Psyllid ID: psy15782

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
Protein Sequence
MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR
Secondary Structure (PSIPRED)
ccccccccccEEEEEEccccEEEEEEcEEcccccEEEEEEEEEEccccEEEccEEEEEccEEEEEEccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
HHHHHcccccEEEEEEccccEEEEEEEEEcccccEEEEEEEEEccccccEEEEEEEEcHHHEEEEEccccccHHHHcccccccHHHHHHHccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MNFLMKLSHETVTIElkngtqvhgTIQGVDVAMNTHLKTVKMtvkgkepttldsislrgnniryyilpdslpletlliddaprskgkrdsrrgggaggargrggrggrgggrggrgrggprgrggpprr
Flexible Loop (DISEMBL)
MNFLMKLSHETVTielkngtqvhgTIQGVDVAMNTHLKTVkmtvkgkepttldsislrgNNIRYYILPDSLPLETLLIddaprskgkrdsrrgggaggargrggrggrgggrggrgrggprgrggpprr
Low Complexity Region (SEG)
MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDDAPRSKGKRDSrrgggaggargrggrggrgggrggrgrggprgrggpprr
Disordered region (IsUnstruct)
********HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLI***************************************************
Disordered Region (DISOPRED)
MNFLMK*SHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETL*****************************************************
Disordered Region (DISEMBL)
MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDDA************************************************
Disordered Region (DISPRO)
MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDDA************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	129	2.2.26 [Sep-21-2011]
Q9VU02	124	Probable small nuclear ri	yes	N/A	0.666	0.693	0.779	2e-36
P62315	119	Small nuclear ribonucleop	yes	N/A	0.666	0.722	0.755	9e-35
Q4R5F6	119	Small nuclear ribonucleop	N/A	N/A	0.666	0.722	0.755	9e-35
P62314	119	Small nuclear ribonucleop	yes	N/A	0.666	0.722	0.755	9e-35
Q3ZC10	119	Small nuclear ribonucleop	yes	N/A	0.666	0.722	0.755	9e-35
Q10013	126	Probable small nuclear ri	yes	N/A	0.643	0.658	0.783	4e-32
O42661	117	Small nuclear ribonucleop	yes	N/A	0.666	0.735	0.720	1e-31
Q02260	146	Small nuclear ribonucleop	yes	N/A	0.891	0.787	0.376	3e-14
Q43582	146	Probable U6 snRNA-associa	N/A	N/A	0.782	0.691	0.351	2e-08
Q9UUC6	97	Small nuclear ribonucleop	no	N/A	0.550	0.731	0.346	6e-07

>sp|Q9VU02|SMD1_DROME Probable small nuclear ribonucleoprotein Sm D1 OS=Drosophila melanogaster GN=SmD1 PE=1 SV=1

 Score =  150 bits (379), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 67/86 (77%), Positives = 80/86 (93%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQ+HGTI GVDVAMNTHLK+V+MT+K ++P  L+++S+RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQIHGTITGVDVAMNTHLKSVRMTIKNRDPVHLETLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGKR 88
          RY+ILPDSLPLETLLIDD P+SK K+
Sbjct: 66 RYFILPDSLPLETLLIDDTPKSKTKK 91

Essential for pre-mRNA splicing. Implicated in the formation of stable, biologically active snRNP structures.
Drosophila melanogaster (taxid: 7227)

>sp|P62315|SMD1_MOUSE Small nuclear ribonucleoprotein Sm D1 OS=Mus musculus GN=Snrpd1 PE=2 SV=1

 Score =  145 bits (365), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 65/86 (75%), Positives = 77/86 (89%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGKR 88
          RY+ILPDSLPL+TLL+D  P+ K K+
Sbjct: 66 RYFILPDSLPLDTLLVDVEPKVKSKK 91

May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA.

Mus musculus (taxid: 10090)

>sp|Q4R5F6|SMD1_MACFA Small nuclear ribonucleoprotein Sm D1 OS=Macaca fascicularis GN=SNRPD1 PE=3 SV=1

 Score =  145 bits (365), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 65/86 (75%), Positives = 77/86 (89%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGKR 88
          RY+ILPDSLPL+TLL+D  P+ K K+
Sbjct: 66 RYFILPDSLPLDTLLVDVEPKVKSKK 91

May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA.

Macaca fascicularis (taxid: 9541)

>sp|P62314|SMD1_HUMAN Small nuclear ribonucleoprotein Sm D1 OS=Homo sapiens GN=SNRPD1 PE=1 SV=1

 Score =  145 bits (365), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 65/86 (75%), Positives = 77/86 (89%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGKR 88
          RY+ILPDSLPL+TLL+D  P+ K K+
Sbjct: 66 RYFILPDSLPLDTLLVDVEPKVKSKK 91

May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA.

Homo sapiens (taxid: 9606)

>sp|Q3ZC10|SMD1_BOVIN Small nuclear ribonucleoprotein Sm D1 OS=Bos taurus GN=SNRPD1 PE=3 SV=1

 Score =  145 bits (365), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 65/86 (75%), Positives = 77/86 (89%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGKR 88
          RY+ILPDSLPL+TLL+D  P+ K K+
Sbjct: 66 RYFILPDSLPLDTLLVDVEPKVKSKK 91

May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA.

Bos taurus (taxid: 9913)

>sp|Q10013|SMD1_CAEEL Probable small nuclear ribonucleoprotein Sm D1 OS=Caenorhabditis elegans GN=snr-3 PE=3 SV=1

 Score =  136 bits (342), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 65/83 (78%), Positives = 70/83 (84%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETV IELKNGTQV GTI GVDVAMNTHL+ V MTVK KEP  LD++S+RGNNI
Sbjct: 6  FLMKLSHETVNIELKNGTQVSGTIMGVDVAMNTHLRAVSMTVKNKEPVKLDTLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSK 85
          RY ILPD L L+TLLIDD PR K
Sbjct: 66 RYIILPDPLALDTLLIDDEPRKK 88

Essential for pre-mRNA splicing. Implicated in the formation of stable, biologically active snRNP structures.

Caenorhabditis elegans (taxid: 6239)

>sp|O42661|SMD1_SCHPO Small nuclear ribonucleoprotein Sm D1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smd1 PE=1 SV=1

 Score =  135 bits (339), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 62/86 (72%), Positives = 76/86 (88%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKL++ETV+IELKNGT VHGTI  VD+ MNTHLK VKMTVKG+EP  ++++S+RGNNI
Sbjct: 6  FLMKLTNETVSIELKNGTIVHGTITSVDMQMNTHLKAVKMTVKGREPVPVETLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGKR 88
          RYYILPDSLPL+TLLIDD+ + K K+
Sbjct: 66 RYYILPDSLPLDTLLIDDSTKPKQKK 91

Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site.

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

>sp|Q02260|SMD1_YEAST Small nuclear ribonucleoprotein Sm D1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SMD1 PE=1 SV=1

 Score = 77.0 bits (188), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 55/146 (37%), Positives = 69/146 (47%), Gaps = 31/146 (21%)

Query: 1   MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK--------------- 45
           +NFL KL +E VTIELKNGT V GT+Q V   MN  L  VK+T+                
Sbjct: 4   VNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQPRLNKLNSNGIAMA 63

Query: 46  ------GKEPT------TLDSISLRGNNIRYYILPDSLPLETLLIDDAPRSKGKRDSRRG 93
                 G++PT      +L  I++RGN IR  ILPDSL L++LL+D     K     RR 
Sbjct: 64  SLYLTGGQQPTASDNIASLQYINIRGNTIRQIILPDSLNLDSLLVD----QKQLNSLRRS 119

Query: 94  GGAGGARGRGGRGGRGGGRGGRGRGG 119
           G       +  R   G     R R G
Sbjct: 120 GQIANDPSKKRRRDFGAPANKRPRRG 145

Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Also binds telomerase RNA and is required for its accumulation.

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

>sp|Q43582|LSM4_TOBAC Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1

 Score = 57.8 bits (138), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/108 (35%), Positives = 50/108 (46%), Gaps = 7/108 (6%)

Query: 12  VTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEPTTLDSISLRGNNIRYYILPDS 70
           + +ELKNG   +G +   D  MN HL+ V  T K G     +    +RGN I+Y  +PD 
Sbjct: 15  MLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYVRGNTIKYLRVPDE 74

Query: 71  LPLETLLIDDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRG 118
           +      ID        R  R+  G G AR RGGR     GR  +G G
Sbjct: 75  V------IDKVQEEAKSRTDRKPPGVGRARARGGRDDSAVGRQPKGIG 116

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

Nicotiana tabacum (taxid: 4097)

>sp|Q9UUC6|SMD3_SCHPO Small nuclear ribonucleoprotein Sm D3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smd3 PE=1 SV=1

 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 4/75 (5%)

Query: 1  MNFLMKLSHET----VTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSIS 56
          M+  +KL HET    VT+EL+NG+   G +   +  MN  ++ + +T +    + LD + 
Sbjct: 1  MSLCIKLLHETQGHIVTMELENGSTYRGKLIEAEDNMNCQMRDISVTARDGRVSHLDQVY 60

Query: 57 LRGNNIRYYILPDSL 71
          +RG++IR+ I+PD L
Sbjct: 61 IRGSHIRFLIVPDML 75

Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site.

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

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	129
158285999	126	AGAP007246-PA [Anopheles gambiae str. PE	0.666	0.682	0.837	4e-37
170064026	126	small nuclear ribonucleoprotein Sm D1 [C	0.697	0.714	0.824	2e-36
242022404	122	small nuclear ribonucleoprotein sm D1, p	0.666	0.704	0.813	2e-36
157105264	126	small nuclear ribonucleoprotein sm d1 [A	0.697	0.714	0.802	1e-35
198464926	125	GA10544 [Drosophila pseudoobscura pseudo	0.666	0.688	0.790	8e-35
66509459	123	PREDICTED: probable small nuclear ribonu	0.620	0.650	0.875	1e-34
156538102	123	PREDICTED: probable small nuclear ribonu	0.620	0.650	0.875	1e-34
17864386	124	small ribonucleoprotein particle protein	0.666	0.693	0.779	2e-34
194870009	124	GG13810 [Drosophila erecta] gi|190654350	0.666	0.693	0.779	2e-34
391333356	120	PREDICTED: probable small nuclear ribonu	0.674	0.725	0.784	2e-34

>gi|158285999|ref|XP_308555.4| AGAP007246-PA [Anopheles gambiae str. PEST] gi|157020260|gb|EAA04383.5| AGAP007246-PA [Anopheles gambiae str. PEST]

 Score =  159 bits (402), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 72/86 (83%), Positives = 81/86 (94%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQVHGTI GVDVAMNTHLK VKMT+K ++P TLDS+S+RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVAMNTHLKAVKMTIKNRDPVTLDSLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGKR 88
          RYYILPDSLPLETLLIDDAP+++ K+
Sbjct: 66 RYYILPDSLPLETLLIDDAPKTRAKK 91

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170064026|ref|XP_001867355.1| small nuclear ribonucleoprotein Sm D1 [Culex quinquefasciatus] gi|167881462|gb|EDS44845.1| small nuclear ribonucleoprotein Sm D1 [Culex quinquefasciatus]

 Score =  157 bits (396), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 75/91 (82%), Positives = 83/91 (91%), Gaps = 1/91 (1%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQVHGTI GVDVAMNTHLK VKMT+K ++P  LDS+S+RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVAMNTHLKAVKMTIKNRDPVQLDSLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGK-RDSRR 92
          RYYILPDSLPLETLLIDDAP+++ K RDS R
Sbjct: 66 RYYILPDSLPLETLLIDDAPKTRAKKRDSNR 96

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242022404|ref|XP_002431630.1| small nuclear ribonucleoprotein sm D1, putative [Pediculus humanus corporis] gi|212516938|gb|EEB18892.1| small nuclear ribonucleoprotein sm D1, putative [Pediculus humanus corporis]

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 70/86 (81%), Positives = 79/86 (91%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQVHGTI GVDVAMNTHLK VKMT+K KEP  L+++++RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVAMNTHLKAVKMTIKNKEPVMLETLTIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGKR 88
          RY+ILPDSLPLETLLIDD P+SK K+
Sbjct: 66 RYFILPDSLPLETLLIDDTPKSKAKK 91

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157105264|ref|XP_001648790.1| small nuclear ribonucleoprotein sm d1 [Aedes aegypti] gi|157118312|ref|XP_001653165.1| small nuclear ribonucleoprotein sm d1 [Aedes aegypti] gi|108880134|gb|EAT44359.1| AAEL004263-PA [Aedes aegypti] gi|108883288|gb|EAT47513.1| AAEL001382-PA [Aedes aegypti]

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 73/91 (80%), Positives = 83/91 (91%), Gaps = 1/91 (1%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQVHGTI GVDVAMNTHLK VKMT+K ++P  LDS+S+RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVAMNTHLKAVKMTIKNRDPVQLDSLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGK-RDSRR 92
          RYYILPDSLPLETLLIDDAP+++ K R++ R
Sbjct: 66 RYYILPDSLPLETLLIDDAPKTRAKKREANR 96

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198464926|ref|XP_001353417.2| GA10544 [Drosophila pseudoobscura pseudoobscura] gi|198149939|gb|EAL30924.2| GA10544 [Drosophila pseudoobscura pseudoobscura]

 Score =  151 bits (382), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 68/86 (79%), Positives = 80/86 (93%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQ+HGTI GVDVAMNTHLK+V+MT+K ++P  L+S+S+RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQIHGTITGVDVAMNTHLKSVRMTIKNRDPVHLESLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGKR 88
          RY+ILPDSLPLETLLIDD P+SK K+
Sbjct: 66 RYFILPDSLPLETLLIDDTPKSKTKK 91

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66509459|ref|XP_624938.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D1-like [Apis mellifera] gi|340728072|ref|XP_003402355.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D1-like [Bombus terrestris] gi|350424394|ref|XP_003493781.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D1-like [Bombus impatiens] gi|383861733|ref|XP_003706339.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D1-like [Megachile rotundata]

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 70/80 (87%), Positives = 75/80 (93%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQVHGTI GVDVAMNTHLKTVKMT+K ++P  LD++SLRGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVAMNTHLKTVKMTIKNRDPVQLDTLSLRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAP 82
          RYYILPDSLPLETLLIDD P
Sbjct: 66 RYYILPDSLPLETLLIDDTP 85

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156538102|ref|XP_001608160.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D1-like [Nasonia vitripennis]

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 70/80 (87%), Positives = 75/80 (93%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQVHGTI GVDVAMNTHLKTVKMT+K ++P  LD++SLRGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVAMNTHLKTVKMTIKNRDPVQLDTLSLRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAP 82
          RYYILPDSLPLETLLIDD P
Sbjct: 66 RYYILPDSLPLETLLIDDTP 85

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17864386|ref|NP_524774.1| small ribonucleoprotein particle protein SmD1 [Drosophila melanogaster] gi|194747611|ref|XP_001956245.1| GF25112 [Drosophila ananassae] gi|195327205|ref|XP_002030312.1| GM24635 [Drosophila sechellia] gi|195493908|ref|XP_002094615.1| GE20102 [Drosophila yakuba] gi|195589894|ref|XP_002084684.1| GD12704 [Drosophila simulans] gi|33112453|sp|Q9VU02.1|SMD1_DROME RecName: Full=Probable small nuclear ribonucleoprotein Sm D1; Short=Sm-D1; AltName: Full=snRNP core protein D1 gi|7294552|gb|AAF49893.1| small ribonucleoprotein particle protein SmD1 [Drosophila melanogaster] gi|189181777|gb|ACD81665.1| FI02845p [Drosophila melanogaster] gi|190623527|gb|EDV39051.1| GF25112 [Drosophila ananassae] gi|194119255|gb|EDW41298.1| GM24635 [Drosophila sechellia] gi|194180716|gb|EDW94327.1| GE20102 [Drosophila yakuba] gi|194196693|gb|EDX10269.1| GD12704 [Drosophila simulans]

 Score =  150 bits (379), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 67/86 (77%), Positives = 80/86 (93%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQ+HGTI GVDVAMNTHLK+V+MT+K ++P  L+++S+RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQIHGTITGVDVAMNTHLKSVRMTIKNRDPVHLETLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGKR 88
          RY+ILPDSLPLETLLIDD P+SK K+
Sbjct: 66 RYFILPDSLPLETLLIDDTPKSKTKK 91

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194870009|ref|XP_001972567.1| GG13810 [Drosophila erecta] gi|190654350|gb|EDV51593.1| GG13810 [Drosophila erecta]

 Score =  150 bits (379), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 67/86 (77%), Positives = 80/86 (93%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          FLMKLSHETVTIELKNGTQ+HGTI GVDVAMNTHLK+V+MT+K ++P  L+++S+RGNNI
Sbjct: 6  FLMKLSHETVTIELKNGTQIHGTITGVDVAMNTHLKSVRMTIKNRDPVHLETLSIRGNNI 65

Query: 63 RYYILPDSLPLETLLIDDAPRSKGKR 88
          RY+ILPDSLPLETLLIDD P+SK K+
Sbjct: 66 RYFILPDSLPLETLLIDDTPKSKTKK 91

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|391333356|ref|XP_003741082.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D1-like [Metaseiulus occidentalis]

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 69/88 (78%), Positives = 80/88 (90%), Gaps = 1/88 (1%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEPTTLDSISLRGNN 61
          FLMKLSHETVTIELKNGTQVHGT+ GVDVAMNTHLK VKMT+K   EP +L+++S+RGNN
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTVTGVDVAMNTHLKNVKMTLKNAAEPVSLETLSIRGNN 65

