=54.8

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec----------CccccccccEEE
Q psy800           13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD----------SHLLSYFASDLI   72 (204)
Q Consensus        13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~----------~~~~~~lG~vlI   72 (204)
                      .++...|++++||+|+|+|+|||+|+|+|+|||+||||||+||+|+..          .+.++++|.+||
T Consensus         3 v~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~I   72 (231)
T 3pgw_B            3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL   72 (231)
T ss_pred             cCchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEE
Confidence            567889999999999999999999999999999999999999999862          246788999999

>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1

Probab=99.37  E-value=4.7e-13  Score=105.18  Aligned_cols=55  Identities=16%  Similarity=0.397  Sum_probs=49.8

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        16 ~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      .++|+++++++|.|+|+||++|.|+|.|||+|||++|+||+|+.    ...+|.++|+.
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~----~~~lg~v~IRG   56 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA----GEKFNRVFIMY   56 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT----CCEEEEEEECG
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc----CCEeceEEEeC
Confidence            46899999999999999999999999999999999999999983    25789998854

>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}

Probab=98.27  E-value=2.8e-06  Score=62.13  Aligned_cols=62  Identities=18%  Similarity=0.223  Sum_probs=52.6

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      .|+ .|..++||+|.|.|.||+.|+|+|.+|| ...|+||.||.|     ++    ....++|.|..|.-|-.
T Consensus         8 ~p~-el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~~-----~~----~~~~~iI~G~aI~eI~v   70 (86)
T 1y96_A            8 GPL-EWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLE-----DG----SMSVTGIMGHAVQTVET   70 (86)
T ss_dssp             CHH-HHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEECT-----TS----CEEEEEECGGGEEEEEE
T ss_pred             CHH-HHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeeccc-----CC----eEEEEEEecceEEEEEE
Confidence            455 5889999999999999999999999999 999999999921     22    34789999999988744

>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}

Probab=97.98  E-value=1.5e-05  Score=58.19  Aligned_cols=42  Identities=21%  Similarity=0.229  Sum_probs=38.7

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeec-CeeeeEecce
Q psy800           13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDV   55 (204)
Q Consensus        13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD-~~mNlvL~~~   55 (204)
                      .+|.++ +.+++|+|.|.+.+|++|.|.|.+|| .-.|++|.|+
T Consensus         7 ~~p~el-~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~   49 (86)
T 1y96_A            7 KGPLEW-QDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF   49 (86)
T ss_dssp             SCHHHH-HHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE
T ss_pred             CCHHHH-HhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec
Confidence            567755 57999999999999999999999999 9999999999

>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A

Probab=96.58  E-value=0.0031  Score=45.52  Aligned_cols=34  Identities=24%  Similarity=0.458  Sum_probs=28.0

Q ss_pred             HHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceE
Q psy800          121 LVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNML  154 (204)
Q Consensus       121 ~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlV  154 (204)
                      +|+.+.  ..+|+|.|.||-.+.|++.|||+|+=+.
T Consensus        11 fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL   46 (82)
T 1u1s_A           11 YLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILL   46 (82)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEE
Confidence            455544  5679999999999999999999999443

>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A*

Probab=96.55  E-value=0.0033  Score=44.47  Aligned_cols=54  Identities=19%  Similarity=0.352  Sum_probs=40.0

Q ss_pred             HHHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          120 ELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       120 ~~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      .+|+.+.  ..+|+|.|.||..++|++.+||+|+ +.|++.               ...+|-=..|..|.|.
T Consensus        12 ~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~-vlL~~~---------------~~~LIYKhAIsTI~p~   67 (74)
T 2ylb_A           12 PFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLKNT---------------VSQMVYKHAISTVVPS   67 (74)
T ss_dssp             HHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSE-EEEESS---------------SEEEEEGGGEEEEEES
T ss_pred             HHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEECC---------------ceEEEEeeeEEEEeEc
Confidence            3666666  5679999999999999999999999 444431               2445666667777654

>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2

Probab=96.29  E-value=0.0057  Score=43.79  Aligned_cols=53  Identities=17%  Similarity=0.317  Sum_probs=38.9

Q ss_pred             HHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          121 LVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       121 ~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +|+.+.  ..+|+|.|.||..+.|++.+||+|+ +.|++         |      ...+|-=..|..|.|.
T Consensus        12 fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~-VlL~~---------g------~~qLIYKhAISTI~P~   66 (79)
T 3sb2_A           12 FLNALRKEHVPVSIYLVNGIKLQGHVESFDQYV-VLLRN---------T------VTQMVYKHAISTVVPA   66 (79)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEES---------S------SEEEEEGGGEEEEEES
T ss_pred             HHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcE-EEEEC---------C------ceEEEEeeeEEEEeec
Confidence            555555  3569999999999999999999999 44431         2      1346666777887765

>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A

Probab=96.27  E-value=0.0041  Score=46.75  Aligned_cols=34  Identities=24%  Similarity=0.472  Sum_probs=28.4

Q ss_pred             HHHhhcC--CEEEEEEeCCeEEEEEEEEEcCccceE
Q psy800          121 LVDKCIG--SRIHIIMKNDKEIVGTLNGFDDFVNML  154 (204)
Q Consensus       121 ~L~~~i~--k~V~V~Lk~gr~i~G~L~gfD~~mNlV  154 (204)
                      +|+.+..  .+|+|.|.||-.++|++.+||+|+=++
T Consensus        13 fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL   48 (104)
T 2y90_A           13 FLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILL   48 (104)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            5666654  479999999999999999999999444

>1kq1_A HFQ, HOST factor for Q beta; hexamer, RNA binding protein, translational regulator, SM motif; 1.55A {Staphylococcus aureus} SCOP: b.38.1.2 PDB: 1kq2_A

Probab=96.27  E-value=0.0071  Score=43.09  Aligned_cols=37  Identities=14%  Similarity=0.375  Sum_probs=31.2

Q ss_pred             HHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEec
Q psy800           16 LELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLE   53 (204)
Q Consensus        16 ~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~   53 (204)
                      -.||+.+.  +.+|.|.|.+|..++|.+.+||.|+ +.|+
T Consensus         9 d~fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~-VlL~   47 (77)
T 1kq1_A            9 DKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYV-VSLN   47 (77)
T ss_dssp             HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcE-EEEE
Confidence            45676666  6799999999999999999999999 4444

>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A

Probab=96.26  E-value=0.006  Score=43.99  Aligned_cols=37  Identities=24%  Similarity=0.450  Sum_probs=30.7

Q ss_pred             HHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEec
Q psy800           16 LELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLE   53 (204)
Q Consensus        16 ~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~   53 (204)
                      -.||+.+-  +.+|.|.|.+|..++|.+.|||.|+ +.|+
T Consensus         9 d~fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ft-VlL~   47 (82)
T 1u1s_A            9 DPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   47 (82)
T ss_dssp             HHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceE-EEEe
Confidence            45666555  5689999999999999999999999 5554

>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A*

Probab=96.23  E-value=0.0065  Score=42.94  Aligned_cols=40  Identities=25%  Similarity=0.443  Sum_probs=33.2

Q ss_pred             CCcHHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEec
Q psy800           13 LLPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLE   53 (204)
Q Consensus        13 ~~P~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~   53 (204)
                      ..--.||+.+.  +.+|.|.|.+|..++|.+.+||.|+ +.|+
T Consensus         8 ~lQd~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~-vlL~   49 (74)
T 2ylb_A            8 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   49 (74)
T ss_dssp             CCHHHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             ccHHHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEE
Confidence            34456777776  6799999999999999999999999 5555

>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A

Probab=96.06  E-value=0.0093  Score=42.58  Aligned_cols=34  Identities=21%  Similarity=0.551  Sum_probs=28.6

Q ss_pred             HHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceE
Q psy800          121 LVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNML  154 (204)
Q Consensus       121 ~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlV  154 (204)
                      +|+.+.  ..+|+|.|.||..+.|++.|||+|+=+.
T Consensus        15 fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL   50 (78)
T 3ahu_A           15 FLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLL   50 (78)
T ss_dssp             HHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            555555  6789999999999999999999999444

>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2

Probab=96.05  E-value=0.0089  Score=42.79  Aligned_cols=37  Identities=22%  Similarity=0.410  Sum_probs=30.6

Q ss_pred             cHHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEe
Q psy800           15 PLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLL   52 (204)
Q Consensus        15 P~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL   52 (204)
                      --.||+.+.  +.+|.|.|.+|..++|.+.+||.|+ +.|
T Consensus         9 Qd~fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~-VlL   47 (79)
T 3sb2_A            9 QDPFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYV-VLL   47 (79)
T ss_dssp             HHHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEE
T ss_pred             HHHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcE-EEE
Confidence            356777666  4579999999999999999999999 445

>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii}

Probab=96.04  E-value=0.0081  Score=42.17  Aligned_cols=29  Identities=14%  Similarity=0.579  Sum_probs=25.7

Q ss_pred             CCEEEEEEeCCeEEEEEEEeecCeeeeEec
Q psy800           24 GSRIHIIMKNDKEIVGTLNGFDDFVNMLLE   53 (204)
Q Consensus        24 ~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~   53 (204)
                      +.+|.|.|.+|..++|.+.|||.|+ +.|+
T Consensus        25 ~~~Vtv~L~NG~~l~G~I~~fD~ft-Vll~   53 (71)
T 2qtx_A           25 GKKVKIFLRNGEVLDAEVTGVSNYE-IMVK   53 (71)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             CCcEEEEEeCCeEEEEEEEEEcceE-EEEE
Confidence            4689999999999999999999999 4444

>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii}

Probab=95.96  E-value=0.011  Score=41.55  Aligned_cols=28  Identities=18%  Similarity=0.540  Sum_probs=25.1

Q ss_pred             CCEEEEEEeCCeEEEEEEEEEcCccceE
Q psy800          127 GSRIHIIMKNDKEIVGTLNGFDDFVNML  154 (204)
Q Consensus       127 ~k~V~V~Lk~gr~i~G~L~gfD~~mNlV  154 (204)
                      ..+|+|.|.||..+.|.+.|||+|+=+.
T Consensus        25 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll   52 (71)
T 2qtx_A           25 GKKVKIFLRNGEVLDAEVTGVSNYEIMV   52 (71)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             CCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            5679999999999999999999999444

>1kq1_A HFQ, HOST factor for Q beta; hexamer, RNA binding protein, translational regulator, SM motif; 1.55A {Staphylococcus aureus} SCOP: b.38.1.2 PDB: 1kq2_A

Probab=95.93  E-value=0.013  Score=41.63  Aligned_cols=34  Identities=15%  Similarity=0.396  Sum_probs=28.8

Q ss_pred             HHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceE
Q psy800          121 LVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNML  154 (204)
Q Consensus       121 ~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlV  154 (204)
                      +|+.+.  ..+|+|.|.||-.+.|++.+||+|+=+.
T Consensus        11 fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL   46 (77)
T 1kq1_A           11 ALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSL   46 (77)
T ss_dssp             HHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            566665  6789999999999999999999999443

>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A

Probab=95.92  E-value=0.0075  Score=45.29  Aligned_cols=40  Identities=25%  Similarity=0.443  Sum_probs=32.6

Q ss_pred             CCcHHHHHhhcC--CEEEEEEeCCeEEEEEEEeecCeeeeEec
Q psy800           13 LLPLELVDKCIG--SRIHIIMKNDKEIVGTLNGFDDFVNMLLE   53 (204)
Q Consensus        13 ~~P~~~L~~~~~--k~V~V~l~~g~~~~G~L~gfD~~mNlvL~   53 (204)
                      ..--.||+.+..  .+|.|.|.+|..++|.+.+||.|+ +.|+
T Consensus         8 nlQd~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~-VlL~   49 (104)
T 2y90_A            8 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   49 (104)
T ss_dssp             CCHHHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             ccHHHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEE
Confidence            344567777764  489999999999999999999999 5554

>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A

Probab=95.91  E-value=0.0085  Score=42.80  Aligned_cols=37  Identities=24%  Similarity=0.563  Sum_probs=30.4

Q ss_pred             HHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEec
Q psy800           16 LELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLE   53 (204)
Q Consensus        16 ~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~   53 (204)
                      -.||+.+-  +.+|.|.|.+|..++|.+.|||.|+ +.|+
T Consensus        13 d~fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~-VlL~   51 (78)
T 3ahu_A           13 DQFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFT-VLLE   51 (78)
T ss_dssp             HHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceE-EEEE
Confidence            45666555  6799999999999999999999999 4444

>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis SP}

Probab=94.73  E-value=0.089  Score=36.73  Aligned_cols=42  Identities=24%  Similarity=0.252  Sum_probs=34.4

Q ss_pred             CCCc-HHHHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800          115 TLLP-LELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLED  157 (204)
Q Consensus       115 ~~~P-l~~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d  157 (204)
                      +.+| ...|.+++  ..+|.|+|-+|..++|.+.-+|.|. +.|.+
T Consensus         6 t~lPsvR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~c-l~L~~   50 (70)
T 3hfo_A            6 SGLPSVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDG-LGLVD   50 (70)
T ss_dssp             CSCHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE-EEEEC
T ss_pred             CCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCE-EEEEc
Confidence            4566 77888888  4569999999999999999999998 44443

>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP}

Probab=94.38  E-value=0.12  Score=36.28  Aligned_cols=60  Identities=20%  Similarity=0.231  Sum_probs=42.8

Q ss_pred             CCCc-HHHHHhhcC--CEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          115 TLLP-LELVDKCIG--SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       115 ~~~P-l~~L~~~i~--k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      +.+| ...|.+++.  .+|.|+|-+|..++|++.-+|.|. +.|.+..+             ..++|.-..|.+|.|
T Consensus         8 t~lPsvR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~c-l~L~~~~~-------------~~~LI~R~AI~~Ikp   70 (72)
T 3hfn_A            8 TSLPSIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTC-VCIADENS-------------RQTTIWKQAIAYLQP   70 (72)
T ss_dssp             -CHHHHHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSE-EEEEC----------------CEEEEEGGGEEEEEE
T ss_pred             CCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCE-EEEEcCCC-------------CeEEEEeeeeEEEEe
Confidence            4556 778999985  459999999999999999999998 55554332             135566666666654

>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster}

Probab=94.10  E-value=0.34  Score=35.17  Aligned_cols=63  Identities=27%  Similarity=0.410  Sum_probs=51.1