Query: 62 IRYYILPDSLPLETLLIDDAPRSKGKRD 89
          IRYYILPDSLPLETLLIDD P++K K++
Sbjct: 66 IRYYILPDSLPLETLLIDDTPKAKKKKE 93

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

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	129
FB|FBgn0261933	124	SmD1 "Small ribonucleoprotein	0.697	0.725	0.758	9.5e-34
ZFIN|ZDB-GENE-020419-14	119	snrpd1 "small nuclear ribonucl	0.682	0.739	0.761	8.5e-33
UNIPROTKB|Q3ZC10	119	SNRPD1 "Small nuclear ribonucl	0.682	0.739	0.738	6e-32
UNIPROTKB|E2RIW7	119	SNRPD1 "Uncharacterized protei	0.682	0.739	0.738	6e-32
UNIPROTKB|P62314	119	SNRPD1 "Small nuclear ribonucl	0.682	0.739	0.738	6e-32
UNIPROTKB|F2Z5G9	119	SNRPD1 "Uncharacterized protei	0.682	0.739	0.738	6e-32
MGI|MGI:98344	119	Snrpd1 "small nuclear ribonucl	0.682	0.739	0.738	6e-32
RGD|1306345	119	Snrpd1 "small nuclear ribonucl	0.682	0.739	0.738	6e-32
UNIPROTKB|F1NLM5	121	SNRPD1 "Uncharacterized protei	0.666	0.710	0.755	7.7e-32
TAIR|locus:2091102	114	AT3G07590 "AT3G07590" [Arabido	0.682	0.771	0.761	7.7e-32

FB|FBgn0261933 SmD1 "Small ribonucleoprotein particle protein SmD1" [Drosophila melanogaster (taxid:7227)]

 Score = 367 (134.2 bits), Expect = 9.5e-34, P = 9.5e-34
 Identities = 69/91 (75%), Positives = 83/91 (91%)

Query:     1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
             + FLMKLSHETVTIELKNGTQ+HGTI GVDVAMNTHLK+V+MT+K ++P  L+++S+RGN
Sbjct:     4 VRFLMKLSHETVTIELKNGTQIHGTITGVDVAMNTHLKSVRMTIKNRDPVHLETLSIRGN 63

Query:    61 NIRYYILPDSLPLETLLIDDAPRSKGKR-DS 90
             NIRY+ILPDSLPLETLLIDD P+SK K+ DS
Sbjct:    64 NIRYFILPDSLPLETLLIDDTPKSKTKKKDS 94

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

GO:0005681 "spliceosomal complex" evidence=ISS

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

GO:0005634 "nucleus" evidence=IDA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0071011 "precatalytic spliceosome" evidence=IDA

ZFIN|ZDB-GENE-020419-14 snrpd1 "small nuclear ribonucleoprotein D1 polypeptide" [Danio rerio (taxid:7955)]

 Score = 358 (131.1 bits), Expect = 8.5e-33, P = 8.5e-33
 Identities = 67/88 (76%), Positives = 79/88 (89%)

Query:     1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
             + FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EPT L+S+S+RGN
Sbjct:     4 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPTQLESLSIRGN 63

Query:    61 NIRYYILPDSLPLETLLIDDAPRSKGKR 88
             NIRY+ILPDSLPL+TLL+D  P+ K K+
Sbjct:    64 NIRYFILPDSLPLDTLLVDIEPKVKSKK 91

GO:0007507 "heart development" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|Q3ZC10 SNRPD1 "Small nuclear ribonucleoprotein Sm D1" [Bos taurus (taxid:9913)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 65/88 (73%), Positives = 78/88 (88%)

Query:     1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
             + FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGN
Sbjct:     4 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGN 63

Query:    61 NIRYYILPDSLPLETLLIDDAPRSKGKR 88
             NIRY+ILPDSLPL+TLL+D  P+ K K+
Sbjct:    64 NIRYFILPDSLPLDTLLVDVEPKVKSKK 91

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|E2RIW7 SNRPD1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 65/88 (73%), Positives = 78/88 (88%)

Query:     1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
             + FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGN
Sbjct:     4 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGN 63

Query:    61 NIRYYILPDSLPLETLLIDDAPRSKGKR 88
             NIRY+ILPDSLPL+TLL+D  P+ K K+
Sbjct:    64 NIRYFILPDSLPLDTLLVDVEPKVKSKK 91

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

UNIPROTKB|P62314 SNRPD1 "Small nuclear ribonucleoprotein Sm D1" [Homo sapiens (taxid:9606)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 65/88 (73%), Positives = 78/88 (88%)

Query:     1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
             + FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGN
Sbjct:     4 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGN 63

Query:    61 NIRYYILPDSLPLETLLIDDAPRSKGKR 88
             NIRY+ILPDSLPL+TLL+D  P+ K K+
Sbjct:    64 NIRYFILPDSLPLDTLLVDVEPKVKSKK 91

GO:0005515 "protein binding" evidence=IPI

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0005689 "U12-type spliceosomal complex" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;TAS

GO:0003723 "RNA binding" evidence=TAS

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

GO:0005634 "nucleus" evidence=TAS

GO:0000245 "spliceosomal complex assembly" evidence=TAS

GO:0000387 "spliceosomal snRNP assembly" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0034660 "ncRNA metabolic process" evidence=TAS

UNIPROTKB|F2Z5G9 SNRPD1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 65/88 (73%), Positives = 78/88 (88%)

Query:     1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
             + FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGN
Sbjct:     4 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGN 63

Query:    61 NIRYYILPDSLPLETLLIDDAPRSKGKR 88
             NIRY+ILPDSLPL+TLL+D  P+ K K+
Sbjct:    64 NIRYFILPDSLPLDTLLVDVEPKVKSKK 91

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

MGI|MGI:98344 Snrpd1 "small nuclear ribonucleoprotein D1" [Mus musculus (taxid:10090)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 65/88 (73%), Positives = 78/88 (88%)

Query:     1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
             + FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGN
Sbjct:     4 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGN 63

Query:    61 NIRYYILPDSLPLETLLIDDAPRSKGKR 88
             NIRY+ILPDSLPL+TLL+D  P+ K K+
Sbjct:    64 NIRYFILPDSLPLDTLLVDVEPKVKSKK 91

GO:0005634 "nucleus" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=ISO

GO:0005737 "cytoplasm" evidence=IDA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

RGD|1306345 Snrpd1 "small nuclear ribonucleoprotein D1" [Rattus norvegicus (taxid:10116)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 65/88 (73%), Positives = 78/88 (88%)

Query:     1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
             + FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGN
Sbjct:     4 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGN 63

Query:    61 NIRYYILPDSLPLETLLIDDAPRSKGKR 88
             NIRY+ILPDSLPL+TLL+D  P+ K K+
Sbjct:    64 NIRYFILPDSLPLDTLLVDVEPKVKSKK 91

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005689 "U12-type spliceosomal complex" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA;ISO

UNIPROTKB|F1NLM5 SNRPD1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 349 (127.9 bits), Expect = 7.7e-32, P = 7.7e-32
 Identities = 65/86 (75%), Positives = 77/86 (89%)

Query:     3 FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
             FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGNNI
Sbjct:     8 FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 67

Query:    63 RYYILPDSLPLETLLIDDAPRSKGKR 88
             RY+ILPDSLPL+TLL+D  P+ K K+
Sbjct:    68 RYFILPDSLPLDTLLVDVEPKVKSKK 93

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

TAIR|locus:2091102 AT3G07590 "AT3G07590" [Arabidopsis thaliana (taxid:3702)]

 Score = 349 (127.9 bits), Expect = 7.7e-32, P = 7.7e-32
 Identities = 67/88 (76%), Positives = 78/88 (88%)

Query:     1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
             + FLMKL++ETV+IELKNGT VHGTI GVDV+MNTHLKTVKM++KGK P TLD +SLRGN
Sbjct:     4 VRFLMKLNNETVSIELKNGTVVHGTITGVDVSMNTHLKTVKMSLKGKNPVTLDHLSLRGN 63

Query:    61 NIRYYILPDSLPLETLLIDDAPRSKGKR 88
             NIRYYILPDSL LETLL++D PR K K+
Sbjct:    64 NIRYYILPDSLNLETLLVEDTPRVKPKK 91

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

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

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0010388 "cullin deneddylation" evidence=RCA

---

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)
Q10013	SMD1_CAEEL	No assigned EC number	0.7831	0.6434	0.6587	yes	N/A
Q4R5F6	SMD1_MACFA	No assigned EC number	0.7558	0.6666	0.7226	N/A	N/A
Q02260	SMD1_YEAST	No assigned EC number	0.3767	0.8914	0.7876	yes	N/A
P62314	SMD1_HUMAN	No assigned EC number	0.7558	0.6666	0.7226	yes	N/A
P62315	SMD1_MOUSE	No assigned EC number	0.7558	0.6666	0.7226	yes	N/A
Q9VU02	SMD1_DROME	No assigned EC number	0.7790	0.6666	0.6935	yes	N/A
Q3ZC10	SMD1_BOVIN	No assigned EC number	0.7558	0.6666	0.7226	yes	N/A
O42661	SMD1_SCHPO	No assigned EC number	0.7209	0.6666	0.7350	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	129
cd01724	92	cd01724, Sm_D1, Sm protein D1	8e-59
pfam01423	66	pfam01423, LSM, LSM domain	5e-20
smart00651	67	smart00651, Sm, snRNP Sm proteins	7e-19
cd01721	70	cd01721, Sm_D3, Sm protein D3	1e-14
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	1e-13
cd00600	63	cd00600, Sm_like, Sm and related proteins	5e-13
cd01723	76	cd01723, LSm4, Like-Sm protein 4	2e-10
cd01725	89	cd01725, LSm2, Like-Sm protein 2	6e-10
cd01733	78	cd01733, LSm10, Like-Sm protein 10	3e-09
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	5e-09
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	3e-07
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	5e-07
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	7e-07
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	9e-07
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	1e-06
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	3e-06
cd01722	69	cd01722, Sm_F, Sm protein F	4e-06
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	1e-05
cd01726	68	cd01726, LSm6, Like-Sm protein 6	4e-05
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	6e-05
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	1e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	3e-04
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	3e-04
pfam05918	543	pfam05918, API5, Apoptosis inhibitory protein 5 (A	4e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	5e-04
cd01732	76	cd01732, LSm5, Like-Sm protein 5	7e-04
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	8e-04
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	0.001
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	0.001

>gnl|CDD|212471 cd01724, Sm_D1, Sm protein D1

 Score =  176 bits (448), Expect = 8e-59
 Identities = 64/88 (72%), Positives = 78/88 (88%)

Query: 1  MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
          + FLMKLS+ETVTIELKNGT VHGTI GVDV+MNTHLK VK+T+KGK P +LD++S+RGN
Sbjct: 3  VRFLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGN 62

Query: 61 NIRYYILPDSLPLETLLIDDAPRSKGKR 88
          NIRY ILPDSL L+TLL+DD P++K K+
Sbjct: 63 NIRYIILPDSLNLDTLLVDDTPKAKAKK 90

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 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. Length = 92

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

 Score = 76.8 bits (190), Expect = 5e-20
 Identities = 27/66 (40%), Positives = 38/66 (57%)

Query: 2  NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNN 61
           FL KL  + VT+ELKNG ++ GT++G D  MN  L  V+ T+K  +   L  + +RGNN
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60

Query: 62 IRYYIL 67
          I     
Sbjct: 61 IVLISP 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|197820 smart00651, Sm, snRNP Sm proteins

 Score = 74.1 bits (183), Expect = 7e-19
 Identities = 31/67 (46%), Positives = 42/67 (62%), Gaps = 1/67 (1%)

Query: 2  NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEPTTLDSISLRGN 60
           FL KL  + V +ELKNG +  GT++G D  MN  L+ V+ TVK G++   L  + +RGN
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60

Query: 61 NIRYYIL 67
          NI Y IL
Sbjct: 61 NIVYIIL 67

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

>gnl|CDD|212468 cd01721, Sm_D3, Sm protein D3

 Score = 63.7 bits (156), Expect = 1e-14
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 4/68 (5%)

Query: 6  KLSHE----TVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNN 61
          KL HE     VT+ELK G    G +   +  MN  LK V +T +  + + L+ + +RG+ 
Sbjct: 3  KLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGKVSKLEQVYIRGSQ 62

Query: 62 IRYYILPD 69
          IR+ ILPD
Sbjct: 63 IRFIILPD 70

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 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. Length = 70

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

 Score = 61.2 bits (149), Expect = 1e-13
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 4/71 (5%)

Query: 1  MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTT----LDSIS 56
          ++FL KL ++ V ++LKNG +  GT+ G D  MN  L  V+  +              + 
Sbjct: 9  LSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVL 68

Query: 57 LRGNNIRYYIL 67
          +RG+NI     
Sbjct: 69 IRGDNIVLISP 79

Length = 79

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

 Score = 59.2 bits (144), Expect = 5e-13
 Identities = 20/63 (31%), Positives = 31/63 (49%)

Query: 4  LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIR 63
          L     +TV++ELK+G  + GT+   D  MN  L  V  T +  +   L  + +RG+NI 
Sbjct: 1  LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIV 60

Query: 64 YYI 66
             
Sbjct: 61 SIR 63

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|212470 cd01723, LSm4, Like-Sm protein 4

 Score = 53.0 bits (128), Expect = 2e-10
 Identities = 25/61 (40%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 12 VTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEPTTLDSISLRGNNIRYYILPDS 70
          V +ELKNG   +G +   D  MN HLK V  T K G     +    +RGN I+Y  LPD 
Sbjct: 14 VLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRGNTIKYLRLPDE 73

Query: 71 L 71
          +
Sbjct: 74 V 74

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|212472 cd01725, LSm2, Like-Sm protein 2

 Score = 51.8 bits (125), Expect = 6e-10
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 12 VTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEP--TTLDSISLRGNNIRYYILPD 69
          VT+ELKN   + GT+  VD  +N  L  + +    K P   ++ +  +RG+ +RY  LP 
Sbjct: 14 VTVELKNDLSITGTLHSVDQYLNIKLTNISVNDPEKYPHLLSVKNCFIRGSVVRYVQLPA 73

Query: 70 SLPLETLLIDDAPR 83
             ++T L+ DA R
Sbjct: 74 D-EVDTELLQDATR 86

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 = 89

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

 Score = 49.8 bits (120), Expect = 3e-09
 Identities = 22/55 (40%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 11 TVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMT-VKGKEPTTLDSISLRGNNIRY 64
            T+EL+N T V G I  VD  MN  L     T  +GK+    D   ++G NIRY
Sbjct: 21 VTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQ-HHFDEFFVQGRNIRY 74

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 52.0 bits (125), Expect = 5e-09
 Identities = 25/41 (60%), Positives = 25/41 (60%)

Query: 85  KGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
            G R   RGGG GG RG GGRGG  GG  GRGRGG  G  G
Sbjct: 7   GGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRG 47

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 19/42 (45%), Positives = 19/42 (45%)

Query: 86  GKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPP 127
                  G G G   G GG  G GG  GGRG G  RGRGG  
Sbjct: 2   MGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGG 43

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 46.6 bits (111), Expect = 5e-07
 Identities = 24/43 (55%), Positives = 24/43 (55%)

Query: 83  RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
           R  G    R GGG GG RG G   GRGGG GGRG GG  G G 
Sbjct: 14  RGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 46.3 bits (110), Expect = 7e-07
 Identities = 24/39 (61%), Positives = 24/39 (61%)

Query: 91  RRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
             GGG GG RG G  GG GGGRGG GRGG RG G    R
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGR 39

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 45.9 bits (109), Expect = 9e-07
 Identities = 24/38 (63%), Positives = 24/38 (63%)

Query: 92  RGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
            GGG GG RG GG GGRGGG  G GRGG RGRG     
Sbjct: 6   FGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGG 43

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 21/43 (48%), Positives = 21/43 (48%)

Query: 83  RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
              G    R GG  GG  G  G GGRGGGRGG    G  G GG
Sbjct: 2   MGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGG 44

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 44.3 bits (105), Expect = 3e-06
 Identities = 20/44 (45%), Positives = 20/44 (45%)

Query: 86  GKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
           G R    GGG GG    GGRGG  G   G G GG  G GG    
Sbjct: 12  GGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPG 55

Length = 293

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

 Score = 41.4 bits (98), Expect = 4e-06
 Identities = 21/63 (33%), Positives = 32/63 (50%)

Query: 2  NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNN 61
           FL  L+ + V ++LK G +  GT+  VD  MN  L   +  + GK    L  + +R NN
Sbjct: 4  PFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIRCNN 63

Query: 62 IRY 64
          + Y
Sbjct: 64 VLY 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 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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 22/46 (47%), Positives = 22/46 (47%)

Query: 83  RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPR 128
              G     RGGG GG  G G  GG  GG  G GRG  RG GG  R
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGR 46

Length = 293

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

 Score = 38.7 bits (91), Expect = 4e-05
 Identities = 20/64 (31%), Positives = 32/64 (50%)

Query: 1  MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
            FL K+  + V ++LKNG +  G +  +D  MN  L+  +  V G+         +RGN
Sbjct: 3  SKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIRGN 62

Query: 61 NIRY 64
          N+ Y
Sbjct: 63 NVLY 66

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|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 21/70 (30%), Positives = 26/70 (37%), Gaps = 12/70 (17%)