Q ss_pred             hcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecCCCe--------eeeeeCeEEEeCCcEEEEccc
Q psy800          125 CIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTPEGR--------RITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       125 ~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~~~~--------~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +++++|.+..+.+-+|+|+|...| +-.-+.|.|+.-+-++  |.        ...-+..++.||+.|.-+...
T Consensus        11 yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTE--gR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~   82 (88)
T 2vxe_A           11 ELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTE--DRDTQFQIAPQSQIYDYILFRGSDIKDIRVV   82 (88)
T ss_dssp             CTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCT--TTCCSSCCCCCCSCEEEEEEETTTEEEEEEC
T ss_pred             ccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCc--CCCCCcccCCCCceeeEEEEccCCccEEEEe
Confidence            799999999999999999999999 6678999998876432  21        234468999999999987654

>1ycy_A Conserved hypothetical protein; structural genomics, southeast collaboratory for structural genomics, secsg, protein structure initiative; 2.80A {Pyrococcus furiosus} SCOP: b.38.1.4

Probab=92.06  E-value=0.77  Score=31.47  Aligned_cols=59  Identities=27%  Similarity=0.529  Sum_probs=42.1

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEE
Q psy800          120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITML  186 (204)
Q Consensus       120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I  186 (204)
                      +.|+++.+++|-|-......+.|+|..||+-. +.|.|+..+.    |   .+-..++++=|.|--|
T Consensus         9 ktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~----G---Nk~k~liv~idDinWi   67 (71)
T 1ycy_A            9 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI----G---NRGKQMLIGLEDINWI   67 (71)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT----E---EEEEEEEEEGGGEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHh----c---cccceeEEEeccceEE
Confidence            47899999999999999999999999999987 7889999864    2   1223556665555544

>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387, stronGly BENT five-stranded antiparallel beta- sheet, structural genomics, PSI; NMR {Danio rerio} SCOP: b.38.1.5 PDB: 2vxf_A

Probab=91.60  E-value=0.37  Score=35.43  Aligned_cols=65  Identities=28%  Similarity=0.447  Sum_probs=51.1

Q ss_pred             HhhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecCCCe--------eeeeeCeEEEeCCcEEEEccc
Q psy800          123 DKCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTPEGR--------RITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       123 ~~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~~~~--------~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      ..++|++|.+..+.+-+|+|+|...| +-.-+.|.|+.-+-+  +|.        ...-+..++.||+-|.-+...
T Consensus        15 ~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGT--EgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~   88 (95)
T 2fb7_A           15 TPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGT--EDRPTDRPIAPRDETFEYIIFRGSDIKDLTVC   88 (95)
T ss_dssp             -CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSC--CSSSCSSCCCSCCCCSSCEEECSTTEEEEEES
T ss_pred             CcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecc--cCCCCCCccCCCCcceeEEEEcCCCcceEEEe
Confidence            45899999999999999999999999 567799999775433  221        234568999999999987543

>1y96_B Gemin7, SIP3, GEM-associated protein 7; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}

Probab=91.50  E-value=0.63  Score=33.55  Aligned_cols=63  Identities=16%  Similarity=0.308  Sum_probs=49.3

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      -|..|....+++|.+.+.++.++.|+..++| +..|+..++-.-    +=|    .++..+||+.-|+.++-
T Consensus        20 fLr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T----PiG----v~~eAlLR~~Dii~~sF   83 (85)
T 1y96_B           20 YLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQT----PIG----VQAEALLRCSDIISYTF   83 (85)
T ss_dssp             HHHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEECC----TTC----CEEEEEEEGGGEEEEEE
T ss_pred             HHHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcCC----Ccc----cchhhhhhcCCEEEEEe
Confidence            3667777889999999999999999999999 557776655431    112    25688999999998864

>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP}

Probab=90.55  E-value=0.45  Score=33.30  Aligned_cols=45  Identities=20%  Similarity=0.247  Sum_probs=34.5

Q ss_pred             CCCCCc-HHHHHhhcC--CEEEEEEeCCeEEEEEEEeecCeeeeEecce
Q psy800           10 PSTLLP-LELVDKCIG--SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV   55 (204)
Q Consensus        10 ~~~~~P-~~~L~~~~~--k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~   55 (204)
                      --+..| ...|..++.  ++|.|+|.+|..+.|++.-+|.|. |-|.+.
T Consensus         6 fdt~lPsvR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~c-l~L~~~   53 (72)
T 3hfn_A            6 FDTSLPSIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTC-VCIADE   53 (72)
T ss_dssp             ---CHHHHHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSE-EEEEC-
T ss_pred             cCCCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCE-EEEEcC
Confidence            334556 678888884  589999999999999999999998 555544

>4a53_A EDC3; RNA binding protein; NMR {Schizosaccharomyces pombe} PDB: 4a54_A

Probab=90.53  E-value=0.37  Score=37.04  Aligned_cols=37  Identities=27%  Similarity=0.515  Sum_probs=31.7

Q ss_pred             HHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEE--cceE
Q psy800          122 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL--EDVT  159 (204)
Q Consensus       122 L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL--~da~  159 (204)
                      ..+|++..|.|+|+||..+.|++..+|.- +|+|  .+|.
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd~k-~LtL~~~~a~   45 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFDSS-NSILQLRLAN   45 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEETT-TTEEEEEETT
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeecCC-eeEEeccccc
Confidence            56899999999999999999999999843 4666  8884

>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis SP}

Probab=89.51  E-value=0.68  Score=32.20  Aligned_cols=42  Identities=24%  Similarity=0.252  Sum_probs=34.3

Q ss_pred             CCCc-HHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEecc
Q psy800           12 TLLP-LELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLED   54 (204)
Q Consensus        12 ~~~P-~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~   54 (204)
                      +..| ...|..++  ..+|.|+|.+|..+.|.+.-+|.|. +-|.+
T Consensus         6 t~lPsvR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~c-l~L~~   50 (70)
T 3hfo_A            6 SGLPSVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDG-LGLVD   50 (70)
T ss_dssp             CSCHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE-EEEEC
T ss_pred             CCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCE-EEEEc
Confidence            4456 67788888  4689999999999999999999998 54443

>1ycy_A Conserved hypothetical protein; structural genomics, southeast collaboratory for structural genomics, secsg, protein structure initiative; 2.80A {Pyrococcus furiosus} SCOP: b.38.1.4

Probab=89.35  E-value=0.56  Score=32.18  Aligned_cols=44  Identities=30%  Similarity=0.539  Sum_probs=35.3

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec
Q psy800           16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD   60 (204)
Q Consensus        16 ~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~   60 (204)
                      -+.|++.-+++|-|-..+...|.|+|.-||+-. +.|.|+..+..
T Consensus         8 dktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~G   51 (71)
T 1ycy_A            8 EKVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIG   51 (71)
T ss_dssp             HHHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTE
T ss_pred             HHHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHhc
Confidence            357788889999999999999999999999998 88899998764

>2vc8_A Enhancer of mRNA-decapping protein 3; P-BODY component, cytoplasm, SM-like protein, protein-binding; 1.31A {Homo sapiens}

Probab=83.62  E-value=3.1  Score=29.83  Aligned_cols=57  Identities=18%  Similarity=0.244  Sum_probs=45.7

Q ss_pred             hhcCCEEEEEEeCCe-EEEEEEEEEcCc-cceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEE
Q psy800          124 KCIGSRIHIIMKNDK-EIVGTLNGFDDF-VNMLLEDVTEYESTPEGRRITKLDQILLNGNNITML  186 (204)
Q Consensus       124 ~~i~k~V~V~Lk~gr-~i~G~L~gfD~~-mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I  186 (204)
                      +++++.|.|..++.- .|.|.|...|.. -||.|.+|..     +|- +.....+.+|+.-|.-+
T Consensus         6 ~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f~-----NG~-~~~s~eVtls~~DI~~L   64 (84)
T 2vc8_A            6 DWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPFH-----NGV-KCLVPEVTFRAGDITEL   64 (84)
T ss_dssp             TTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEEE-----TTE-ECSSSEEEEEGGGCSEE
T ss_pred             cccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhhh-----CCC-CCCCcEEEEEecChhhe
Confidence            689999999999999 999999999966 6899999952     453 33445688888776554

---

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	204
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	2e-18
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	2e-12
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	5e-16
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	7e-10
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-15
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-09
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	3e-15
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	8e-10
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	3e-15
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	3e-09
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	6e-15
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	6e-09
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	3e-14
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	1e-09
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	3e-12
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	1e-08
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	6e-12
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	5e-07
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	6e-12
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	4e-08
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	7e-12
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	3e-07
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	3e-11
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	2e-05
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	4e-10
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	7e-05

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Length = 92

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

 Score = 74.1 bits (182), Expect = 2e-18
 Identities = 39/85 (45%), Positives = 56/85 (65%), Gaps = 12/85 (14%)

Query: 114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRIT-- 171
           + +LPL L+DKCIG+RI+++MK DKE  G L GFD++VNM+L+DV EY    +   I+  
Sbjct: 2   NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGG 61

Query: 172 ----------KLDQILLNGNNITML 186
                     +L+ ILL+GNN+ ML
Sbjct: 62  NKKLKRVMVNRLETILLSGNNVAML 86

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Length = 92

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

 Score = 58.3 bits (141), Expect = 2e-12
 Identities = 27/47 (57%), Positives = 39/47 (82%)

Query: 11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
          + +LPL L+DKCIG+RI+++MK DKE  G L GFD++VNM+L+DV +
Sbjct: 2  NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQE 48

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

 Score = 67.5 bits (165), Expect = 5e-16
 Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 4/74 (5%)

Query: 114 STLLPLELVDKCIGSRIHIIMKNDK-EIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITK 172
           + +LP ++V   +G  I + MK ++ ++VG L G DD++N+ L +  E +   + R    
Sbjct: 2   AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVR---S 58

Query: 173 LDQILLNGNNITML 186
           L +I+L GNN+ ++
Sbjct: 59  LGEIVLRGNNVVLI 72

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

 Score = 51.3 bits (123), Expect = 7e-10
 Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 11 STLLPLELVDKCIGSRIHIIMKNDK-EIVGTLNGFDDFVNMLLEDVTDCHDS 61
          + +LP ++V   +G  I + MK ++ ++VG L G DD++N+ L +  +C   
Sbjct: 2  AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE 53

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score = 65.9 bits (161), Expect = 2e-15
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 3/69 (4%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
           PL+ +   + S + I +K D+E  G L  FD  +N++L D  E E   +G    +L  +L
Sbjct: 7   PLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTRRLGTVL 63

Query: 178 LNGNNITML 186
           + G+NI  +
Sbjct: 64  IRGDNIVYI 72

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score = 50.5 bits (121), Expect = 2e-09
 Identities = 15/46 (32%), Positives = 25/46 (54%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
          PL+ +   + S + I +K D+E  G L  FD  +N++L D  +  D
Sbjct: 7  PLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED 52

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

 Score = 65.5 bits (160), Expect = 3e-15
 Identities = 16/69 (23%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
           PL+++ + +   + +I+K   E  G L G+D  +N++L D    +   +G  + +  +I+
Sbjct: 3   PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQ---DGEVVKRYGKIV 59

Query: 178 LNGNNITML 186
           + G+N+  +
Sbjct: 60  IRGDNVLAI 68

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

 Score = 51.2 bits (123), Expect = 8e-10
 Identities = 13/47 (27%), Positives = 25/47 (53%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
          PL+++ + +   + +I+K   E  G L G+D  +N++L D     D 
Sbjct: 3  PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG 49

>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]

 Score = 65.1 bits (159), Expect = 3e-15
 Identities = 17/69 (24%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
           PL+++++ + S + + +K  +E  GTL+G+D  +N++L D  E +    G  + K+  ++
Sbjct: 4   PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQ---NGEVVRKVGSVV 60

Query: 178 LNGNNITML 186
           + G+ +  +
Sbjct: 61  IRGDTVVFV 69

>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]

 Score = 49.7 bits (119), Expect = 3e-09
 Identities = 13/46 (28%), Positives = 30/46 (65%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
          PL+++++ + S + + +K  +E  GTL+G+D  +N++L D  +  +
Sbjct: 4  PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQN 49

>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 64.7 bits (158), Expect = 6e-15
 Identities = 17/69 (24%), Positives = 40/69 (57%), Gaps = 3/69 (4%)

Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
             +++ + + + + + +K +KE+ G L  +D  +N++L D  E +S   G+   KL  I+
Sbjct: 8   AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGK---KLGTIV 64

Query: 178 LNGNNITML 186
           + G+N+ ++
Sbjct: 65  IRGDNVILI 73

>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 48.9 bits (117), Expect = 6e-09
 Identities = 9/43 (20%), Positives = 25/43 (58%)

Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
            +++ + + + + + +K +KE+ G L  +D  +N++L D  +
Sbjct: 8  AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEE 50

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.9 bits (153), Expect = 3e-14
 Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQI 176
           +P++++ +  G  +       +   G L   +D +N  + ++T         R+ +L+Q+
Sbjct: 2   VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVT---YRDGRVAQLEQV 58

Query: 177 LLNGNNITML 186
            + G  I  L
Sbjct: 59  YIRGCKIRFL 68

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (121), Expect = 1e-09
 Identities = 7/48 (14%), Positives = 21/48 (43%)

Query: 14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
          +P++++ +  G  +       +   G L   +D +N  + ++T  +  
Sbjct: 2  VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD 49

>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 59.3 bits (144), Expect = 3e-12
 Identities = 9/70 (12%), Positives = 30/70 (42%), Gaps = 7/70 (10%)

Query: 119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILL 178
           +  ++  +G  + +++ N +   G L+  D+ +N++L + +            K +++ +
Sbjct: 2   VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAG-------EKFNRVFI 54

Query: 179 NGNNITMLGL 188
               I  +  
Sbjct: 55  MYRYIVHIDS 64

>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 49.3 bits (118), Expect = 1e-08
 Identities = 7/42 (16%), Positives = 24/42 (57%)

Query: 16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
          +  ++  +G  + +++ N +   G L+  D+ +N++L + ++
Sbjct: 2  VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASN 43

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.1 bits (138), Expect = 6e-12
 Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 7/70 (10%)

Query: 124 KCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEY-------ESTPEGRRITKLDQI 176
           + I  R+  I+++ +  +GT   FD  +N++L D  E+           E      L  +
Sbjct: 5   QHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLV 64

Query: 177 LLNGNNITML 186
           LL G N+  +
Sbjct: 65  LLRGENLVSM 74

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (103), Expect = 5e-07
 Identities = 10/37 (27%), Positives = 21/37 (56%)

Query: 21 KCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
          + I  R+  I+++ +  +GT   FD  +N++L D  +
Sbjct: 5  QHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDE 41