Query: 72  PLETLLIDDA-PRSKGKR--------DSRRGGG---AGGARGRGGRGGRGGGRGGRGRGG 119
           P+   L+ DA P + G+R          RR GG   +G  R  G   GR      R    
Sbjct: 554 PMNMQLLGDAQPHTGGERRGGGRGFGGERREGGRNFSGERREGGRGDGRRFSGERREGRA 613

Query: 120 PRGRGGPPRR 129
           PR      RR
Sbjct: 614 PRRDDSTGRR 623

Length = 629

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

 Score = 37.6 bits (88), Expect = 1e-04
 Identities = 15/52 (28%), Positives = 31/52 (59%)

Query: 11 TVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
           V ++LK G +V G ++G D  +N  L+  +  ++G+    L ++ +RG+N+
Sbjct: 13 NVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNV 64

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 17/38 (44%), Positives = 18/38 (47%)

Query: 82  PRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGG 119
              +G      G G G  RGRGG GG  GG GG G G 
Sbjct: 19  GGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56

Length = 293

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

 Score = 36.7 bits (85), Expect = 3e-04
 Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 12 VTIELK-NGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          + +E+K +  Q+ G +  VD  MN HL      V  ++  +L ++ LRGNNI
Sbjct: 13 IRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLRGNNI 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|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5)

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 8/44 (18%)

Query: 82  PRSKGKRDSRRGGGAGGARGRG-GRGGRGGGRGGRGRGGPRGRG 124
              +G     + G + G RGR  GRG  GGG    GRG    RG
Sbjct: 505 KSGEG---ISKVGQSYGGRGRTRGRGRGGGG----GRGRGYNRG 541

This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterized by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in human chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors. Length = 543

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 37.8 bits (88), Expect = 5e-04
 Identities = 19/40 (47%), Positives = 21/40 (52%)

Query: 82  PRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPR 121
               G+    RGGG GG RGRG  GG GG  GG G G  +
Sbjct: 17  GGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56

Length = 293

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

 Score = 35.7 bits (83), Expect = 7e-04
 Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 3/52 (5%)

Query: 14 IELKNGTQVHGTIQGVDVAMNTHLKTVK---MTVKGKEPTTLDSISLRGNNI 62
          I +K+  +  GT+ G D  +N  L+ V    +T +G++ T LD I L GNNI
Sbjct: 18 IIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNI 69

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|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score = 37.5 bits (87), Expect = 8e-04
 Identities = 13/42 (30%), Positives = 16/42 (38%)

Query: 88  RDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
           R  R GGG G   GRG + G+     G  +         P R
Sbjct: 391 RQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSR 432

Length = 456

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

 Score = 35.0 bits (81), Expect = 0.001
 Identities = 17/53 (32%), Positives = 27/53 (50%)

Query: 12 VTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRY 64
          V + LK G +  G +QG D+ MN  L   +    G+    L  + +RG+N+ Y
Sbjct: 17 VLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVY 69

Length = 72

>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 19/41 (46%), Positives = 20/41 (48%), Gaps = 3/41 (7%)

Query: 89  DSRRGGG--AGGARGRGGRGGRGGGRGGRGR-GGPRGRGGP 126
           + RRGGG    G   R G  G GG R G G  G PR R  P
Sbjct: 429 EQRRGGGRSGPGGGSRSGSVGGGGRRDGAGADGKPRPRRKP 469

Length = 572

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	129
KOG3428|consensus	109		99.96
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.95
KOG3172|consensus	119		99.93
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
KOG3293|consensus	134		99.9
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.83
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.8
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.79
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.79
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.78
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.75
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.74
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.74
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.72
KOG3448|consensus	96		99.7
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.66
KOG3482|consensus	79		99.66
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.62
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.61
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.59
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.57
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.56
KOG1783|consensus	77		99.54
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.54
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.49
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.45
KOG1780|consensus	77		99.39
KOG3262|consensus	215		99.32
KOG1775|consensus	84		99.17
KOG3460|consensus	91		99.15
KOG1774|consensus	88		98.74
KOG3168|consensus	177		98.35
KOG1781|consensus	108		98.32
KOG1784|consensus	96		98.29
KOG1782|consensus	129		98.09
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	98.02
KOG0947|consensus	1248		97.4
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	97.16
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	97.12
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	96.94
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	96.85
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	96.71
COG1923	77	Hfq Uncharacterized host factor I protein [General	96.4
KOG3459|consensus	114		96.28
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.11
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	96.04
PRK14091	165	RNA-binding protein Hfq; Provisional	95.52
PRK14091	165	RNA-binding protein Hfq; Provisional	95.51
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	93.43
KOG1073|consensus	361		93.23
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	91.62
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	89.13
KOG3262|consensus	215		88.51
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	87.94
PRK14638	150	hypothetical protein; Provisional	87.18
PRK02001	152	hypothetical protein; Validated	86.49
PRK13149	73	H/ACA RNA-protein complex component Gar1; Reviewed	86.46
PRK14639	140	hypothetical protein; Provisional	86.36
PRK14642	197	hypothetical protein; Provisional	83.47
PRK00092	154	ribosome maturation protein RimP; Reviewed	82.98
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	82.18
PRK09618	142	flgD flagellar basal body rod modification protein	81.31
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	80.43
PRK14644	136	hypothetical protein; Provisional	80.29
COG3277	98	GAR1 RNA-binding protein involved in rRNA processi	80.1

>KOG3428|consensus

Probab=99.96  E-value=8.5e-29  Score=168.42  Aligned_cols=98  Identities=67%  Similarity=1.022  Sum_probs=86.7

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCccccccCCC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDD   80 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L~~~   80 (129)
                      |+||++|.+++|+|||||+++++|+|.++|.+||++|.+|+++.+. +|++++.++|+||+|+||++||++++|++|+++
T Consensus         4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l~ld~Llvd~   82 (109)
T KOG3428|consen    4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSLNLDTLLVDD   82 (109)
T ss_pred             HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCcCcceeeeeh
Confidence            6899999999999999999999999999999999999999999876 999999999999999999999999999999999


Q ss_pred             CCccCCCCCCCCCCCCCCC
Q psy15782         81 APRSKGKRDSRRGGGAGGA   99 (129)
Q Consensus        81 ~~~~k~~~~~~~g~g~g~g   99 (129)
                      +|+.+.+...+.++++++|
T Consensus        83 ~~~~~~~~~~~~~rgrgrg  101 (109)
T KOG3428|consen   83 APRLHLRKNEKVGRGRGRG  101 (109)
T ss_pred             hhhhhhhcccccccccccc
Confidence            8877655443333444333

>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=99.95  E-value=5.5e-28  Score=162.22  Aligned_cols=85  Identities=69%  Similarity=1.115  Sum_probs=80.2

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCccccccCCC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDD   80 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L~~~   80 (129)
                      ++||+++.|++|+||||||++|+|+|.+||.|||++|+||+++.+++.+..+++++|||++|+||++||.++++++|.++
T Consensus         3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~~~~~l~~~   82 (90)
T cd01724           3 VRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLNLDTLLVDS   82 (90)
T ss_pred             hHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCCcchhhhhc
Confidence            57999999999999999999999999999999999999999998888899999999999999999999999999999887


Q ss_pred             CCccC
Q psy15782         81 APRSK   85 (129)
Q Consensus        81 ~~~~k   85 (129)
                      ++.++
T Consensus        83 ~~~~~   87 (90)
T cd01724          83 TPKPK   87 (90)
T ss_pred             CCccc
Confidence            66554

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.

>KOG3172|consensus

Probab=99.93  E-value=4.1e-25  Score=150.03  Aligned_cols=80  Identities=29%  Similarity=0.522  Sum_probs=73.0

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCccccccCCC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDD   80 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L~~~   80 (129)
                      |.+|....++-|++|+++|++|+|+|.++|++||++|.|+++|..++...+++++||||+.|+|+++||.|       ++
T Consensus         7 iKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmL-------Kn   79 (119)
T KOG3172|consen    7 IKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDML-------KN   79 (119)
T ss_pred             eeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHh-------hc
Confidence            46788888999999999999999999999999999999999999999999999999999999999999987       46


Q ss_pred             CCccCCC
Q psy15782         81 APRSKGK   87 (129)
Q Consensus        81 ~~~~k~~   87 (129)
                      +|.+|+.
T Consensus        80 APmFkk~   86 (119)
T KOG3172|consen   80 APMFKKG   86 (119)
T ss_pred             Ccccccc
Confidence            6665533

>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=99.92  E-value=1.9e-24  Score=138.79  Aligned_cols=69  Identities=33%  Similarity=0.611  Sum_probs=66.2

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      ++||++++|++|+||||||++|+|+|.+||.|||++|+||+++..+++...++++||||++|+||++||
T Consensus         2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd   70 (70)
T cd01721           2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence            479999999999999999999999999999999999999999888888899999999999999999997

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.

>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=99.90  E-value=1.3e-23  Score=137.55  Aligned_cols=68  Identities=35%  Similarity=0.552  Sum_probs=65.3

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILP   68 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~p   68 (129)
                      +.||+.+.|++|+|||||+.+|+|+|.+||.+||++|+||+++..++.+..+++++|||++|+||++|
T Consensus        11 ~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733          11 IILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             HHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence            46999999999999999999999999999999999999999998888888999999999999999998

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.

>KOG3293|consensus

Probab=99.90  E-value=9.5e-24  Score=146.42  Aligned_cols=74  Identities=27%  Similarity=0.501  Sum_probs=67.8

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcc-eecceEEEecCeEEEEEcCCCCccccc
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEP-TTLDSISLRGNNIRYYILPDSLPLETL   76 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~-~~l~~~~IrGn~Ir~Ii~pd~l~l~~~   76 (129)
                      .+|....++++.|||||+++|.|.|++||.|||++|++|++++++++. +.+.+|+|||++|+|+.+||++ +|.+
T Consensus         5 sLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~i-id~v   79 (134)
T KOG3293|consen    5 SLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEI-IDKV   79 (134)
T ss_pred             hHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHH-HHHH
Confidence            578888999999999999999999999999999999999999998764 7899999999999999999995 4444

>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=99.89  E-value=5.6e-23  Score=133.89  Aligned_cols=71  Identities=31%  Similarity=0.519  Sum_probs=66.3

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcc-eecceEEEecCeEEEEEcCCCC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEP-TTLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~-~~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      ++||+++.+++|+|||||+++|+|+|.+||.|||++|+||+++..+++. ..++++||||++|+||++||++
T Consensus         3 l~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~   74 (76)
T cd01723           3 LSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI   74 (76)
T ss_pred             hHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence            4799999999999999999999999999999999999999999777765 5689999999999999999985

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.

>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=99.88  E-value=1.9e-22  Score=132.91  Aligned_cols=71  Identities=31%  Similarity=0.486  Sum_probs=64.5

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCc--ceecceEEEecCeEEEEEcCCCC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKE--PTTLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~--~~~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      +.||+++.|++|+||||||++|+|+|.+||.|||++|+||+++..+..  ...+++++|||++|+||++||.+
T Consensus         3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~   75 (81)
T cd01725           3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADE   75 (81)
T ss_pred             hHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhH
Confidence            369999999999999999999999999999999999999998865543  35679999999999999999984

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.

>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=6.3e-21  Score=121.38  Aligned_cols=66  Identities=26%  Similarity=0.407  Sum_probs=62.0

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      .+||+++++++|+|+|+|+++|+|+|.+||.|||++|+||+++...+++..++.++|||++|+||.
T Consensus         2 ~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           2 SEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             HHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence            379999999999999999999999999999999999999999877777889999999999999973

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.

>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=99.83  E-value=2.7e-20  Score=118.85  Aligned_cols=66  Identities=32%  Similarity=0.468  Sum_probs=61.1

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      ++||+++++++|+|+|+||.+|.|+|.+||.|||++|+||+++....++..++.++|||++|+||.
T Consensus         3 ~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           3 KPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             HHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence            478999999999999999999999999999999999999998866666788999999999999983

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.80  E-value=3e-19  Score=115.20  Aligned_cols=66  Identities=27%  Similarity=0.487  Sum_probs=60.8

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      ++||.++++++|+|+|+||++|+|+|.+||.|||++|+||+++...+....++.++|||++|.+|.
T Consensus         6 ~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~   71 (72)
T PRK00737          6 LDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVS   71 (72)
T ss_pred             HHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEc
Confidence            368999999999999999999999999999999999999999876656678999999999999985

>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=99.79  E-value=5.7e-19  Score=112.56  Aligned_cols=66  Identities=23%  Similarity=0.418  Sum_probs=62.1

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      ++||+++++++|+|+|+|+++|.|+|.+||.|||++|+||+++..+.+...++.++|||++|.||.
T Consensus         2 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~   67 (68)
T cd01731           2 LDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFIS   67 (68)
T ss_pred             hHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEc
Confidence            368999999999999999999999999999999999999999887777889999999999999985

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.

>smart00651 Sm snRNP Sm proteins

Probab=99.79  E-value=1e-18  Score=110.37  Aligned_cols=66  Identities=45%  Similarity=0.649  Sum_probs=62.1

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC-CcceecceEEEecCeEEEEEc
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG-KEPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~-~~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      .||.++++++|+|+|+|++++.|+|.+||.+||++|+||+++..+ .++..++.++|||++|+||+.
T Consensus         1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence            489999999999999999999999999999999999999999877 678899999999999999874

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=99.78  E-value=9.2e-19  Score=110.68  Aligned_cols=66  Identities=44%  Similarity=0.603  Sum_probs=62.6

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC-cceecceEEEecCeEEEEEc
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK-EPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~-~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      .||+++++++|+|+|+||.+|.|+|.+||.+||++|+||+++.... +...++.++|||++|++|++
T Consensus         1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred             ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence            4899999999999999999999999999999999999999998877 78899999999999999974

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 ....

>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=99.75  E-value=1.2e-17  Score=104.14  Aligned_cols=63  Identities=33%  Similarity=0.490  Sum_probs=59.9

Q ss_pred             hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782          4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      |+++++++|+|+|+|+++|.|+|.+||.+||+.|+|++++.++.++..++.++|||++|++|+
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEEC
Confidence            678999999999999999999999999999999999999988888899999999999999984

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.

>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=99.74  E-value=1.6e-17  Score=107.23  Aligned_cols=68  Identities=24%  Similarity=0.345  Sum_probs=62.5

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      .+|.++++++|.|+|+++.+|.|+|.+||.|||++|+||+++....+...++.++|||++|.+|..-|
T Consensus         3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~   70 (72)
T cd01719           3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALE   70 (72)
T ss_pred             hhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEccc
Confidence            47899999999999999999999999999999999999999876667788999999999999988654

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.

>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=99.74  E-value=1.2e-17  Score=108.81  Aligned_cols=65  Identities=31%  Similarity=0.400  Sum_probs=59.4

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEe---cCCcceecceEEEecCeEEEEE
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTV---KGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~---~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      .||+++++++|+|+|+++++|.|+|.+||.|||++|+||+++.   ..++..+++.++|||++|.+|+
T Consensus         6 ~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~   73 (76)
T cd01732           6 ELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLV   73 (76)
T ss_pred             HHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEE
Confidence            6899999999999999999999999999999999999998886   3334578999999999999987

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.

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

Probab=99.72  E-value=3.9e-17  Score=106.85  Aligned_cols=65  Identities=34%  Similarity=0.475  Sum_probs=57.2

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEec-CCcc--e-ecceEEEecCeEEEEE
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEP--T-TLDSISLRGNNIRYYI   66 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~-~~~~--~-~l~~~~IrGn~Ir~Ii   66 (129)
                      .||.++++++|.|+|+|+++|.|+|.+||.|||++|+||+++.. +++.  . ..+.++|||++|.+|.
T Consensus        10 ~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~   78 (79)
T COG1958          10 SFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLIS   78 (79)
T ss_pred             HHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEe
Confidence            68999999999999999999999999999999999999999874 3232  3 3449999999999986

>KOG3448|consensus

Probab=99.70  E-value=6.1e-17  Score=106.72  Aligned_cols=69  Identities=32%  Similarity=0.535  Sum_probs=64.6

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcc--eecceEEEecCeEEEEEcCCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEP--TTLDSISLRGNNIRYYILPDS   70 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~--~~l~~~~IrGn~Ir~Ii~pd~   70 (129)
                      +|++.++++.|+|||||+..+.|+|.++|+|+|++|.|+.+++.++-|  .....|||||+.|+||.+|..
T Consensus         5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd   75 (96)
T KOG3448|consen    5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKD   75 (96)
T ss_pred             HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChh
Confidence            588999999999999999999999999999999999999999887776  567899999999999999977

>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=99.66  E-value=7e-16  Score=101.60  Aligned_cols=66  Identities=20%  Similarity=0.347  Sum_probs=58.8

Q ss_pred             hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC--------cceecceEEEecCeEEEEEcCC
Q psy15782          4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK--------EPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~--------~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      |.++++++|.|.|+++++|.|+|.+||.|||++|+||++.....        +...++.++|||++|.+|...+
T Consensus         7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            77899999999999999999999999999999999999886532        3567899999999999987654

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.

>KOG3482|consensus

Probab=99.66  E-value=1.6e-16  Score=101.24  Aligned_cols=65  Identities=32%  Similarity=0.448  Sum_probs=61.6

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      .||+.|+|++|.|.||.|.+|.|+|.++|.+||+.|.++++.........+.+++||.|||.||.
T Consensus        11 pFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~   75 (79)
T KOG3482|consen   11 PFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIR   75 (79)
T ss_pred             HHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEe
Confidence            59999999999999999999999999999999999999999877777889999999999999985

>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=99.62  E-value=2.4e-15  Score=99.21  Aligned_cols=65  Identities=17%  Similarity=0.301  Sum_probs=57.6

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC-------------cceecceEEEecCeEEEEE
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK-------------EPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~-------------~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      .||.+.++++|.|.|+++++|.|+|.+||.|||++|+||++.....             ....++.++|||++|.+|.
T Consensus         4 ~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~   81 (82)
T cd01730           4 DLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS   81 (82)
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence            6889999999999999999999999999999999999999886431             1347899999999999875

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.