>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.2 bits (138), Expect = 6e-12
 Identities = 17/82 (20%), Positives = 41/82 (50%), Gaps = 13/82 (15%)

Query: 118 PLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITK--- 172
           PL ++ + +   +++ I  +N+K+++G +  FD   NM+LE+V E  +        K   
Sbjct: 3   PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKS 62

Query: 173 --------LDQILLNGNNITML 186
                   + ++ L G+++ ++
Sbjct: 63  KPVNKDRYISKMFLRGDSVIVV 84

>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (111), Expect = 4e-08
 Identities = 13/45 (28%), Positives = 29/45 (64%), Gaps = 2/45 (4%)

Query: 15 PLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
          PL ++ + +   +++ I  +N+K+++G +  FD   NM+LE+V +
Sbjct: 3  PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKE 47

>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 56.6 bits (137), Expect = 7e-12
 Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 4/65 (6%)

Query: 123 DKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNN 182
              IG ++ + +++  EI G L  FD  VN+LLED  E           K   +++ G N
Sbjct: 8   QDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNV----YKRGTMVVRGEN 63

Query: 183 ITMLG 187
           +  + 
Sbjct: 64  VLFIS 68

>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 43.9 bits (104), Expect = 3e-07
 Identities = 15/43 (34%), Positives = 24/43 (55%)

Query: 20 DKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH 62
             IG ++ + +++  EI G L  FD  VN+LLED  +  D +
Sbjct: 8  QDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN 50

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.7 bits (132), Expect = 3e-11
 Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 4/65 (6%)

Query: 124 KCIGSRIHIIMK-NDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNN 182
             +  R+ + +K N  E  GTL   D++ N+ L +  E+     G     L +I +  NN
Sbjct: 3   GLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV---AGVSHGTLGEIFIRCNN 59

Query: 183 ITMLG 187
           +  + 
Sbjct: 60  VLYIR 64

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.9 bits (91), Expect = 2e-05
 Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 21 KCIGSRIHIIMK-NDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
            +  R+ + +K N  E  GTL   D++ N+ L +  +    
Sbjct: 3  GLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG 44

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (125), Expect = 4e-10
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNG 180
            + K     + I +KN  ++ GT+ G D  +N  L+ V     T + R   +L+ + + G
Sbjct: 5   FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKM---TLKNREPVQLETLSIRG 61

Query: 181 NNITMLGL 188
           NNI    L
Sbjct: 62  NNIRYFIL 69

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (88), Expect = 7e-05
 Identities = 11/39 (28%), Positives = 19/39 (48%)

Query: 18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
           + K     + I +KN  ++ GT+ G D  +N  L+ V 
Sbjct: 5  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVK 43

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	204
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.87
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.87
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.86
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.86
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.84
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.83
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.83
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.82
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.8
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.8
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.78
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.71
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.71
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.7
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.7
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.68
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.67
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.63
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.59
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.59
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.58
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.56
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.54
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.49
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.37
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.18
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	95.97
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	95.83
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	95.44
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	95.22
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	94.7
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	93.88
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	92.29
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	90.02
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	88.61
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	82.19

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=99.87  E-value=2.7e-22  Score=140.46  Aligned_cols=71  Identities=23%  Similarity=0.516  Sum_probs=65.9

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +.|+++|+++++++|+|+|+||+.|+|+|.+||+|||++|+||.|..   ++++.+++|.++|||++|++|+|.
T Consensus         1 ~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~l~~~~IRG~~I~~Isp~   71 (71)
T d1h641_           1 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQ---DGEVVKRYGKIVIRGDNVLAISPT   71 (71)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEEC
T ss_pred             CCchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEe---cCCcEeEcCcEEEECCeEEEEeCC
Confidence            36999999999999999999999999999999999999999999986   345688999999999999999874

>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]

Probab=99.87  E-value=2.2e-22  Score=141.49  Aligned_cols=71  Identities=24%  Similarity=0.556  Sum_probs=65.5

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      ..|+++|+++++++|+|+|+||+.|.|+|.|||+|||++|+||+|+.   +++..+++|.++|||++|.+|+|.
T Consensus         2 ~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~~g~~~IRG~~I~~Ispa   72 (72)
T d1i4k1_           2 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQ---NGEVVRKVGSVVIRGDTVVFVSPA   72 (72)
T ss_dssp             CCHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEES---SSSEEEEEEEEEECGGGEEEEECC
T ss_pred             CChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEe---cCCeEeEcceEEEeCCeEEEEEcC
Confidence            46999999999999999999999999999999999999999999985   334678999999999999999863

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

Probab=99.86  E-value=7.1e-22  Score=140.15  Aligned_cols=73  Identities=30%  Similarity=0.650  Sum_probs=66.3

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCC-eEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          114 STLLPLELVDKCIGSRIHIIMKND-KEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       114 ~~~~Pl~~L~~~i~k~V~V~Lk~g-r~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +...|+++|+++++++|+|+|++| +.|.|+|.|||+|||++|+||+|+.   ++.+.+++|.++|||++|.+|+|.
T Consensus         2 ~~~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~~g~~~IRG~~I~~I~p~   75 (75)
T d1ljoa_           2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECK---GEEKVRSLGEIVLRGNNVVLIQPQ   75 (75)
T ss_dssp             CCCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEEC
T ss_pred             CccccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEc---CCCcEeEcceEEEeCCEEEEEECC
Confidence            457899999999999999999976 7999999999999999999999986   334688999999999999999873

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=99.86  E-value=1e-21  Score=138.63  Aligned_cols=71  Identities=31%  Similarity=0.579  Sum_probs=66.0

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       115 ~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      ...|+++|+++++++|.|+|+||+.|.|+|.+||+|||++|+||+|..   ++...+++|.++|||++|.+|+|
T Consensus         4 ~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~---~~~~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           4 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             TTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEC
T ss_pred             ccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEe---CCCeEeEcceEEEeCCEEEEEeC
Confidence            467999999999999999999999999999999999999999999986   34568899999999999999986

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

Probab=99.84  E-value=1.1e-21  Score=143.70  Aligned_cols=75  Identities=51%  Similarity=0.907  Sum_probs=66.3

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCC------------CeeeeeeCeEEEeCCc
Q psy800          115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE------------GRRITKLDQILLNGNN  182 (204)
Q Consensus       115 ~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~------------~~~~~~lg~ilIRGdn  182 (204)
                      ..+|+++|+++++++|+|.|+||+.|.|+|.+||+||||+|+||.|++...+            +...+++|.++|||++
T Consensus         3 ~~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~   82 (92)
T d2fwka1           3 IILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNN   82 (92)
T ss_dssp             CCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGG
T ss_pred             ccChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCE
Confidence            5789999999999999999999999999999999999999999999875311            1346789999999999


Q ss_pred             EEEEccc
Q psy800          183 ITMLGLH  189 (204)
Q Consensus       183 I~~I~~~  189 (204)
                      |++|+|.
T Consensus        83 Vv~I~p~   89 (92)
T d2fwka1          83 VAMLVPG   89 (92)
T ss_dssp             EEEEESS
T ss_pred             EEEEEeC
Confidence            9999983

>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=3.8e-21  Score=141.56  Aligned_cols=76  Identities=21%  Similarity=0.427  Sum_probs=63.4