>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=99.61  E-value=3.1e-15  Score=99.77  Aligned_cols=65  Identities=20%  Similarity=0.306  Sum_probs=56.5

Q ss_pred             hhhhhcC--CCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCc-------------ceecceEEEecCeEEEEE
Q psy15782          2 NFLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKE-------------PTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         2 ~~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~-------------~~~l~~~~IrGn~Ir~Ii   66 (129)
                      .||.+++  +++|.|.|+++.+|.|+|.+||.|||+.|+||+++.+...             ...++.+||||++|.+|.
T Consensus         5 ~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~Is   84 (87)
T cd01720           5 SLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVILVL   84 (87)
T ss_pred             HHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEEEe
Confidence            5788885  8999999999999999999999999999999998764422             236899999999999975

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=99.59  E-value=6.1e-15  Score=96.68  Aligned_cols=65  Identities=28%  Similarity=0.367  Sum_probs=57.0

Q ss_pred             hhhhhcCCC--eEEEEEc--CCcEEEEEEEEecccccceEeeEEEEec-CCcceecceEEEecCeEEEEE
Q psy15782          2 NFLMKLSHE--TVTIELK--NGTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         2 ~~L~~l~~~--~V~VeLk--ng~~~~G~L~~~D~~mNl~Lkdv~~~~~-~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      .+|++++.+  +|.|+|+  ++.+|.|+|.+||.|||++|+|+++... ..+...++.++|||+||.+|+
T Consensus         9 ~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~   78 (79)
T cd01718           9 NLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQ   78 (79)
T ss_pred             HHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEc
Confidence            467888888  6888887  8999999999999999999999998875 445678999999999999976

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.

>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=99.57  E-value=2.1e-14  Score=93.09  Aligned_cols=66  Identities=17%  Similarity=0.175  Sum_probs=57.6

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC---cceecceEEEecCeEEEEEc
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK---EPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~---~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      ..|.++++++|.|.|+++++|.|+|.+||.|||+.|+||++....+   ....++.++|||++|.+|.+
T Consensus         5 ~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728           5 ASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             HHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence            4688899999999999999999999999999999999998775432   24678899999999998753

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.

>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=99.56  E-value=2.1e-14  Score=94.01  Aligned_cols=64  Identities=28%  Similarity=0.367  Sum_probs=56.8

Q ss_pred             hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC----------CcceecceEEEecCeEEEEEc
Q psy15782          4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG----------KEPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~----------~~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      |.++++++|.|.|+++.+|.|+|.+||.|||++|+||+++...          .++..++.++|||++|.+|.+
T Consensus         5 l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           5 MLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             hHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            6789999999999999999999999999999999999987532          234678999999999999864

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.

>KOG1783|consensus

Probab=99.54  E-value=1e-15  Score=97.62  Aligned_cols=68  Identities=28%  Similarity=0.425  Sum_probs=64.1

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      +||.+.+|++|.|+|.++..|+|+|.++|.+||+.|+.+++....+.+..+...|||||+|.||...+
T Consensus         9 ~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~~   76 (77)
T KOG1783|consen    9 EFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQK   76 (77)
T ss_pred             HHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEecc
Confidence            69999999999999999999999999999999999999998888888899999999999999998754

>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=99.54  E-value=6.1e-14  Score=90.77  Aligned_cols=67  Identities=28%  Similarity=0.303  Sum_probs=58.8

Q ss_pred             hhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC---C-cceecceEEEecCeEEEEEcCC
Q psy15782          3 FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG---K-EPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~---~-~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      -|.++++++|.|.|+++..|.|+|.+||.|||+.|++|++....   + +...++.+++||++|.+|..-|
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            47889999999999999999999999999999999999887532   1 3567899999999999988654

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.

>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=99.49  E-value=2.1e-13  Score=88.67  Aligned_cols=66  Identities=21%  Similarity=0.249  Sum_probs=59.5

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC------CcceecceEEEecCeEEEEEc
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG------KEPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~------~~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      +-|.++++++|.|.|+||.+|.|+|.++|.+||+.|+||++....      .+...++.++|+|++|..+..
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            468899999999999999999999999999999999999998654      345789999999999998864

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.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.45  E-value=5.1e-13  Score=89.40  Aligned_cols=66  Identities=27%  Similarity=0.380  Sum_probs=54.4

Q ss_pred             hhhhhcCCC--eEEEEEcC--CcEEEEEEEEecccccceEeeEEEEecC-CcceecceEEEecCeEEEEEc
Q psy15782          2 NFLMKLSHE--TVTIELKN--GTQVHGTIQGVDVAMNTHLKTVKMTVKG-KEPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         2 ~~L~~l~~~--~V~VeLkn--g~~~~G~L~~~D~~mNl~Lkdv~~~~~~-~~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      .+|.+++.+  +|.|+|.+  +.+|.|+|.+||.|||++|+|++++..+ .+...++.++||||||.+|..
T Consensus        17 ~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~   87 (89)
T PTZ00138         17 NQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA   87 (89)
T ss_pred             HHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEc
Confidence            456666554  58888877  4899999999999999999999988653 345789999999999999864

>KOG1780|consensus

Probab=99.39  E-value=9.1e-13  Score=84.34  Aligned_cols=65  Identities=23%  Similarity=0.341  Sum_probs=61.0

Q ss_pred             hhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEc
Q psy15782          3 FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      -|.|+.++++.+.|..+..+.|.|.+||.|||++|+++++...+++...+...+||||+|..+-.
T Consensus         8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~ea   72 (77)
T KOG1780|consen    8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEA   72 (77)
T ss_pred             hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEee
Confidence            48899999999999999999999999999999999999999999889999999999999987654

>KOG3262|consensus

Probab=99.32  E-value=2.9e-12  Score=95.44  Aligned_cols=70  Identities=26%  Similarity=0.457  Sum_probs=57.1

Q ss_pred             hhhhcCCCeE-----EEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCC-Cccccc
Q psy15782          3 FLMKLSHETV-----TIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDS-LPLETL   76 (129)
Q Consensus         3 ~L~~l~~~~V-----~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~-l~l~~~   76 (129)
                      ++|++.+++|     .|+|+|.++| |+|++|...||-    ++++++..+.+...++..   ..+++|.||+ |+++.|
T Consensus        67 ~Vck~~~~kIPyfNAPIylenk~qI-GKVDEIfG~i~d----~~fsIK~~dgv~assfk~---g~k~fi~p~KllPl~RF  138 (215)
T KOG3262|consen   67 LVCKLTNKKIPYFNAPIYLENKEQI-GKVDEIFGPIND----VHFSIKPSDGVQASSFKP---GDKLFIDPDKLLPLDRF  138 (215)
T ss_pred             eEEeeccccCCCCCCceeecchhhh-cchhhhcccccc----cEEEEecCCCceeecccC---CCeEEecccccCcHhhc
Confidence            5667777776     8999999999 999999999995    667777777776666554   4788899999 999999


Q ss_pred             cCCC
Q psy15782         77 LIDD   80 (129)
Q Consensus        77 L~~~   80 (129)
                      |+.+
T Consensus       139 LP~p  142 (215)
T KOG3262|consen  139 LPQP  142 (215)
T ss_pred             CCCC
Confidence            9754

>KOG1775|consensus

Probab=99.17  E-value=1.6e-11  Score=79.07  Aligned_cols=66  Identities=29%  Similarity=0.333  Sum_probs=58.0

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEec--C-CcceecceEEEecCeEEEEEc
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK--G-KEPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~--~-~~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      +++.|++|.+|.|.+|+.+++.|+|.+||+|.|+.|+||+++..  + +...+++.+++.||+|..++.
T Consensus        10 EliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvP   78 (84)
T KOG1775|consen   10 ELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVP   78 (84)
T ss_pred             HHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEec
Confidence            57889999999999999999999999999999999999976632  2 345789999999999998654

>KOG3460|consensus

Probab=99.15  E-value=1.4e-11  Score=80.60  Aligned_cols=69  Identities=23%  Similarity=0.352  Sum_probs=58.7

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCc-------------ceecceEEEecCeEEEEEcC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKE-------------PTTLDSISLRGNNIRYYILP   68 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~-------------~~~l~~~~IrGn~Ir~Ii~p   68 (129)
                      .||.-.+.+.|-|+|+++.++.|+|.+||+|+|+.|.||+++.+.-+             ....+.+|+||++|.+|..|
T Consensus         8 dllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvspp   87 (91)
T KOG3460|consen    8 DLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVSPP   87 (91)
T ss_pred             HHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEcCc
Confidence            57777899999999999999999999999999999999987754211             24577999999999999887


Q ss_pred             CC
Q psy15782         69 DS   70 (129)
Q Consensus        69 d~   70 (129)
                      -.
T Consensus        88 ~~   89 (91)
T KOG3460|consen   88 LR   89 (91)
T ss_pred             cc
Confidence            54

>KOG1774|consensus

Probab=98.74  E-value=2.1e-08  Score=65.47  Aligned_cols=58  Identities=31%  Similarity=0.367  Sum_probs=49.3

Q ss_pred             eEEEEEcC--CcEEEEEEEEecccccceEeeEEEEec-CCcceecceEEEecCeEEEEEcC
Q psy15782         11 TVTIELKN--GTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEPTTLDSISLRGNNIRYYILP   68 (129)
Q Consensus        11 ~V~VeLkn--g~~~~G~L~~~D~~mNl~Lkdv~~~~~-~~~~~~l~~~~IrGn~Ir~Ii~p   68 (129)
                      .|.|+|..  +..++|.+.+||+|||+++++++++.. .+...+++.++++|+||..|...
T Consensus        26 ~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~~   86 (88)
T KOG1774|consen   26 RVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQSA   86 (88)
T ss_pred             ceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEeec
Confidence            58888887  689999999999999999999987754 34445899999999999988653

>KOG3168|consensus

Probab=98.35  E-value=4.5e-07  Score=66.58  Aligned_cols=72  Identities=22%  Similarity=0.327  Sum_probs=59.5

Q ss_pred             hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEec---------C-CcceecceEEEecCeEEEEEcCCCCcc
Q psy15782          4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK---------G-KEPTTLDSISLRGNNIRYYILPDSLPL   73 (129)
Q Consensus         4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~---------~-~~~~~l~~~~IrGn~Ir~Ii~pd~l~l   73 (129)
                      |..++|..+.|.|.|++++.|++..||.|||+.|.||++.-.         + .+...+..+++||.+|......+....
T Consensus         9 ml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp~   88 (177)
T KOG3168|consen    9 MLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPPP   88 (177)
T ss_pred             HHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCCC
Confidence            556789999999999999999999999999999998875421         1 234678999999999999988877554


Q ss_pred             cc
Q psy15782         74 ET   75 (129)
Q Consensus        74 ~~   75 (129)
                      ++
T Consensus        89 s~   90 (177)
T KOG3168|consen   89 SD   90 (177)
T ss_pred             cc
Confidence            43

>KOG1781|consensus

Probab=98.32  E-value=8.8e-08  Score=64.56  Aligned_cols=68  Identities=19%  Similarity=0.321  Sum_probs=58.0

Q ss_pred             hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC-C-------cceecceEEEecCeEEEEEcCCCC
Q psy15782          4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG-K-------EPTTLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~-~-------~~~~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      |.++++++|.|.+..|.++.|+|.+||+.||++|+|+.+...+ .       +...++.+.+||..+..|...|-.
T Consensus        22 Lsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~   97 (108)
T KOG1781|consen   22 LSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGS   97 (108)
T ss_pred             HHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcch
Confidence            5678999999999999999999999999999999999765432 1       236789999999999988887764

>KOG1784|consensus

Probab=98.29  E-value=9.1e-07  Score=58.95  Aligned_cols=74  Identities=22%  Similarity=0.332  Sum_probs=62.5

Q ss_pred             hhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEe----cCCcceecceEEEecCeEEEEEcCCCCcccccc
Q psy15782          3 FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTV----KGKEPTTLDSISLRGNNIRYYILPDSLPLETLL   77 (129)
Q Consensus         3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~----~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L   77 (129)
                      -|..++++.|.|-..+|+.+.|.|.+||...|+.++++.+-.    ...+...++.++|||.|+-.|-.-|+ .+|+.|
T Consensus         4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDE-e~d~~l   81 (96)
T KOG1784|consen    4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDE-ELDSRL   81 (96)
T ss_pred             hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecch-hhhhhh
Confidence            367889999999999999999999999999999999985432    23456789999999999999988887 466666

>KOG1782|consensus

Probab=98.09  E-value=5.7e-07  Score=62.88  Aligned_cols=66  Identities=18%  Similarity=0.224  Sum_probs=53.9

Q ss_pred             hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCc---ceecceEEEecCeEEEEEcCC
Q psy15782          4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKE---PTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~---~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      |.+.+.+++.|-|++|..+.|.|.|||+|-|+.|.++++-+--++   ..+.+.|+|||.||..+-.-|
T Consensus        14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid   82 (129)
T KOG1782|consen   14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEID   82 (129)
T ss_pred             HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCC
Confidence            456688999999999999999999999999999999875332222   256788999999999986544

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

Probab=98.02  E-value=1.8e-05  Score=51.09  Aligned_cols=44  Identities=25%  Similarity=0.372  Sum_probs=35.2

Q ss_pred             hhhhcCCCeEEEEEcCCcEEEEEEEEecc---cccceEeeEEEEecC
Q psy15782          3 FLMKLSHETVTIELKNGTQVHGTIQGVDV---AMNTHLKTVKMTVKG   46 (129)
Q Consensus         3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~---~mNl~Lkdv~~~~~~   46 (129)
                      ++..++|++|.|.++||.+|+|.+.+++.   -+.+.|+-+..+...
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            56789999999999999999999999998   899999998876543

>KOG0947|consensus

Probab=97.40  E-value=0.00034  Score=63.54  Aligned_cols=44  Identities=18%  Similarity=0.171  Sum_probs=39.3

Q ss_pred             cceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCcccccc
Q psy15782         34 NTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLL   77 (129)
Q Consensus        34 Nl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L   77 (129)
                      =++.+++++|++.++|++|++|++-+.+...|+....+++..-+
T Consensus       456 RtK~K~IyViST~kRPVPLEh~l~t~~~l~kiidq~g~fl~~~~  499 (1248)
T KOG0947|consen  456 RTKQKTIYVISTSKRPVPLEHYLYTKKSLFKIIDQNGIFLLKGI  499 (1248)
T ss_pred             hccCceEEEEecCCCccceEEEEEeccceehhhcccchhhhhcc
Confidence            47889999999999999999999999999999999998875544

>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=97.16  E-value=0.0016  Score=40.60  Aligned_cols=34  Identities=35%  Similarity=0.389  Sum_probs=28.3

Q ss_pred             hhhhhcC--CCeEEEEEcCCcEEEEEEEEecccccc
Q psy15782          2 NFLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNT   35 (129)
Q Consensus         2 ~~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl   35 (129)
                      .||..+-  ..+|+|+|.||-.+.|++.+||.|+=+
T Consensus         2 ~fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVl   37 (61)
T cd01716           2 QFLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVL   37 (61)
T ss_pred             HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEE
Confidence            3677664  457999999999999999999999843

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.

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=97.12  E-value=0.0019  Score=42.27  Aligned_cols=33  Identities=36%  Similarity=0.469  Sum_probs=27.7

Q ss_pred             hhhhc--CCCeEEEEEcCCcEEEEEEEEecccccc
Q psy15782          3 FLMKL--SHETVTIELKNGTQVHGTIQGVDVAMNT   35 (129)
Q Consensus         3 ~L~~l--~~~~V~VeLkng~~~~G~L~~~D~~mNl   35 (129)
                      ||..+  ...+|+|+|.||-.+.|+|.+||.|+=+
T Consensus        11 fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVl   45 (79)
T PRK00395         11 FLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVL   45 (79)
T ss_pred             HHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEE
Confidence            56655  3557999999999999999999999843

>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=96.94  E-value=0.00086  Score=42.28  Aligned_cols=36  Identities=22%  Similarity=0.263  Sum_probs=28.5

Q ss_pred             CCeEEEEEcC--C--cEEEEEEEEecccccceEeeEEEEe
Q psy15782          9 HETVTIELKN--G--TQVHGTIQGVDVAMNTHLKTVKMTV   44 (129)
Q Consensus         9 ~~~V~VeLkn--g--~~~~G~L~~~D~~mNl~Lkdv~~~~   44 (129)
                      ...|.|.++.  +  -.++|.|++||.|||+.|.||.++.
T Consensus         8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y   47 (66)
T cd01739           8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETY   47 (66)
T ss_pred             CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhh
Confidence            3457776665  2  4677999999999999999998764

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.

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

Probab=96.85  E-value=0.0074  Score=40.89  Aligned_cols=65  Identities=17%  Similarity=0.229  Sum_probs=53.9

Q ss_pred             hhcCCCeEEEEEcCCcEEEEEEEEecc-cccceEeeEEEEecCCc---------ceecceEEEecCeEEEEEcCC
Q psy15782          5 MKLSHETVTIELKNGTQVHGTIQGVDV-AMNTHLKTVKMTVKGKE---------PTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         5 ~~l~~~~V~VeLkng~~~~G~L~~~D~-~mNl~Lkdv~~~~~~~~---------~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      ..++|++|.+.-+++..|+|+|..+|. .-.+.|++|...-+.++         ...++.+..+|+.|+-+.+-+
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e   78 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIE   78 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEc
Confidence            467999999999999999999999995 67899999988766554         245788889999999776644

>TIGR02383 Hfq RNA chaperone Hfq

Probab=96.71  E-value=0.0035  Score=39.14  Aligned_cols=33  Identities=36%  Similarity=0.430  Sum_probs=27.6

Q ss_pred             hhhhcC--CCeEEEEEcCCcEEEEEEEEecccccc
Q psy15782          3 FLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNT   35 (129)
Q Consensus         3 ~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl   35 (129)
                      ||..+-  ..+|+|+|.||..+.|++.+||.|+=+
T Consensus         7 fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVl   41 (61)
T TIGR02383         7 FLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVL   41 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEE
Confidence            566553  557999999999999999999999843

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.

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

Probab=96.40  E-value=0.014  Score=37.93  Aligned_cols=32  Identities=34%  Similarity=0.463  Sum_probs=27.3

Q ss_pred             hhhhhc--CCCeEEEEEcCCcEEEEEEEEecccc
Q psy15782          2 NFLMKL--SHETVTIELKNGTQVHGTIQGVDVAM   33 (129)
Q Consensus         2 ~~L~~l--~~~~V~VeLkng~~~~G~L~~~D~~m   33 (129)
                      .||..+  ...+|+|+|-||-..+|.+.+||.|.
T Consensus        10 ~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~   43 (77)
T COG1923          10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFV   43 (77)
T ss_pred             HHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEE
Confidence            366655  45689999999999999999999987

>KOG3459|consensus

Probab=96.28  E-value=0.00078  Score=46.43  Aligned_cols=58  Identities=21%  Similarity=0.316  Sum_probs=47.2

Q ss_pred             CCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC-------c------ceecceEEEecCeEEEEE
Q psy15782          9 HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK-------E------PTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         9 ~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~-------~------~~~l~~~~IrGn~Ir~Ii   66 (129)
                      +.+|.|-++|...+.|.+.+||-|.|++|+++.+..+..       .      ...+..+||||+++..+.
T Consensus        36 ~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~  106 (114)
T KOG3459|consen   36 NTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVL  106 (114)
T ss_pred             CceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEE
Confidence            567999999999999999999999999999997654321       1      134678999999988765

>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=96.11  E-value=0.043  Score=35.48  Aligned_cols=58  Identities=19%  Similarity=0.312  Sum_probs=45.0

Q ss_pred             hcCCCeEEEEEcCCcEEEEEEEEecc-cccceEeeEEEEecCCcc----------eecceEEEecCeEE
Q psy15782          6 KLSHETVTIELKNGTQVHGTIQGVDV-AMNTHLKTVKMTVKGKEP----------TTLDSISLRGNNIR   63 (129)
Q Consensus         6 ~l~~~~V~VeLkng~~~~G~L~~~D~-~mNl~Lkdv~~~~~~~~~----------~~l~~~~IrGn~Ir   63 (129)
                      .++|++|.+--|.+..|.|+|.++|. ---+.|+||...-+.+++          ..++.+..||+.|+
T Consensus         3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIk   71 (74)
T cd01736           3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIK   71 (74)
T ss_pred             cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccc
Confidence            57899999999999999999999995 446789999877665543          33556666666664

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.

>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=96.04  E-value=0.048  Score=35.79  Aligned_cols=60  Identities=17%  Similarity=0.261  Sum_probs=45.2

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecc-cccceEeeEEEEecCCcc-eecceEEEecCeEEEEEc
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDV-AMNTHLKTVKMTVKGKEP-TTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~-~mNl~Lkdv~~~~~~~~~-~~l~~~~IrGn~Ir~Ii~   67 (129)
                      ++|.++.+++|.+.|.+.+++.|+...+|. ..|+..+|-.      .| -..++-.+|.+.|..+..
T Consensus        17 r~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~------TPlGv~~eAlLR~~DVi~~~f   78 (80)
T PF11095_consen   17 RSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ------TPLGVQPEALLRCSDVISISF   78 (80)
T ss_dssp             HHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE------TTTTEEEEEEEEGGGEEEEEE
T ss_pred             HHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC------CCcccChhheeecCCEEEEEe
Confidence            567788999999999999999999999994 5577666542      33 134778899999988765

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=95.52  E-value=0.036  Score=40.95  Aligned_cols=32  Identities=31%  Similarity=0.356  Sum_probs=26.8

Q ss_pred             hhhhcC--CCeEEEEEcCCcEEEEEEEEeccccc
Q psy15782          3 FLMKLS--HETVTIELKNGTQVHGTIQGVDVAMN   34 (129)
Q Consensus         3 ~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mN   34 (129)
                      ||..+-  ..+|+|+|.||-.++|+|.+||.|.=
T Consensus        16 fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftV   49 (165)
T PRK14091         16 FLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSI   49 (165)
T ss_pred             HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEE
Confidence            566654  44699999999999999999999873

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=95.51  E-value=0.045  Score=40.44  Aligned_cols=33  Identities=33%  Similarity=0.435  Sum_probs=27.4

Q ss_pred             hhhhcC--CCeEEEEEcCCcEEEEEEEEecccccc
Q psy15782          3 FLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNT   35 (129)
Q Consensus         3 ~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl   35 (129)
                      ||..+-  ..+|+|+|.||-.++|+|.+||.|+=+
T Consensus        96 fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvl  130 (165)
T PRK14091         96 FLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCML  130 (165)
T ss_pred             HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEE
Confidence            566553  457999999999999999999999844

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

Probab=93.43  E-value=0.45  Score=30.08  Aligned_cols=50  Identities=16%  Similarity=0.184  Sum_probs=35.5

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEec-ccccceEeeEEEEecCCcceecceEEEecCeEEEE
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVD-VAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYY   65 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D-~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~I   65 (129)
                      +.|++++|++|.|++-.|+. +|+|.++. +|+=+  +     . .     -..+|||=..|.+|
T Consensus        14 q~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhIvl--~-----~-~-----~~~~~IR~~~IV~v   64 (66)
T PF10842_consen   14 QTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHIVL--E-----E-N-----GTPFFIRIAQIVWV   64 (66)
T ss_pred             HHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEEEE--E-----e-C-----CcEEEEEeeeEEEE
Confidence            56889999999999988877 69999987 34421  1     0 0     24577776666655

>KOG1073|consensus

Probab=93.23  E-value=0.23  Score=41.03  Aligned_cols=68  Identities=16%  Similarity=0.235  Sum_probs=54.9

Q ss_pred             hhhcCCCeEEEEEcCCcEEEEEEEEec-ccccceEeeEEEEecCCcc---------e-ecceEEEecCeEEEEEcCCCC
Q psy15782          4 LMKLSHETVTIELKNGTQVHGTIQGVD-VAMNTHLKTVKMTVKGKEP---------T-TLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         4 L~~l~~~~V~VeLkng~~~~G~L~~~D-~~mNl~Lkdv~~~~~~~~~---------~-~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      ...++|++|.+.=|++..|+|.|.-+| +---|-|++|...-+.+++         . .++.++.||+.|+-+++-+..
T Consensus         4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p   82 (361)
T KOG1073|consen    4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETP   82 (361)
T ss_pred             ccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCc
Confidence            346799999999999999999999999 5668889999766554431         2 678999999999977776653

>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=91.62  E-value=0.75  Score=26.78  Aligned_cols=31  Identities=19%  Similarity=0.318  Sum_probs=25.9

Q ss_pred             CCCeEEEEEcCCcEEEEEEEEecccccceEee
Q psy15782          8 SHETVTIELKNGTQVHGTIQGVDVAMNTHLKT   39 (129)
Q Consensus         8 ~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkd   39 (129)
                      +|++|+|++ ++..++|+...+|..=.+.++.
T Consensus         2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~   32 (48)
T PF02237_consen    2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRT   32 (48)
T ss_dssp             TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEE
T ss_pred             CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEE
Confidence            689999999 5666689999999988886654

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 ....

>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=89.13  E-value=3.5  Score=25.59  Aligned_cols=30  Identities=10%  Similarity=0.068  Sum_probs=26.6

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEecccccce
Q psy15782          7 LSHETVTIELKNGTQVHGTIQGVDVAMNTH   36 (129)
Q Consensus         7 l~~~~V~VeLkng~~~~G~L~~~D~~mNl~   36 (129)
                      .+|..|.+++-.+.+++|.|..||...++.
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~l   33 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKML   33 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEE
Confidence            468899999999999999999999887653

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.

>KOG3262|consensus

Probab=88.51  E-value=1.8  Score=32.82  Aligned_cols=10  Identities=10%  Similarity=0.119  Sum_probs=5.4

Q ss_pred             EEEEec-cccc
Q psy15782         25 TIQGVD-VAMN   34 (129)
Q Consensus        25 ~L~~~D-~~mN   34 (129)
                      +|.+.| .|.|
T Consensus        70 k~~~~kIPyfN   80 (215)
T KOG3262|consen   70 KLTNKKIPYFN   80 (215)
T ss_pred             eeccccCCCCC
Confidence            355555 4555

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

Probab=87.94  E-value=3  Score=30.92  Aligned_cols=60  Identities=10%  Similarity=0.121  Sum_probs=37.2

Q ss_pred             hhhhcCCCeEEEEEcCCcEEEEEEEEecc-cccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782          3 FLMKLSHETVTIELKNGTQVHGTIQGVDV-AMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~-~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      .+..++++.|.|.+.| +++.|-|..+|. .-|++|-+...   +++   ...-+|-|-.|+.|..-+
T Consensus        11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~---~sv~~I~ghaVk~vevl~   71 (166)
T PF06372_consen   11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGK---RSVKVIMGHAVKSVEVLS   71 (166)
T ss_dssp             HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS----EEEEEE-GGGEEEEEEEE
T ss_pred             HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCc---eeEEEEEccceEEEEEcc
Confidence            3567899999999999 999999999995 55765553321   221   123556677777665443

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=87.18  E-value=1.2  Score=32.36  Aligned_cols=29  Identities=17%  Similarity=0.284  Sum_probs=26.0

Q ss_pred             hhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782          4 LMKLSHETVTIELKNGTQVHGTIQGVDVA   32 (129)
Q Consensus         4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~   32 (129)
                      +.+.+|++|.|.|++.+.+.|+|.++|..
T Consensus        95 f~r~~G~~v~V~~~~~k~~~G~L~~~~~~  123 (150)
T PRK14638         95 YVRFTGKLAKIVTKDGKTFIGRIESFVDG  123 (150)
T ss_pred             HHHhCCCEEEEEECCCcEEEEEEEEEeCC
Confidence            45678999999999999999999999964

>PRK02001 hypothetical protein; Validated

Probab=86.49  E-value=4.6  Score=29.42  Aligned_cols=29  Identities=21%  Similarity=0.336  Sum_probs=26.2

Q ss_pred             hhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782          4 LMKLSHETVTIELKNGTQVHGTIQGVDVA   32 (129)
Q Consensus         4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~   32 (129)
                      +.+.+|+.|.|.|.++..+.|+|.++|+.
T Consensus        85 f~r~~G~~v~V~l~~~~~~~G~L~~~~~~  113 (152)
T PRK02001         85 YKKNIGRELEVLTKNGKKIEGELKSADEN  113 (152)
T ss_pred             HHHhCCCEEEEEECCCCEEEEEEEEEeCC
Confidence            45678999999999999999999999975

>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed

Probab=86.46  E-value=1.9  Score=27.54  Aligned_cols=34  Identities=15%  Similarity=0.099  Sum_probs=26.0

Q ss_pred             EEEEcCCcEEEEEEEEecccccceEeeEEEEecCCccee
Q psy15782         13 TIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTT   51 (129)
Q Consensus        13 ~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~   51 (129)
                      .|.++|.+.+ |+|.++..+.|-    .|++.+..+...
T Consensus        29 ~V~~~~~~~I-GkV~dIfGPV~~----pY~~Vk~~~~~~   62 (73)
T PRK13149         29 VVYDKKLKKI-GKVVDVFGPVKE----PYVLVKPDKKDP   62 (73)
T ss_pred             EeECCCCCEe-EEEEEEECCCCC----cEEEEEeCCCCC
Confidence            6788999999 999999999985    566555444433

>PRK14639 hypothetical protein; Provisional

Probab=86.36  E-value=1.4  Score=31.60  Aligned_cols=29  Identities=28%  Similarity=0.288  Sum_probs=26.1

Q ss_pred             hhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782          4 LMKLSHETVTIELKNGTQVHGTIQGVDVA   32 (129)
Q Consensus         4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~   32 (129)
                      +.+.+|++|.|.|.+...+.|+|.++|..
T Consensus        83 f~r~~G~~v~v~l~~~~~~~G~L~~~~~~  111 (140)
T PRK14639         83 FAKSIGELVKITTNEKEKFEGKIVSVDDE  111 (140)
T ss_pred             HHHhCCCEEEEEECCCcEEEEEEEEEeCC
Confidence            45778999999999999999999999984

>PRK14642 hypothetical protein; Provisional

Probab=83.47  E-value=4.7  Score=30.72  Aligned_cols=29  Identities=24%  Similarity=0.486  Sum_probs=25.2

Q ss_pred             hhhcCCCeEEEEEc-------------CCcEEEEEEEEeccc
Q psy15782          4 LMKLSHETVTIELK-------------NGTQVHGTIQGVDVA   32 (129)
Q Consensus         4 L~~l~~~~V~VeLk-------------ng~~~~G~L~~~D~~   32 (129)
                      +.+.+|+.|.|.|+             +.+.++|+|.++|..
T Consensus        95 f~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~  136 (197)
T PRK14642         95 FERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG  136 (197)
T ss_pred             HHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence            35678999999998             679999999999974

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=82.98  E-value=5.8  Score=28.62  Aligned_cols=28  Identities=18%  Similarity=0.349  Sum_probs=24.1

Q ss_pred             hhhcCCCeEEEEE----cCCcEEEEEEEEecc
Q psy15782          4 LMKLSHETVTIEL----KNGTQVHGTIQGVDV   31 (129)
Q Consensus         4 L~~l~~~~V~VeL----kng~~~~G~L~~~D~   31 (129)
                      +.+.+|+.|.|.|    .+...+.|+|.++|.
T Consensus        93 f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         93 FRRFIGREVKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             HHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence            4567899999997    467899999999998

>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes []

Probab=82.18  E-value=3.3  Score=29.34  Aligned_cols=28  Identities=21%  Similarity=0.382  Sum_probs=21.6

Q ss_pred             hhhcCCCeEEEEEc----CCcEEEEEEEEecc
Q psy15782          4 LMKLSHETVTIELK----NGTQVHGTIQGVDV   31 (129)
Q Consensus         4 L~~l~~~~V~VeLk----ng~~~~G~L~~~D~   31 (129)
                      +.+.+|+.|.|.|+    +...+.|+|.+++.
T Consensus        82 ~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~  113 (141)
T PF02576_consen   82 FERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE  113 (141)
T ss_dssp             HHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred             HHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence            45678999999994    45789999999998

; PDB: 1IB8_A.

>PRK09618 flgD flagellar basal body rod modification protein; Provisional

Probab=81.31  E-value=6.2  Score=28.53  Aligned_cols=25  Identities=32%  Similarity=0.421  Sum_probs=23.4

Q ss_pred             hcCCCeEEEEEcCCcEEEEEEEEec
Q psy15782          6 KLSHETVTIELKNGTQVHGTIQGVD   30 (129)
Q Consensus         6 ~l~~~~V~VeLkng~~~~G~L~~~D   30 (129)
                      .|+|++|.+++.++..+.|++.+|.
T Consensus        89 slVGk~V~~~~~~g~~~tG~V~~V~  113 (142)
T PRK09618         89 ELIGKEVEWEGEDGEIVSGTVTSVK  113 (142)
T ss_pred             HHhCCEEEEEeCCCCEEEEEEEEEE
Confidence            5899999999999999999999997

>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold

Probab=80.43  E-value=3.7  Score=26.50  Aligned_cols=29  Identities=28%  Similarity=0.468  Sum_probs=24.1

Q ss_pred             hhhcCCCeEEEEEc---CC-cEEEEEEEEeccc
Q psy15782          4 LMKLSHETVTIELK---NG-TQVHGTIQGVDVA   32 (129)
Q Consensus         4 L~~l~~~~V~VeLk---ng-~~~~G~L~~~D~~   32 (129)
                      +.+.+|+.|.|+|+   ++ +.+.|.|.++|+.
T Consensus        20 ~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~   52 (83)
T cd01734          20 FERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD   52 (83)
T ss_pred             HHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence            35678999999997   55 6899999999983

The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.