Q ss_pred             CCcHHHHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCC-----------eeeeeeCeEEEeCCc
Q psy800          116 LLPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG-----------RRITKLDQILLNGNN  182 (204)
Q Consensus       116 ~~Pl~~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~-----------~~~~~lg~ilIRGdn  182 (204)
                      ++|+++|.+++  +++|.|.|++|+.+.|+|.|||+||||||+||.|++...+.           ...+.+|.++|||||
T Consensus         1 tGPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdn   80 (93)
T d1b34b_           1 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDS   80 (93)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGG
T ss_pred             CCcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCE
Confidence            47999999999  89999999999999999999999999999999998763111           135789999999999


Q ss_pred             EEEEccccC
Q psy800          183 ITMLGLHTH  191 (204)
Q Consensus       183 I~~I~~~~~  191 (204)
                      |++|...+.
T Consensus        81 Vv~I~~~p~   89 (93)
T d1b34b_          81 VIVVLRNPL   89 (93)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEcChh
Confidence            999976653

>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.83  E-value=9.8e-21  Score=132.82  Aligned_cols=68  Identities=28%  Similarity=0.531  Sum_probs=62.0

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800          119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHT  190 (204)
Q Consensus       119 l~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~  190 (204)
                      -..|+++++++|+|+|+||+.|.|+|.+||+|||++|+||+|+.   ++ +.+++|.++|||++|++|++.+
T Consensus         4 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~---~~-~~~~~g~v~iRG~~I~~I~~~P   71 (71)
T d1i8fa_           4 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII---DG-NVYKRGTMVVRGENVLFISPVP   71 (71)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEE---TT-EEEEEEEEEECGGGEEEEEECC
T ss_pred             hHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEE---CC-CEEEcceEEEeCCeEEEEeCCC
Confidence            35899999999999999999999999999999999999999986   23 5788999999999999998753

>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.82  E-value=1.4e-20  Score=133.45  Aligned_cols=70  Identities=23%  Similarity=0.471  Sum_probs=64.4

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800          116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL  188 (204)
Q Consensus       116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~  188 (204)
                      ..|.++|+++++++|+|+|+||+.|.|+|.|||+|||++|+||+|+..  + .+.+.+|.++|||++|++|+|
T Consensus         6 ~~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~--~-~~~~~~~~v~iRG~~I~~I~~   75 (76)
T d1th7a1           6 ETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQS--D-GSGKKLGTIVIRGDNVILISP   75 (76)
T ss_dssp             HHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECS--S-SCEEEEEEEEECGGGEEEEEE
T ss_pred             ccHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEec--C-CcccCcceEEEECCEEEEEEe
Confidence            458999999999999999999999999999999999999999999862  3 357899999999999999987

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=6.6e-20  Score=128.75  Aligned_cols=70  Identities=21%  Similarity=0.384  Sum_probs=64.1

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      .|+++|+++.+++|+|+||||+.|+|+|.+||+|||++|+||++..  .++ +..++|.++|||++|.+|...
T Consensus         2 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~--~~~-~~~~~~~v~IRG~~I~~i~lp   71 (72)
T d1d3ba_           2 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY--RDG-RVAQLEQVYIRGCKIRFLILP   71 (72)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC--TTS-CEEEEEEEEECGGGEEEEEEC
T ss_pred             CchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEc--CCC-cEeEcCeEEEECCEEEEEEcC
Confidence            6999999999999999999999999999999999999999999875  333 567899999999999999754

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.80  E-value=5e-20  Score=128.19  Aligned_cols=65  Identities=25%  Similarity=0.425  Sum_probs=58.4

Q ss_pred             HHhhcCCEEEEEEe-CCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          122 VDKCIGSRIHIIMK-NDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       122 L~~~i~k~V~V~Lk-~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      |+++++++|.|+|| +|++|+|+|.|||+|||++|+||+|+.   +++..+++|.++|||++|.+|++.
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~lg~~~IRG~nI~~I~~~   66 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV---AGVSHGTLGEIFIRCNNVLYIREL   66 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEE---TTEEEEECCSEEECGGGEEEEEEC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEe---cCCcccCcCeEEEECCEEEEEEeC
Confidence            56789999999999 667899999999999999999999986   445788999999999999999754

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1.7e-19  Score=129.17  Aligned_cols=69  Identities=25%  Similarity=0.476  Sum_probs=60.3

Q ss_pred             HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecC-------CCeeeeeeCeEEEeCCcEEEEccc
Q psy800          121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP-------EGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~-------~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      .|.++++++|.|.|+|||.+.|+|.|||+||||||+||.|++...       .+...+.+|.++|||++|++|+.+
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEcc
Confidence            367899999999999999999999999999999999999986421       123568999999999999999754

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=99.71  E-value=9.4e-18  Score=117.00  Aligned_cols=62  Identities=23%  Similarity=0.430  Sum_probs=58.9

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      +.|+++|+++++++|.|+|+||++|.|+|.+||+|||++|+||.|+.+++....+|.++|+.
T Consensus         1 ~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~l~~~~IRG   62 (71)
T d1h641_           1 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRG   62 (71)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECG
T ss_pred             CCchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCcEeEcCcEEEEC
Confidence            47999999999999999999999999999999999999999999999888888999999955

>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]

Probab=99.71  E-value=7e-18  Score=118.10  Aligned_cols=62  Identities=24%  Similarity=0.465  Sum_probs=58.9

Q ss_pred             CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ..|+++|+++++++|.|+|+||++|+|+|.|||+|||++|+||.|+.+++....+|.++|+.
T Consensus         2 ~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG   63 (72)
T d1i4k1_           2 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRG   63 (72)
T ss_dssp             CCHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEEEEECG
T ss_pred             CChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcceEEEeC
Confidence            57999999999999999999999999999999999999999999999888888999999955

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

Probab=99.70  E-value=1.4e-17  Score=117.68  Aligned_cols=64  Identities=25%  Similarity=0.566  Sum_probs=59.8

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCC-eEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           11 STLLPLELVDKCIGSRIHIIMKND-KEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        11 ~~~~P~~~L~~~~~k~V~V~l~~g-~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ++..|+++|+++++++|+|+|++| ++|.|+|.|||+|||++|+||+|+.+++....+|+++|+.
T Consensus         2 ~~~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG   66 (75)
T d1ljoa_           2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRG   66 (75)
T ss_dssp             CCCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECG
T ss_pred             CccccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCcEeEcceEEEeC
Confidence            567899999999999999999976 8999999999999999999999999888889999999955

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=99.70  E-value=2.3e-17  Score=116.01  Aligned_cols=64  Identities=27%  Similarity=0.446  Sum_probs=60.1

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        11 ~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ....|+++|+++++|+|.|+|+||++|.|+|.|||+|||++|+||.|+.+++...++|.++|+.
T Consensus         3 ~~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~IRG   66 (74)
T d1mgqa_           3 NVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRG   66 (74)
T ss_dssp             CTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECG
T ss_pred             cccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEEEeC
Confidence            3567999999999999999999999999999999999999999999999888889999999955

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=5.9e-17  Score=115.71  Aligned_cols=68  Identities=25%  Similarity=0.337  Sum_probs=61.3