>PRK14644 hypothetical protein; Provisional

Probab=80.29  E-value=3.2  Score=29.65  Aligned_cols=29  Identities=14%  Similarity=0.200  Sum_probs=25.3

Q ss_pred             hhhcCCCeEEEEEcCC----cEEEEEEEEeccc
Q psy15782          4 LMKLSHETVTIELKNG----TQVHGTIQGVDVA   32 (129)
Q Consensus         4 L~~l~~~~V~VeLkng----~~~~G~L~~~D~~   32 (129)
                      +.+.+|+.|.|.|++.    ..+.|+|.++|+.
T Consensus        80 f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~  112 (136)
T PRK14644         80 LENHIGEIIDVSLNKEVNKTDFITGELLENNPE  112 (136)
T ss_pred             HHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC
Confidence            4567899999999886    9999999999973

>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis]

Probab=80.10  E-value=14  Score=25.07  Aligned_cols=34  Identities=15%  Similarity=0.129  Sum_probs=26.9

Q ss_pred             EEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcce
Q psy15782         12 VTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPT   50 (129)
Q Consensus        12 V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~   50 (129)
                      -.|.+++...+ |+|..|..++|-    .|++.+..+..
T Consensus        29 ~~V~~~~~k~I-G~V~dVfGPv~~----PY~~Vkp~~~~   62 (98)
T COG3277          29 APVYDANLKRI-GKVVDVFGPVDE----PYILVKPDDRD   62 (98)
T ss_pred             CeeEecCCCEE-EEEEEEEccCCC----CEEEEeccccc
Confidence            37888999999 999999999984    77776664433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	129
1b34_A	119	Crystal Structure Of The D1d2 Sub-Complex From The		9e-35

>pdb|1B34|A Chain A, Crystal Structure Of The D1d2 Sub-Complex From The Human Snrnp Core Domain Length = 119

Iteration: 1
 Score =  141 bits (356), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 78/88 (88%)
Query: 1  MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
          + FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGN
Sbjct: 4  VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGN 63
Query: 61 NIRYYILPDSLPLETLLIDDAPRSKGKR 88
          NIRY+ILPDSLPL+TLL+D  P+ K K+
Sbjct: 64 NIRYFILPDSLPLDTLLVDVEPKVKSKK 91

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	129
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.97
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.95
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.9
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.88
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.84
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.84
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.83
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.83
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.83
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.82
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.81
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.81
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.8
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.8
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.79
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.74
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.73
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.72
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.71
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.71
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.68
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.68
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.68
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.64
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	98.59
3u28_C	114	H/ACA ribonucleoprotein complex subunit 1; pseudou	98.03
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	97.25
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	97.08
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	97.08
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	97.01
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	96.94
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	96.92
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.92
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	96.63
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.32
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	96.14
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	95.81
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	94.28
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	93.89
1ycy_A	71	Conserved hypothetical protein; structural genomic	93.59
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	93.37

>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=99.97  E-value=7.2e-32  Score=188.36  Aligned_cols=87  Identities=75%  Similarity=1.158  Sum_probs=75.5

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCccccccCCC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDD   80 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L~~~   80 (129)
                      ++||+++++++|+|+|+|+.+|+|+|.+||.|||++|+||+++..++++.+++.++|||+||.||++||.|++|++|.++
T Consensus         4 ~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~~lg~v~IRG~nI~~I~~pd~l~~d~~l~~~   83 (119)
T 1b34_A            4 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVDV   83 (119)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTCCHHHHTC--
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEEEcCCeEEEEEeccccccchhHhhh
Confidence            37999999999999999999999999999999999999999998888889999999999999999999999999999999


Q ss_pred             CCccCCC
Q psy15782         81 APRSKGK   87 (129)
Q Consensus        81 ~~~~k~~   87 (129)
                      +||+|.+
T Consensus        84 ~pK~k~~   90 (119)
T 1b34_A           84 EPKVKSK   90 (119)
T ss_dssp             -------
T ss_pred             ccccccc
Confidence            9887654

>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=99.95  E-value=1.1e-28  Score=173.77  Aligned_cols=85  Identities=24%  Similarity=0.418  Sum_probs=78.7

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCccccccCCC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDD   80 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L~~~   80 (129)
                      ++||+++++++|+|||||+++|+|+|.+||.|||++|+||+++..+++...++++|||||+|+||++||.++++++|.++
T Consensus         7 ~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd~l~~~~~l~~~   86 (126)
T 2y9a_D            7 IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNAPMLKSM   86 (126)
T ss_dssp             HHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCSSCSSSSHHHHH
T ss_pred             HHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEccccccchHHhhhh
Confidence            37999999999999999999999999999999999999999998888899999999999999999999999999999765


Q ss_pred             CCccC
Q psy15782         81 APRSK   85 (129)
Q Consensus        81 ~~~~k   85 (129)
                      .++.|
T Consensus        87 ~~k~~   91 (126)
T 2y9a_D           87 KNKNQ   91 (126)
T ss_dssp             HHHHC
T ss_pred             hhccc
Confidence            54443

>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=99.90  E-value=8e-24  Score=136.60  Aligned_cols=68  Identities=26%  Similarity=0.472  Sum_probs=66.0

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      +||+++++++|+|||||+++|+|+|.+||.|||++|+||+++.++++...++.++|||++|+||++||
T Consensus         8 ~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            8 KVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             HHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             HHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEEEeCCEEEEEEcCC
Confidence            69999999999999999999999999999999999999999988888999999999999999999997

>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=99.88  E-value=1e-22  Score=139.18  Aligned_cols=71  Identities=30%  Similarity=0.458  Sum_probs=56.5

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC-cceecceEEEecCeEEEEEcCCCC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK-EPTTLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~-~~~~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      ++||+++++++|+|+|+|+++|.|+|.+||.|||++|+||+++..++ +...++.++|||++|+||++||.+
T Consensus        18 ~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG~nI~~I~~pd~l   89 (105)
T 4emh_A           18 LTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNIKYLRIQDEV   89 (105)
T ss_dssp             --------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECGGGEEEEEC----
T ss_pred             HHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeCCeEEEEecCHHH
Confidence            47999999999999999999999999999999999999999997776 478999999999999999999986

>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=99.84  E-value=5.1e-21  Score=123.70  Aligned_cols=69  Identities=25%  Similarity=0.367  Sum_probs=64.6

Q ss_pred             hhhhhcCCCeEEEEEcCC-cEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCC
Q psy15782          2 NFLMKLSHETVTIELKNG-TQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDS   70 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng-~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~   70 (129)
                      .||.++++++|+|+|+|+ ++|.|+|.+||.|||++|+||+++.+.++...++.++|||++|.||+.||+
T Consensus         8 ~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~nI~~i~~~de   77 (77)
T 1ljo_A            8 QMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQEE   77 (77)
T ss_dssp             HHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             HHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEEEeCCeEEEEEeCCC
Confidence            689999999999999999 999999999999999999999999887778899999999999999999984

>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=99.84  E-value=1.2e-20  Score=124.57  Aligned_cols=70  Identities=27%  Similarity=0.349  Sum_probs=64.1

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      +||+++++++|+|+|+||++|.|+|.+||.|||++|+||+++...++...++.++|||++|+||+.||..
T Consensus         9 ~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~IRG~nI~~i~~~d~~   78 (86)
T 3s6n_F            9 PFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEE   78 (86)
T ss_dssp             HHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEEECGGGEEEEEECC--
T ss_pred             HHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEEEeCCeEEEEEeCCcc
Confidence            6899999999999999999999999999999999999999876655678999999999999999999873

>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=99.83  E-value=1.1e-20  Score=121.99  Aligned_cols=69  Identities=23%  Similarity=0.408  Sum_probs=65.6

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDS   70 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~   70 (129)
                      .||.++++++|+|+|+|+++|.|+|.+||.|||++|+||+++..+.+...++.++|||++|.||+.||.
T Consensus         7 ~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~   75 (77)
T 1i4k_A            7 DVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSPAPG   75 (77)
T ss_dssp             HHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEECC-
T ss_pred             HHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCcEeECCEEEECCCEEEEEEeCCC
Confidence            689999999999999999999999999999999999999999888788899999999999999999986

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

Probab=99.83  E-value=1.1e-20  Score=121.53  Aligned_cols=69  Identities=22%  Similarity=0.375  Sum_probs=64.5

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDS   70 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~   70 (129)
                      .||.++++++|+|+|+||++|.|+|.+||.|||++|+||+++..+.+...++.++|||++|.+|..||+
T Consensus         7 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~e   75 (75)
T 1h64_1            7 DVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTEE   75 (75)
T ss_dssp             HHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             HHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEEECCCEEEEEEeCCC
Confidence            689999999999999999999999999999999999999999888778899999999999999999874

>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=99.83  E-value=2.2e-20  Score=125.04  Aligned_cols=69  Identities=30%  Similarity=0.342  Sum_probs=63.1

Q ss_pred             ChhhhhcCCCeEEEEEcCC-cEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782          1 MNFLMKLSHETVTIELKNG-TQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng-~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      ++||.++++++|+|+|+|+ ++|.|+|.+||.|||++|+||+++..+++...++.++|||++|+||..++
T Consensus        23 ~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~IRG~nI~~I~~~~   92 (93)
T 1n9r_A           23 KPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELP   92 (93)
T ss_dssp             ---CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECC
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEEEcCCeEEEEEeCC
Confidence            4689999999999999999 99999999999999999999999987777789999999999999999886

>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=99.82  E-value=3.6e-20  Score=120.82  Aligned_cols=69  Identities=22%  Similarity=0.300  Sum_probs=64.7

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDS   70 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~   70 (129)
                      .||.++++++|+|+|+||++|.|+|.+||.|||++|+||+++..+.+...++.++|||++|.+|..+|.
T Consensus        12 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   80 (81)
T 1th7_A           12 KVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             HHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEEC--
T ss_pred             HHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEEECCCEEEEEEecCC
Confidence            689999999999999999999999999999999999999999888888999999999999999999874

>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=6.4e-20  Score=118.42  Aligned_cols=69  Identities=20%  Similarity=0.346  Sum_probs=53.8

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDS   70 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~   70 (129)
                      .||.++++++|+|+|+||++|.|+|.+||.|||++|+||+++..+++...++.++|||++|.+|...|.
T Consensus         7 ~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            7 PELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             -------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEEECSSSEEEEEC---
T ss_pred             HHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEEECCCeEEEEEeccC
Confidence            589999999999999999999999999999999999999999888888899999999999999998775

>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=99.81  E-value=5.6e-20  Score=118.34  Aligned_cols=68  Identities=31%  Similarity=0.438  Sum_probs=63.1

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      +||+++++++|+|+|+||++|.|+|.+||.|||++|+||+++...++...++.++|||++|.||...|
T Consensus         7 ~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 4emk_B            7 EFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVLYVSALD   74 (75)
T ss_dssp             HHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEEEEGGGSSEEEEC-
T ss_pred             HHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEEEcCCeEEEEEecC
Confidence            68999999999999999999999999999999999999999877667789999999999999998754

>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=99.80  E-value=1.1e-19  Score=118.50  Aligned_cols=67  Identities=15%  Similarity=0.244  Sum_probs=63.4

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      .||.++++++|+|+|+|+++|.|+|.+||.|||++|+||+++ +..+...++.++|||++|.+|+.+|
T Consensus        14 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~~~~lg~v~iRG~~I~~i~~~d   80 (81)
T 1i8f_A           14 ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTMVVRGENVLFISPVP   80 (81)
T ss_dssp             HHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETTEEEEEEEEEECGGGEEEEEECC
T ss_pred             HHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCCcccCCCEEEECCCEEEEEEeCC
Confidence            589999999999999999999999999999999999999999 6667789999999999999999887

>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=99.80  E-value=2.5e-19  Score=117.39  Aligned_cols=66  Identities=26%  Similarity=0.416  Sum_probs=62.9

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      +.||.++++++|+|+|+|+++|.|+|.+||.|||++|+||+++..+.+...++.++|||++|.||+
T Consensus        17 ~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~IRG~~I~~i~   82 (83)
T 1mgq_A           17 LDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYIS   82 (83)
T ss_dssp             THHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEE
T ss_pred             HHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEEECCCEEEEEE
Confidence            468999999999999999999999999999999999999999988878889999999999999986

>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=99.79  E-value=4.4e-19  Score=118.91  Aligned_cols=68  Identities=21%  Similarity=0.197  Sum_probs=63.2

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEe-cCCcceecceEEEecCeEEEEEcCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTV-KGKEPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~-~~~~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      .||.++++++|+|+|+|+++|.|+|.+||.|||++|+||+++. +.++...++.++|||++|.||+...
T Consensus        23 ~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG~nI~~i~p~~   91 (94)
T 4emk_A           23 ELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGNGMCMLIPGG   91 (94)
T ss_dssp             HHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECSTTEEEEEECC
T ss_pred             HHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcCCEEEEEEeCC
Confidence            6899999999999999999999999999999999999999998 5667789999999999999998643

>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=99.74  E-value=2.7e-18  Score=121.20  Aligned_cols=67  Identities=18%  Similarity=0.167  Sum_probs=62.5

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      ++||.++++++|+|+|+||++|.|+|.+||.|||++|+||+++.    ...++.++|||++|.+|+.||..
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~----~~~lg~v~IRG~nI~~I~~~d~~   68 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA----GEKFNRVFIMYRYIVHIDSTERR   68 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT----CCEEEEEEECGGGEEEEEECCCC
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc----CCEeceEEEeCCeEEEEEcCCcc
Confidence            36899999999999999999999999999999999999999873    36789999999999999999986

>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=99.73  E-value=6.3e-18  Score=112.24  Aligned_cols=69  Identities=22%  Similarity=0.242  Sum_probs=61.8

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEec----------CCcceecceEEEecCeEEEEEcCCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK----------GKEPTTLDSISLRGNNIRYYILPDS   70 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~----------~~~~~~l~~~~IrGn~Ir~Ii~pd~   70 (129)
                      .+|.++++++|+|+|+||++|.|+|.+||.|||++|+||+++.+          ..+...++.++|||++|.+|.+++.
T Consensus         7 ~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~~~~~   85 (91)
T 1d3b_B            7 SKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGP   85 (91)
T ss_dssp             CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEEEC
T ss_pred             HHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEEcCCC
Confidence            47899999999999999999999999999999999999998642          1235789999999999999999876

>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=99.72  E-value=2.8e-17  Score=110.36  Aligned_cols=70  Identities=21%  Similarity=0.285  Sum_probs=61.8

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC-------CcceecceEEEecCeEEEEEcCCCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG-------KEPTTLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~-------~~~~~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      .+|.++++++|.|+|+|+.+|.|+|.+||.|||++|+||+++...       .....++.++|||++|.+|..++..
T Consensus        13 ~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d~~   89 (96)
T 3bw1_A           13 DLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPSED   89 (96)
T ss_dssp             HHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC--
T ss_pred             HHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecCcc
Confidence            589999999999999999999999999999999999999988643       2246799999999999999998873

>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=99.71  E-value=4.8e-17  Score=123.94  Aligned_cols=70  Identities=21%  Similarity=0.228  Sum_probs=62.5

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEec----------CCcceecceEEEecCeEEEEEcCCCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK----------GKEPTTLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~----------~~~~~~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      .+|.++++++|.|+|+|+++|.|+|.+||.|||++|+|++++..          ..+...++.++|||+||.+|.+.+.-
T Consensus         7 ~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isve~pP   86 (231)
T 3pgw_B            7 SKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGPP   86 (231)
T ss_pred             HHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEecCCC
Confidence            47899999999999999999999999999999999999999753          12457899999999999999987663

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

Probab=99.71  E-value=5.7e-17  Score=108.34  Aligned_cols=68  Identities=16%  Similarity=0.283  Sum_probs=60.7

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC----C---------cceecceEEEecCeEEEEEc
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG----K---------EPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~----~---------~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      +.||..+++++|+|+|+++.+|.|+|.+||.|||++|+||+++...    +         +...++.++|||++|.+|..
T Consensus        11 l~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nVv~I~p   90 (93)
T 4emg_A           11 LDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVILIAP   90 (93)
T ss_dssp             THHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGEEEEEC
T ss_pred             HHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeEEEEEe
Confidence            4689999999999999999999999999999999999999988752    2         24789999999999999987


Q ss_pred             C
Q psy15782         68 P   68 (129)
Q Consensus        68 p   68 (129)
                      |
T Consensus        91 ~   91 (93)
T 4emg_A           91 P   91 (93)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=99.68  E-value=2.8e-17  Score=114.66  Aligned_cols=69  Identities=20%  Similarity=0.295  Sum_probs=61.6

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC---------C-c-----ceecceEEEecCeEEEEE
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG---------K-E-----PTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~---------~-~-----~~~l~~~~IrGn~Ir~Ii   66 (129)
                      .||.++++++|+|+|+|+.+|.|+|.+||.|||++|+||+++..+         + .     ...++.++|||++|.+|.
T Consensus        31 ~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~nVv~I~  110 (121)
T 2fwk_A           31 ALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAMLV  110 (121)
T ss_dssp             HHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEEEEE
T ss_pred             HHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCEEEEEE
Confidence            689999999999999999999999999999999999999988743         2 2     567999999999999999


Q ss_pred             cCCC
Q psy15782         67 LPDS   70 (129)
Q Consensus        67 ~pd~   70 (129)
                      ..+.
T Consensus       111 ~~~~  114 (121)
T 2fwk_A          111 PGGD  114 (121)
T ss_dssp             SSSC
T ss_pred             ecCC
Confidence            8775

>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=99.68  E-value=3.4e-17  Score=109.32  Aligned_cols=68  Identities=24%  Similarity=0.347  Sum_probs=61.4

Q ss_pred             hhhhhcCCCeEEEEE----cCCcEEEEEEEEecccccceEeeEEEEec-CCcceecceEEEecCeEEEEEcCC
Q psy15782          2 NFLMKLSHETVTIEL----KNGTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         2 ~~L~~l~~~~V~VeL----kng~~~~G~L~~~D~~mNl~Lkdv~~~~~-~~~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      .||.++++++|+|+|    +++.+|.|+|.+||.|||++|+||+++.. ..+...++.++|||++|.+|..++
T Consensus        19 ~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~nV~~i~~~~   91 (92)
T 3s6n_E           19 NLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSVS   91 (92)
T ss_dssp             HHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGGGEEEEEEC-
T ss_pred             HHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCCEEEEEEeCC
Confidence            689999999999998    99999999999999999999999999874 455678999999999999998764