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       119 l~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +.+|+++.|++|.|+||||..|+|+|.++|.|||++|+||++..  .++ +..+++.++|||++|.+|...
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~--~~~-~~~~~~~v~IRG~~Ir~i~lP   70 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTL--KNR-EPVQLETLSIRGNNIRYFILP   70 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEEC--TTS-CCEEEEEEEECGGGEEEEECC
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEc--CCC-CEEEcccEEEcCCEEEEEECC
Confidence            46899999999999999999999999999999999999999975  333 567899999999999999654

>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.67  E-value=6.3e-17  Score=114.31  Aligned_cols=63  Identities=16%  Similarity=0.295  Sum_probs=58.8

Q ss_pred             CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           12 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        12 ~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ...|.++|+++++++|+|+|+||++|.|+|.|||+|||++|+||.|+..++....+|.++|+.
T Consensus         5 ~~~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~~~v~iRG   67 (76)
T d1th7a1           5 AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRG   67 (76)
T ss_dssp             CHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECG
T ss_pred             cccHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCcccCcceEEEEC
Confidence            345999999999999999999999999999999999999999999999888888999999965

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

Probab=99.63  E-value=1.3e-16  Score=116.39  Aligned_cols=72  Identities=42%  Similarity=0.775  Sum_probs=60.7

Q ss_pred             CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec---------------CccccccccEEEeee
Q psy800           11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD---------------SHLLSYFASDLINFI   75 (204)
Q Consensus        11 ~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~---------------~~~~~~lG~vlIn~~   75 (204)
                      .+..|+++|+++++|+|+|++++|++|.|+|.|||+||||+|+||.|+..               ....+++|.+||.. 
T Consensus         2 ~~~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG-   80 (92)
T d2fwka1           2 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSG-   80 (92)
T ss_dssp             CCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECG-
T ss_pred             CccChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeC-
Confidence            46789999999999999999999999999999999999999999999852               12456789999955 


Q ss_pred             cccceeec
Q psy800           76 WGLPMITP   83 (204)
Q Consensus        76 ~g~~~~~P   83 (204)
                      ..++++.|
T Consensus        81 ~~Vv~I~p   88 (92)
T d2fwka1          81 NNVAMLVP   88 (92)
T ss_dssp             GGEEEEES
T ss_pred             CEEEEEEe
Confidence            23355555

>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.59  E-value=9.9e-16  Score=106.89  Aligned_cols=59  Identities=25%  Similarity=0.413  Sum_probs=53.2

Q ss_pred             cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      +-.+|+++++|+|.|+|+||++|.|+|.|||+|||++|+||+|+.+++ ...+|.++|+.
T Consensus         3 ~~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~~-~~~~g~v~iRG   61 (71)
T d1i8fa_           3 LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN-VYKRGTMVVRG   61 (71)
T ss_dssp             HHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETTE-EEEEEEEEECG
T ss_pred             HhHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECCC-EEEcceEEEeC
Confidence            357899999999999999999999999999999999999999998765 45689999854

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.1e-15  Score=106.90  Aligned_cols=61  Identities=13%  Similarity=0.167  Sum_probs=57.1

Q ss_pred             CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      .|+++|+++.|++|.|+|+||++|.|+|.+||.|||++|+||.|+..++....+|+++|+.
T Consensus         2 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~v~IRG   62 (72)
T d1d3ba_           2 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRG   62 (72)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECG
T ss_pred             CchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCeEEEEC
Confidence            5999999999999999999999999999999999999999999998777777889999954

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.58  E-value=1.4e-15  Score=105.40  Aligned_cols=56  Identities=20%  Similarity=0.313  Sum_probs=51.7

Q ss_pred             HHhhcCCEEEEEEe-CCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           19 VDKCIGSRIHIIMK-NDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        19 L~~~~~k~V~V~l~-~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      |+++++++|.|+|| +|++|+|+|.|||+|||++|+||+|..+++....+|.++|+.
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~IRG   57 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRC   57 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECG
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCcccCcCeEEEEC
Confidence            57899999999999 568999999999999999999999999988888999999954

>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.56  E-value=3.6e-15  Score=114.92  Aligned_cols=64  Identities=16%  Similarity=0.410  Sum_probs=57.0

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800          119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       119 l~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      +..|++++|++|.|+|+||+.|.|+|.+||+|||++|+||++.    ++   .+++.++|||++|.+|...
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~----~~---~k~~~v~IRG~~I~~I~~~   65 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK----AG---EKFNRVFIMYRYIVHIDST   65 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEET----TC---CEEEEEEECGGGEEEEEEC
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEEC----CC---CcccEEEEeCCeEEEEEcc
Confidence            4689999999999999999999999999999999999999984    22   2578999999999999643

>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=4.8e-15  Score=108.45  Aligned_cols=61  Identities=23%  Similarity=0.467  Sum_probs=51.5

Q ss_pred             CcHHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC--------------ccccccccEEEee
Q psy800           14 LPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS--------------HLLSYFASDLINF   74 (204)
Q Consensus        14 ~P~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~--------------~~~~~lG~vlIn~   74 (204)
                      .|+++|.+++  +++|+|.+++|+.+.|+|.|||+||||||+||+|++..              ...+.+|.+||+.
T Consensus         2 GPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRG   78 (93)
T d1b34b_           2 GPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRG   78 (93)
T ss_dssp             CHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECG
T ss_pred             CcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeC
Confidence            5999999999  89999999999999999999999999999999998631              1235688888843

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1.1e-14  Score=103.82  Aligned_cols=55  Identities=20%  Similarity=0.390  Sum_probs=47.4

Q ss_pred             HHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec----------CccccccccEEEe
Q psy800           19 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD----------SHLLSYFASDLIN   73 (204)
Q Consensus        19 L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~----------~~~~~~lG~vlIn   73 (204)
                      |.++++++|.|+++|||+|.|+|.|||+||||+|+||+|+..          ....+.+|.++|.
T Consensus         3 L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IR   67 (81)
T d1d3bb_           3 MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLR   67 (81)
T ss_dssp             CGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEEC
T ss_pred             hHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEe
Confidence            468999999999999999999999999999999999999852          1134678888883

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=4.5e-13  Score=95.21  Aligned_cols=59  Identities=20%  Similarity=0.189  Sum_probs=54.6

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        16 ~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      ..||+++.|++|.|+|++|.+|.|+|.++|.|||++|+||.+...++....+++++|+.
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG   61 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRG   61 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECG
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcC
Confidence            47899999999999999999999999999999999999999998777778899999944

>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.18  E-value=1.2e-11  Score=94.90  Aligned_cols=55  Identities=16%  Similarity=0.424  Sum_probs=48.3

Q ss_pred             HHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800           16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF   74 (204)
Q Consensus        16 ~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~   74 (204)
                      +..|+++++++|.|+|+||++|.|+|.+||+|||++|+||.+..++    .+++++|+.
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~~~----k~~~v~IRG   56 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGE----KFNRVFIMY   56 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETTCC----EEEEEEECG
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECCCC----cccEEEEeC
Confidence            4689999999999999999999999999999999999999985433    467888744

>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.97  E-value=0.0053  Score=40.87  Aligned_cols=33  Identities=21%  Similarity=0.431  Sum_probs=26.6

Q ss_pred             HHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccce
Q psy800          121 LVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNM  153 (204)
Q Consensus       121 ~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNl  153 (204)
                      +|+++.  ..+|+|.|.||-.+.|.+.|||+|.=|
T Consensus         6 fLn~~rk~~~~VtifL~nGvkl~G~I~~fD~ftvL   40 (66)
T d1u1sa1           6 YLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVIL   40 (66)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEE
T ss_pred             HHHHHHHcCCcEEEEEEcCcEEEEEEEEEcceEEE
Confidence            344443  456999999999999999999999743