>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=99.68  E-value=1.9e-16  Score=109.30  Aligned_cols=69  Identities=20%  Similarity=0.322  Sum_probs=56.6

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC-------CcceecceEEEecCeEEEEEcCCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG-------KEPTTLDSISLRGNNIRYYILPDS   70 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~-------~~~~~l~~~~IrGn~Ir~Ii~pd~   70 (129)
                      ..|.++++++|.|+|+|+.+|.|+|.+||.|||++|+||+++..+       .....++.++|||++|.+|..+|.
T Consensus        26 ~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~  101 (113)
T 4emk_C           26 LDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDG  101 (113)
T ss_dssp             ------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC-
T ss_pred             HHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCc
Confidence            468899999999999999999999999999999999999998754       246789999999999999999886

>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=99.64  E-value=3.3e-16  Score=108.70  Aligned_cols=69  Identities=19%  Similarity=0.251  Sum_probs=58.6

Q ss_pred             hhhhhcC--CCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC--------------cceecceEEEecCeEEEE
Q psy15782          2 NFLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK--------------EPTTLDSISLRGNNIRYY   65 (129)
Q Consensus         2 ~~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~--------------~~~~l~~~~IrGn~Ir~I   65 (129)
                      .||.+++  +++|.|+|+|+.+|.|+|.+||.|||++|+||+++....              ....++.++|||++|.+|
T Consensus        30 ~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~nVv~I  109 (118)
T 1b34_B           30 SVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVV  109 (118)
T ss_dssp             HHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEEEE
T ss_pred             HHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCCEEEEE
Confidence            5788888  599999999999999999999999999999999875321              023589999999999999


Q ss_pred             EcCCC
Q psy15782         66 ILPDS   70 (129)
Q Consensus        66 i~pd~   70 (129)
                      ..++.
T Consensus       110 ~~~~~  114 (118)
T 1b34_B          110 LRNPL  114 (118)
T ss_dssp             EECCC
T ss_pred             EeCch
Confidence            99876

>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}

Probab=98.59  E-value=2.1e-07  Score=60.92  Aligned_cols=62  Identities=13%  Similarity=0.132  Sum_probs=53.1

Q ss_pred             hhhhcCCCeEEEEEcCCcEEEEEEEEec-ccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCC
Q psy15782          3 FLMKLSHETVTIELKNGTQVHGTIQGVD-VAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDS   70 (129)
Q Consensus         3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D-~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~   70 (129)
                      .|+++++|+|.|.|.|+++|+|.|.+|| ..+|+.|.|+      .+...+..++|.|..|..|.+-+.
T Consensus        11 el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~------~~~~~~~~~iI~G~aI~eI~v~~~   73 (86)
T 1y96_A           11 EWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF------LEDGSMSVTGIMGHAVQTVETMNE   73 (86)
T ss_dssp             HHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE------CTTSCEEEEEECGGGEEEEEEEEC
T ss_pred             HHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec------ccCCeEEEEEEecceEEEEEEecc
Confidence            4788999999999999999999999999 8999999998      233444678999999998877655

>3u28_C H/ACA ribonucleoprotein complex subunit 1; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_C

Probab=98.03  E-value=2.2e-06  Score=58.68  Aligned_cols=67  Identities=28%  Similarity=0.434  Sum_probs=53.8

Q ss_pred             hhhhcCCCeE-----EEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCC-Cccccc
Q psy15782          3 FLMKLSHETV-----TIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDS-LPLETL   76 (129)
Q Consensus         3 ~L~~l~~~~V-----~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~-l~l~~~   76 (129)
                      +++++.+++|     .|.|+|.+.| |+|.+|...+|-    +|++.+..+.+...++..   ..++++.|++ |+|+.|
T Consensus        41 lV~k~~~~~VP~fNapVy~enK~~I-GKVdEIFGPin~----~YfsVK~~~gv~a~Sfk~---gdk~YId~~kllPl~rF  112 (114)
T 3u28_C           41 IVCRSINTKIPYFNAPIYLENKTQV-GKVDEILGPLNE----VFFTIKCGDGVQATSFKE---GDKFYIAADKLLPIERF  112 (114)
T ss_dssp             EEEEECSSSEECTTCEEECTTCCEE-EEEEEEESBTTS----CEEEEEECTTCCGGGCCT---TCEEEEEGGGEECGGGG
T ss_pred             EEEEeCCCCCCCCCCEeEccCCccc-eeEeEEeCCCCc----cEEEEEecCCCccccccc---CCEEEECccccCcHHhc
Confidence            5667776666     8999999999 999999999995    777777777777776654   3666778887 899998


Q ss_pred             c
Q psy15782         77 L   77 (129)
Q Consensus        77 L   77 (129)
                      |
T Consensus       113 l  113 (114)
T 3u28_C          113 L  113 (114)
T ss_dssp             C
T ss_pred             C
Confidence            8

>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A

Probab=97.25  E-value=0.0014  Score=41.92  Aligned_cols=58  Identities=21%  Similarity=0.295  Sum_probs=40.2

Q ss_pred             hhhhcC--CCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCc
Q psy15782          3 FLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLP   72 (129)
Q Consensus         3 ~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~   72 (129)
                      ||..+.  ..+|+|+|.||..++|+|.+||.|+=+      +.. ++.     ..+|-...|..|.....++
T Consensus        15 fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~Vl------L~~-~g~-----qqlIYKhAISTI~p~~~v~   74 (78)
T 3ahu_A           15 FLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVL------LES-EGK-----QQLIYKHAISTFAPQKNVQ   74 (78)
T ss_dssp             HHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEE------EES-SSC-----EEEEEGGGEEEEEESSCCC
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEE------EEE-CCe-----eEEEEcceEEEEeeccccc
Confidence            666664  678999999999999999999999833      221 211     2345556677776555443

>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii}

Probab=97.08  E-value=0.00081  Score=42.28  Aligned_cols=33  Identities=24%  Similarity=0.281  Sum_probs=27.4

Q ss_pred             hhhhc--CCCeEEEEEcCCcEEEEEEEEecccccc
Q psy15782          3 FLMKL--SHETVTIELKNGTQVHGTIQGVDVAMNT   35 (129)
Q Consensus         3 ~L~~l--~~~~V~VeLkng~~~~G~L~~~D~~mNl   35 (129)
                      ||..+  ...+|+|+|.||..++|+|.+||.|+=+
T Consensus        17 fLn~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVl   51 (71)
T 2qtx_A           17 FEYARRLNGKKVKIFLRNGEVLDAEVTGVSNYEIM   51 (71)
T ss_dssp             CCGGGGGTTCEEEEEETTSCEEEEEEEEECSSEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEE
Confidence            55554  4567999999999999999999999843

>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=97.08  E-value=0.0033  Score=39.77  Aligned_cols=56  Identities=23%  Similarity=0.288  Sum_probs=40.9

Q ss_pred             hhhhcC--CCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCC
Q psy15782          3 FLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         3 ~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      ||+.+.  ..+|+|+|.||..+.|+|.++|.|+=+      +.  ++     ...+|-...|.+|.....+
T Consensus        13 ~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vl------L~--~~-----~~~LIYKhAIsTI~p~~~v   70 (74)
T 2ylb_A           13 FLNALRRERVPVSIYLVNGIKLQGQIESFDQFVIL------LK--NT-----VSQMVYKHAISTVVPSRPV   70 (74)
T ss_dssp             HHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEE------EE--SS-----SEEEEEGGGEEEEEESSCC
T ss_pred             HHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEE------EE--CC-----ceEEEEeeeEEEEeEcccc
Confidence            666665  668999999999999999999999832      22  11     3345666778877765544

>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=97.01  E-value=0.00063  Score=43.91  Aligned_cols=57  Identities=21%  Similarity=0.265  Sum_probs=41.3

Q ss_pred             hhhhcC--CCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCc
Q psy15782          3 FLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLP   72 (129)
Q Consensus         3 ~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~   72 (129)
                      ||..+.  ..+|+|+|.||..++|+|.+||.|+=+      +. .+      ...+|-...|..|.....+.
T Consensus        11 fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVl------L~-~~------~qqLVYKHAISTI~p~~~v~   69 (82)
T 1u1s_A           11 YLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVIL------LK-NT------VSQMVYKHAISTVVPSRPVR   69 (82)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEE------EE-SS------SCEEEEGGGEEEEEESSCCC
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEE------Ee-cC------ceEEEEeeeeEEEeeccccc
Confidence            666664  668999999999999999999999833      21 11      23456667788777666554

>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=96.94  E-value=0.00094  Score=42.63  Aligned_cols=58  Identities=19%  Similarity=0.225  Sum_probs=38.4

Q ss_pred             hhhhhcC--CCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCC
Q psy15782          2 NFLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         2 ~~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      .||+.+.  ..+|+|+|.||..+.|+|.+||.|+=+      +.. ++.     ..+|-...|.+|.....+
T Consensus        10 ~fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~Vl------L~~-~g~-----~qLIYKhAISTI~p~~~v   69 (77)
T 1kq1_A           10 KALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVS------LNS-QGK-----QHLIYKHAISTYTVETEG   69 (77)
T ss_dssp             HHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEE------EEE-TTE-----EEEEEGGGEEEEEC----
T ss_pred             HHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEE------EEE-CCe-----eEEEEeeeEEEEeECccc
Confidence            3677765  678999999999999999999999833      221 221     234555667776654444

>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A

Probab=96.92  E-value=0.0032  Score=42.29  Aligned_cols=58  Identities=24%  Similarity=0.307  Sum_probs=41.8

Q ss_pred             hhhhhcCCC--eEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCc
Q psy15782          2 NFLMKLSHE--TVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLP   72 (129)
Q Consensus         2 ~~L~~l~~~--~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~   72 (129)
                      .||+.+..+  +|+|+|.||..+.|+|.+||.|+=+      +.  +.     ...+|-.-.|.+|.....+.
T Consensus        12 ~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~Vl------L~--~~-----kqqLIYKHAISTI~p~~~v~   71 (104)
T 2y90_A           12 PFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVIL------LK--NT-----VSQMVYKHAISTVVPSRPVS   71 (104)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEE------EE--SS-----SEEEEEGGGEEEEEESSCCC
T ss_pred             HHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEE------EE--CC-----ceEEEEeeeeEEEeeccccc
Confidence            367777544  7999999999999999999999832      22  11     33456667788877666553

>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2

Probab=96.92  E-value=0.0015  Score=41.82  Aligned_cols=58  Identities=22%  Similarity=0.317  Sum_probs=41.0

Q ss_pred             hhhhcC--CCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCcc
Q psy15782          3 FLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPL   73 (129)
Q Consensus         3 ~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l   73 (129)
                      ||..+.  ..+|+|+|.||..+.|+|.+||.|+=+      + . ++.     ..+|-.-.|.+|.....+.+
T Consensus        12 fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~Vl------L-~-~g~-----~qLIYKhAISTI~P~~~v~~   71 (79)
T 3sb2_A           12 FLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVL------L-R-NTV-----TQMVYKHAISTVVPARAVNL   71 (79)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEE------E-E-SSS-----EEEEEGGGEEEEEESSCCCC
T ss_pred             HHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEE------E-E-CCc-----eEEEEeeeEEEEeecCceec
Confidence            666664  456999999999999999999999833      2 1 222     23455677888776665543

>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster}

Probab=96.63  E-value=0.018  Score=37.47  Aligned_cols=63  Identities=17%  Similarity=0.207  Sum_probs=51.6

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEec-ccccceEeeEEEEecCCcc---------eecceEEEecCeEEEEEcCC
Q psy15782          7 LSHETVTIELKNGTQVHGTIQGVD-VAMNTHLKTVKMTVKGKEP---------TTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         7 l~~~~V~VeLkng~~~~G~L~~~D-~~mNl~Lkdv~~~~~~~~~---------~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      ++|++|.+--|.+..|.|+|..+| ..-.+.|+||...-+.+++         ..++.+..||+.|+-+.+-+
T Consensus        11 yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~~   83 (88)
T 2vxe_A           11 ELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVN   83 (88)
T ss_dssp             CTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEECC
T ss_pred             ccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEEec
Confidence            589999999999999999999999 4567899999988765542         34678888999998776543

>4a53_A EDC3; RNA binding protein; NMR {Schizosaccharomyces pombe} PDB: 4a54_A

Probab=96.32  E-value=0.0054  Score=42.30  Aligned_cols=37  Identities=19%  Similarity=0.287  Sum_probs=30.0

Q ss_pred             hhcCCCeEEEEEcCCcEEEEEEEEecc-cccceEeeEE
Q psy15782          5 MKLSHETVTIELKNGTQVHGTIQGVDV-AMNTHLKTVK   41 (129)
Q Consensus         5 ~~l~~~~V~VeLkng~~~~G~L~~~D~-~mNl~Lkdv~   41 (129)
                      ..++|.+|.|+|++++.++|+|..||. .+-+.|.+|.
T Consensus         8 sqFlGy~V~v~LkDgs~~qG~I~~vd~k~LtL~~~~a~   45 (125)
T 4a53_A            8 ADFYGSNVEVLLNNDSKARGVITNFDSSNSILQLRLAN   45 (125)
T ss_dssp             HHHTTCEEEEEETTSCEEEEEEEEEETTTTEEEEEETT
T ss_pred             HHhcCceEEEEECCCCEeeEEEEeecCCeeEEeccccc
Confidence            457899999999999999999999983 3334348884

>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=96.14  E-value=0.013  Score=38.59  Aligned_cols=62  Identities=18%  Similarity=0.275  Sum_probs=51.0

Q ss_pred             hcCCCeEEEEEcCCcEEEEEEEEec-ccccceEeeEEEEecCCcc---------eecceEEEecCeEEEEEc
Q psy15782          6 KLSHETVTIELKNGTQVHGTIQGVD-VAMNTHLKTVKMTVKGKEP---------TTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         6 ~l~~~~V~VeLkng~~~~G~L~~~D-~~mNl~Lkdv~~~~~~~~~---------~~l~~~~IrGn~Ir~Ii~   67 (129)
                      .++|++|.+--|.+..|.|+|..+| ..--+.|+||...-+.+++         ..++.+..||+.|+-+.+
T Consensus        16 ~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V   87 (95)
T 2fb7_A           16 PYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTV   87 (95)
T ss_dssp             CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEE
T ss_pred             cccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEE
Confidence            5789999999999999999999999 4567889999877665442         457888999999987665

>1y96_B Gemin7, SIP3, GEM-associated protein 7; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}

Probab=95.81  E-value=0.032  Score=36.04  Aligned_cols=60  Identities=20%  Similarity=0.329  Sum_probs=47.6

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecc-cccceEeeEEEEecCCcce-ecceEEEecCeEEEEEc
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDV-AMNTHLKTVKMTVKGKEPT-TLDSISLRGNNIRYYIL   67 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~-~mNl~Lkdv~~~~~~~~~~-~l~~~~IrGn~Ir~Ii~   67 (129)
                      ++|..+.+++|.+.|...+++.|+...+|. ..|+..++-      +.|+ ..++-++|.+.|..+..
T Consensus        22 r~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L------~TPiGv~~eAlLR~~Dii~~sF   83 (85)
T 1y96_B           22 RSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQL------QTPIGVQAEALLRCSDIISYTF   83 (85)
T ss_dssp             HHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEE------CCTTCCEEEEEEEGGGEEEEEE
T ss_pred             HHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhc------CCCcccchhhhhhcCCEEEEEe
Confidence            567788999999999999999999999994 557655543      2332 36778899999988765

>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis SP}

Probab=94.28  E-value=0.044  Score=34.19  Aligned_cols=33  Identities=27%  Similarity=0.313  Sum_probs=28.1

Q ss_pred             ChhhhhcC--CCeEEEEEcCCcEEEEEEEEecccc
Q psy15782          1 MNFLMKLS--HETVTIELKNGTQVHGTIQGVDVAM   33 (129)
Q Consensus         1 ~~~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~m   33 (129)
                      ||.|+.++  ..+|.|+|-+|..+.|+|.-.|.++
T Consensus        11 vR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~c   45 (70)
T 3hfo_A           11 VRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDG   45 (70)
T ss_dssp             HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE
T ss_pred             HHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCE
Confidence            45677765  4579999999999999999999987

>2vc8_A Enhancer of mRNA-decapping protein 3; P-BODY component, cytoplasm, SM-like protein, protein-binding; 1.31A {Homo sapiens}

Probab=93.89  E-value=0.24  Score=31.83  Aligned_cols=60  Identities=13%  Similarity=0.168  Sum_probs=45.9

Q ss_pred             hhcCCCeEEEEEcCCc-EEEEEEEEeccc-ccceEeeEEEEecCCcceecceEEEecCeEEEEEc
Q psy15782          5 MKLSHETVTIELKNGT-QVHGTIQGVDVA-MNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         5 ~~l~~~~V~VeLkng~-~~~G~L~~~D~~-mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      .+.+|..|.|+-++.. +|+|.|..+|.. -|+.|.++.   +++-+-+..++.++++.|.-+-+
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f---~NG~~~~s~eVtls~~DI~~L~i   66 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF---HNGVKCLVPEVTFRAGDITELKI   66 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE---ETTEECSSSEEEEEGGGCSEEEE
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh---hCCCCCCCcEEEEEecChhheEE
Confidence            3678999999999999 999999999965 478899984   34444444567777777664433