>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.83  E-value=0.0064  Score=40.42  Aligned_cols=36  Identities=25%  Similarity=0.499  Sum_probs=29.0

Q ss_pred             HHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEec
Q psy800           17 ELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLE   53 (204)
Q Consensus        17 ~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~   53 (204)
                      .||+.+-  +.+|.|.|.+|-.++|.+.|||.|. +.|+
T Consensus         5 ~fLn~~rk~~~~VtifL~nGvkl~G~I~~fD~ft-vLL~   42 (66)
T d1u1sa1           5 PYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   42 (66)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHHHcCCcEEEEEEcCcEEEEEEEEEcceE-EEEE
Confidence            3555544  4689999999999999999999998 4453

>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.44  E-value=0.014  Score=37.98  Aligned_cols=31  Identities=16%  Similarity=0.401  Sum_probs=26.5

Q ss_pred             CCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800          127 GSRIHIIMKNDKEIVGTLNGFDDFVNMLLED  157 (204)
Q Consensus       127 ~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d  157 (204)
                      ..+|+|.|.||-.+.|.+.|||+|.=+.-.+
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~   44 (60)
T d1kq1a_          14 QTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQ   44 (60)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             CCcEEEEEECCcEEEEEEEEEcceEEEEEeC
Confidence            4679999999999999999999998555444

>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: C-terminal domain of transcriptional repressors
family: Biotin repressor (BirA)
domain: Biotin repressor/biotin holoenzyme synthetase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.22  E-value=0.038  Score=33.81  Aligned_cols=32  Identities=38%  Similarity=0.601  Sum_probs=28.3

Q ss_pred             hcCCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800          125 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED  157 (204)
Q Consensus       125 ~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d  157 (204)
                      |++++|.|.. ++++++|+..|+|+.-.|+|+.
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t   32 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQ   32 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEE
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEE
Confidence            5789999976 6678999999999999999975

>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.70  E-value=0.032  Score=36.23  Aligned_cols=35  Identities=14%  Similarity=0.396  Sum_probs=28.4

Q ss_pred             HHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeE
Q psy800           17 ELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNML   51 (204)
Q Consensus        17 ~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlv   51 (204)
                      .||+.+-  +++|.|.|.+|-.++|.+.|||.|.=+.
T Consensus         5 ~fln~lr~~~~~VtifL~nGvkl~G~I~~fD~ftvlL   41 (60)
T d1kq1a_           5 KALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSL   41 (60)
T ss_dssp             HHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHHcCCcEEEEEECCcEEEEEEEEEcceEEEE
Confidence            3454444  5799999999999999999999999443

>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: LSM14 N-terminal domain-like
domain: LSM14 homolog A (Lsm14a)
species: Zebrafish (Danio rerio) [TaxId: 7955]

Probab=93.88  E-value=0.14  Score=34.86  Aligned_cols=65  Identities=25%  Similarity=0.407  Sum_probs=50.8

Q ss_pred             hcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecC---CCe---eeeeeCeEEEeCCcEEEEccc
Q psy800          125 CIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTP---EGR---RITKLDQILLNGNNITMLGLH  189 (204)
Q Consensus       125 ~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~---~~~---~~~~lg~ilIRGdnI~~I~~~  189 (204)
                      |+|++|.+..+.+-+|+|+|...| +---+.|+|+.-.-++.   +++   ...-++.++.||+.|--+...
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~   73 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVC   73 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEES
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEec
Confidence            689999999999999999999999 45668999988764321   110   244578999999999887654

>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: PF1955-like
domain: Hypothetical protein PF1955
species: Pyrococcus furiosus [TaxId: 2261]

Probab=92.29  E-value=0.34  Score=31.18  Aligned_cols=59  Identities=27%  Similarity=0.528  Sum_probs=41.5

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEE
Q psy800          120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITML  186 (204)
Q Consensus       120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I  186 (204)
                      +.|+++.+++|-|-......+.|+|..||+-. +.|+|++.+.    |.   +-..++++=|.|--|
T Consensus         5 ktL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~----GN---k~k~llv~idD~nWi   63 (66)
T d1ycya1           5 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI----GN---RGKQMLIGLEDINWI   63 (66)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT----EE---EEEEEEEEGGGEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHh----cc---ccceeEEEeccceeE
Confidence            46889999999999999999999999999887 7889999864    21   223556665555443

>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: PF1955-like
domain: Hypothetical protein PF1955
species: Pyrococcus furiosus [TaxId: 2261]

Probab=90.02  E-value=0.22  Score=32.11  Aligned_cols=43  Identities=30%  Similarity=0.573  Sum_probs=34.7

Q ss_pred             HHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec
Q psy800           17 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD   60 (204)
Q Consensus        17 ~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~   60 (204)
                      +.|++.-+++|-|-..+...+.|+|.-||+-. +.|+|+..+..
T Consensus         5 ktL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~G   47 (66)
T d1ycya1           5 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIG   47 (66)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTE
T ss_pred             HHHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHhc
Confidence            46788889999999999999999999999988 88899998764

>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: C-terminal domain of transcriptional repressors
family: Biotin repressor (BirA)
domain: Biotin repressor/biotin holoenzyme synthetase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=88.61  E-value=0.38  Score=29.00  Aligned_cols=32  Identities=38%  Similarity=0.553  Sum_probs=28.1

Q ss_pred             hcCCEEEEEEeCCeEEEEEEEeecCeeeeEecc
Q psy800           22 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED   54 (204)
Q Consensus        22 ~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~   54 (204)
                      |++|+|.|. .+++++.|+-.|.|..=.|+|+.
T Consensus         1 f~gk~V~v~-~g~~~i~G~a~gId~~G~Lll~t   32 (47)
T d1biaa2           1 FINRPVKLI-IGDKEIFGISRGIDKQGALLLEQ   32 (47)
T ss_dssp             TTTSEEEEE-ETTEEEEEEEEEECTTSCEEEEE
T ss_pred             CCCCEEEEE-ECCeEEEEEEeeECCCCcEEEEE
Confidence            679999996 46689999999999999999863

>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]}

class: All beta proteins
fold: Sm-like fold
superfamily: YhbC-like, C-terminal domain
family: YhbC-like, C-terminal domain
domain: Hypothetical protein SP14.3 (SP0552)
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=82.19  E-value=0.58  Score=30.47  Aligned_cols=33  Identities=24%  Similarity=0.323  Sum_probs=26.2

Q ss_pred             cHHHHHhhcCCEEEEEEeC---C-eEEEEEEEeecCee
Q psy800           15 PLELVDKCIGSRIHIIMKN---D-KEIVGTLNGFDDFV   48 (204)
Q Consensus        15 P~~~L~~~~~k~V~V~l~~---g-~~~~G~L~gfD~~m   48 (204)
                      |.+| ..++|+.|.|+|+.   | +.+.|.|.++|+-.
T Consensus         6 ~~~f-~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~   42 (74)
T d1ib8a1           6 KDAV-AGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE   42 (74)
T ss_dssp             HHHH-HHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE
T ss_pred             HHHH-HHhCCCEEEEEEecccCCceEEEEEEEeecCCe
Confidence            3444 46899999999873   4 79999999999853