>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=93.59  E-value=0.38  Score=29.37  Aligned_cols=60  Identities=17%  Similarity=0.254  Sum_probs=38.8

Q ss_pred             hhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEc
Q psy15782          3 FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      .|.+-.+++|-|-.-....+.|+|+.||.-. +.|+||+.+.    ......++++=+.|-+|.+
T Consensus        10 tL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~----GNk~k~liv~idDinWimL   69 (71)
T 1ycy_A           10 VLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI----GNRGKQMLIGLEDINWIML   69 (71)
T ss_dssp             HHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT----EEEEEEEEEEGGGEEEEEE
T ss_pred             HHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHh----ccccceeEEEeccceEEEe
Confidence            3556689999999999999999999999865 5688887652    2333445555455555543

>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP}

Probab=93.37  E-value=0.067  Score=33.52  Aligned_cols=33  Identities=24%  Similarity=0.329  Sum_probs=28.3

Q ss_pred             ChhhhhcCC--CeEEEEEcCCcEEEEEEEEecccc
Q psy15782          1 MNFLMKLSH--ETVTIELKNGTQVHGTIQGVDVAM   33 (129)
Q Consensus         1 ~~~L~~l~~--~~V~VeLkng~~~~G~L~~~D~~m   33 (129)
                      ||.|++++-  .+|.|+|-+|..+.|+|.-.|.++
T Consensus        13 vR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~c   47 (72)
T 3hfn_A           13 IRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTC   47 (72)
T ss_dssp             HHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSE
T ss_pred             HHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCE
Confidence            467788764  469999999999999999999987

---

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	129
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	1e-33
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	3e-20
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	2e-17
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	7e-17
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	8e-17
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	2e-16
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	3e-16
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	9e-16
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	4e-15
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-13
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	4e-05
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	2e-04

>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 =  110 bits (277), Expect = 1e-33
 Identities = 61/77 (79%), Positives = 71/77 (92%)

Query: 2  NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNN 61
           FLMKLSHETVTIELKNGTQVHGTI GVDV+MNTHLK VKMT+K +EP  L+++S+RGNN
Sbjct: 4  RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNN 63

Query: 62 IRYYILPDSLPLETLLI 78
          IRY+ILPDSLPL+TLL+
Sbjct: 64 IRYFILPDSLPLDTLLV 80

>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 = 76.4 bits (188), Expect = 3e-20
 Identities = 18/69 (26%), Positives = 30/69 (43%)

Query: 1  MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
          +  L +     VT E   G    G +   +  MN  +  + +T +      L+ + +RG 
Sbjct: 4  IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGC 63

Query: 61 NIRYYILPD 69
           IR+ ILPD
Sbjct: 64 KIRFLILPD 72

>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 = 70.5 bits (173), Expect = 2e-17
 Identities = 14/79 (17%), Positives = 21/79 (26%), Gaps = 4/79 (5%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
           L  L    V + L NG    G +  VD  +N  L         K       + +    I
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFN----RVFIMYRYI 59

Query: 63 RYYILPDSLPLETLLIDDA 81
           +    +           A
Sbjct: 60 VHIDSTERRIDMREFAKQA 78

>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 = 67.4 bits (165), Expect = 7e-17
 Identities = 17/64 (26%), Positives = 31/64 (48%)

Query: 1  MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
          ++ L    +  V I+LK   +  G ++  D+ MN  L   +    G+    L ++ +RG+
Sbjct: 8  LDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGD 67

Query: 61 NIRY 64
          NI Y
Sbjct: 68 NIVY 71

>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 = 67.0 bits (164), Expect = 8e-17
 Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 4  LMKLSHETVTIELK-NGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
          L  L +  V ++LK N T+  GT+   D   N  L   +  V G    TL  I +R NN+
Sbjct: 1  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNV 60

Query: 63 RY 64
           Y
Sbjct: 61 LY 62

>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 = 66.7 bits (163), Expect = 2e-16
 Identities = 16/64 (25%), Positives = 31/64 (48%)

Query: 1  MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
          ++ L +     V + LK G +  GT+ G D+ MN  L   +    G+    + S+ +RG+
Sbjct: 5  LDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGD 64

Query: 61 NIRY 64
           + +
Sbjct: 65 TVVF 68

>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 = 65.9 bits (161), Expect = 3e-16
 Identities = 15/62 (24%), Positives = 27/62 (43%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
           L +  +  V ++LK   +V G ++  D  MN  L   +          L +I +RG+N+
Sbjct: 11 VLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNV 70

Query: 63 RY 64
            
Sbjct: 71 IL 72

>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 = 64.7 bits (158), Expect = 9e-16
 Identities = 15/64 (23%), Positives = 30/64 (46%)

Query: 1  MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
          ++ + +   + V + LK G +  G + G D+ +N  L   +M   G+       I +RG+
Sbjct: 4  LDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGD 63

Query: 61 NIRY 64
          N+  
Sbjct: 64 NVLA 67

>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 = 63.2 bits (154), Expect = 4e-15
 Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 1  MNFLMKLSHETVTIELKNG-TQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRG 59
             +  +  + + +E+K    Q+ G ++GVD  MN +L         ++  +L  I LRG
Sbjct: 7  NQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRG 66

Query: 60 NNIRY 64
          NN+  
Sbjct: 67 NNVVL 71

>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 = 59.0 bits (143), Expect = 1e-13
 Identities = 11/62 (17%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 3  FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
           L     + V ++L++  ++ G ++  D  +N  L+  +  + G       ++ +RG N+
Sbjct: 6  TLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNV-YKRGTMVVRGENV 64

Query: 63 RY 64
           +
Sbjct: 65 LF 66

>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 = 37.5 bits (87), Expect = 4e-05
 Identities = 17/87 (19%), Positives = 32/87 (36%), Gaps = 16/87 (18%)

Query: 1  MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTV---------------KMTVK 45
          +  + K     + + +K   +  G ++G D  +N  L  V                  +K
Sbjct: 7  LALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLK 66

Query: 46 GKEPTTLDSISLRGNNIRYYILPDSLP 72
                L++I L GNN+   ++P   P
Sbjct: 67 RVMVNRLETILLSGNNVA-MLVPGGDP 92

>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 = 35.2 bits (81), Expect = 2e-04
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 11/79 (13%)

Query: 4  LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVK----------MTVKGKEPTTLD 53
          +++     +   L++G    GT +  D  MN  L                 + +E   L 
Sbjct: 3  MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 62

Query: 54 SISLRGNNIRYYILPDSLP 72
           + LRG N+   +  +  P
Sbjct: 63 LVLLRGENL-VSMTVEGPP 80

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	129
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.94
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.91
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.85
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.82
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.82
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.82
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.81
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.8
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.79
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.78
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.6
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.54
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.49
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	96.92
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	96.91
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	96.55
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	93.98
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	89.42

>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=99.94  E-value=2e-27  Score=153.85  Aligned_cols=78  Identities=78%  Similarity=1.215  Sum_probs=75.3

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCccccccC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLI   78 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L~   78 (129)
                      |+||+++.|++|+||||||.+|+|+|.+||.|||++|+||+++..++++..++.+||||++|+||++||+++++++|+
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~lPd~l~~~~~L~   80 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLV   80 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTCCHHHHTC
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEECCCCcccccccC
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999998873

>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=99.91  E-value=1.6e-24  Score=137.41  Aligned_cols=69  Identities=26%  Similarity=0.477  Sum_probs=66.7

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      ++||.+++|+.|+|||||+++|+|+|.+||.|||++|+||+++..+++...++.+||||++|+||++||
T Consensus         4 l~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           4 IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             hHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCeEEEECCEEEEEEcCC
Confidence            368999999999999999999999999999999999999999999999999999999999999999997

>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=99.85  E-value=2.3e-21  Score=121.44  Aligned_cols=66  Identities=35%  Similarity=0.467  Sum_probs=61.5

Q ss_pred             hhhcCCCeEEEEEc-CCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE-cCC
Q psy15782          4 LMKLSHETVTIELK-NGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI-LPD   69 (129)
Q Consensus         4 L~~l~~~~V~VeLk-ng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii-~pd   69 (129)
                      |+++++++|+|+|| ++++|+|+|.+||.|||++|+||+++..++....++.++|||++|+||. +||
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~IRG~nI~~I~~~pd   68 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN   68 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECCC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCcccCcCeEEEECCEEEEEEeCCC
Confidence            68899999999999 5678999999999999999999999988888899999999999999996 776

>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=99.82  E-value=1.7e-20  Score=119.03  Aligned_cols=66  Identities=26%  Similarity=0.416  Sum_probs=63.1

Q ss_pred             ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782          1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      +.||.++++++|+|+|+|+.+|.|+|.+||.+||++|+||+++..+++...++.++|||++|.||+
T Consensus         8 l~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~IRG~~I~~I~   73 (74)
T d1mgqa_           8 LDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYIS   73 (74)
T ss_dssp             THHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEE
T ss_pred             HHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEEEeCCEEEEEe
Confidence            468999999999999999999999999999999999999999998888999999999999999986

>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=99.82  E-value=1.8e-20  Score=118.38  Aligned_cols=65  Identities=25%  Similarity=0.445  Sum_probs=62.6

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      .+|.++++++|+|+|+|+++|.|+|.+||.|||++|+||+++...++...++.++|||++|.||+
T Consensus         6 ~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~Is   70 (72)
T d1i4k1_           6 DVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVS   70 (72)
T ss_dssp             HHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEEEEECGGGEEEEE
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcceEEEeCCeEEEEE
Confidence            68999999999999999999999999999999999999999988888899999999999999986

>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=99.82  E-value=1.8e-20  Score=118.00  Aligned_cols=66  Identities=23%  Similarity=0.377  Sum_probs=62.7

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEc
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      .+|.++++++|+|+|+|+.+|.|+|.+||.+||++|+||+++.++++...++.++|||++|.||+.
T Consensus         5 ~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           5 DVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             HHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             HHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCcEeEcCcEEEECCeEEEEeC
Confidence            689999999999999999999999999999999999999999888888999999999999999863

>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=99.81  E-value=4.4e-20  Score=117.53  Aligned_cols=66  Identities=26%  Similarity=0.369  Sum_probs=62.3

Q ss_pred             hhhhhcCCCeEEEEEcCC-cEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEc
Q psy15782          2 NFLMKLSHETVTIELKNG-TQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng-~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      ++|+++++++|+|+|+|+ ++|.|+|.+||.|||++|+||+++..+++...++.++|||++|+||..
T Consensus         8 ~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           8 QMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             HHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             HHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCcEeEcceEEEeCCEEEEEEC
Confidence            689999999999999987 699999999999999999999999888888999999999999999874

>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=99.80  E-value=8.3e-20  Score=116.41  Aligned_cols=65  Identities=23%  Similarity=0.330  Sum_probs=62.7

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      ++|.++++++|+|+|+||.+|.|+|.+||.|||++|+||+++..++++..++.++|||++|.||.
T Consensus        10 ~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~~~v~iRG~~I~~I~   74 (76)
T d1th7a1          10 KVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILIS   74 (76)
T ss_dssp             HHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEE
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCcccCcceEEEECCEEEEEE
Confidence            68999999999999999999999999999999999999999999989999999999999999986

>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=99.79  E-value=1.5e-19  Score=113.85  Aligned_cols=65  Identities=15%  Similarity=0.292  Sum_probs=59.9

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEc
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      .+|+++++++|+|+|+||.+|.|+|.+||+|||++|+||+++.. ++...++.++|||++|.||..
T Consensus         5 ~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~-~~~~~~g~v~iRG~~I~~I~~   69 (71)
T d1i8fa_           5 ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID-GNVYKRGTMVVRGENVLFISP   69 (71)
T ss_dssp             HHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEET-TEEEEEEEEEECGGGEEEEEE
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEEC-CCEEEcceEEEeCCeEEEEeC
Confidence            47999999999999999999999999999999999999998754 467789999999999999974

>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=99.78  E-value=1.7e-19  Score=125.11  Aligned_cols=66  Identities=18%  Similarity=0.162  Sum_probs=60.2

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCC
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSL   71 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l   71 (129)
                      .+|+++++++|+|+|+||++|.|+|.+||.|||++|+||+++.    ...+..++|||++|+||.+|++.
T Consensus         3 ~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~----~~k~~~v~IRG~~I~~I~~~e~~   68 (127)
T d1m5q1_           3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA----GEKFNRVFIMYRYIVHIDSTERR   68 (127)
T ss_dssp             HHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETT----CCEEEEEEECGGGEEEEEECSCC
T ss_pred             hHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECC----CCcccEEEEeCCeEEEEEcchhh
Confidence            5899999999999999999999999999999999999998753    23577899999999999999983

>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=99.60  E-value=3.9e-16  Score=102.30  Aligned_cols=65  Identities=22%  Similarity=0.332  Sum_probs=56.7

Q ss_pred             hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCc---------------ceecceEEEecCeEEEEE
Q psy15782          2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKE---------------PTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~---------------~~~l~~~~IrGn~Ir~Ii   66 (129)
                      .||.++++++|.|+|+|+.+|.|+|.+||.|||+.|+||+++....+               ..+++.+||||++|.+|.
T Consensus         8 ~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~Vv~I~   87 (92)
T d2fwka1           8 ALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAMLV   87 (92)
T ss_dssp             HHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEEEEE
T ss_pred             HHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEEEEEE
Confidence            68999999999999999999999999999999999999998753211               135789999999999987

>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=99.54  E-value=1.6e-14  Score=92.44  Aligned_cols=64  Identities=25%  Similarity=0.266  Sum_probs=55.5

Q ss_pred             hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC-----C-----cceecceEEEecCeEEEEEc
Q psy15782          4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG-----K-----EPTTLDSISLRGNNIRYYIL   67 (129)
Q Consensus         4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~-----~-----~~~~l~~~~IrGn~Ir~Ii~   67 (129)
                      |.++++++|.|.|+|++.|.|+|.+||.+||+.|+||+++...     .     +...++.++|||++|.+|..
T Consensus         3 L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~   76 (81)
T d1d3bb_           3 MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTV   76 (81)
T ss_dssp             CGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEE
T ss_pred             hHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEc
Confidence            6789999999999999999999999999999999999986421     1     12567899999999999864

>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=99.49  E-value=2.9e-14  Score=93.57  Aligned_cols=69  Identities=19%  Similarity=0.251  Sum_probs=56.0

Q ss_pred             hhhhhcC--CCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC--------------cceecceEEEecCeEEEE
Q psy15782          2 NFLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK--------------EPTTLDSISLRGNNIRYY   65 (129)
Q Consensus         2 ~~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~--------------~~~~l~~~~IrGn~Ir~I   65 (129)
                      .+|.+++  +++|.|.|+++..+.|+|.+||.|||+.|.||+++....              +...++.++|||++|.+|
T Consensus         5 ~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnVv~I   84 (93)
T d1b34b_           5 SVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVV   84 (93)
T ss_dssp             HHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEEEE
T ss_pred             HHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEEEEE
Confidence            3566665  889999999999999999999999999999999875321              124688999999999998


Q ss_pred             EcCCC
Q psy15782         66 ILPDS   70 (129)
Q Consensus        66 i~pd~   70 (129)
                      ..|..
T Consensus        85 ~~~p~   89 (93)
T d1b34b_          85 LRNPL   89 (93)
T ss_dssp             EECCC
T ss_pred             EcChh
Confidence            77654

>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=96.92  E-value=0.0038  Score=38.44  Aligned_cols=63  Identities=17%  Similarity=0.282  Sum_probs=51.1

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEecc-cccceEeeEEEEecCCcc---------eecceEEEecCeEEEEEcCC
Q psy15782          7 LSHETVTIELKNGTQVHGTIQGVDV-AMNTHLKTVKMTVKGKEP---------TTLDSISLRGNNIRYYILPD   69 (129)
Q Consensus         7 l~~~~V~VeLkng~~~~G~L~~~D~-~mNl~Lkdv~~~~~~~~~---------~~l~~~~IrGn~Ir~Ii~pd   69 (129)
                      ++|++|.+--|.+..|.|+|..+|. ---+.|+||...-+.+++         ..++.+..||+.|+-+..-+
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e   74 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   74 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESS
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEecc
Confidence            5799999999999999999999995 446889999988765542         45778888999888766643

>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=96.91  E-value=0.00079  Score=40.22  Aligned_cols=32  Identities=31%  Similarity=0.473  Sum_probs=27.3

Q ss_pred             hhhhc--CCCeEEEEEcCCcEEEEEEEEeccccc
Q psy15782          3 FLMKL--SHETVTIELKNGTQVHGTIQGVDVAMN   34 (129)
Q Consensus         3 ~L~~l--~~~~V~VeLkng~~~~G~L~~~D~~mN   34 (129)
                      ||..+  ...+|+|+|.||-.++|++.+||.|.=
T Consensus         6 fLn~~rk~~~~VtifL~nGvkl~G~I~~fD~ftv   39 (66)
T d1u1sa1           6 YLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVI   39 (66)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEE
T ss_pred             HHHHHHHcCCcEEEEEEcCcEEEEEEEEEcceEE
Confidence            66665  355799999999999999999999974

>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=96.55  E-value=0.0017  Score=38.00  Aligned_cols=33  Identities=27%  Similarity=0.351  Sum_probs=27.8

Q ss_pred             hhhhc--CCCeEEEEEcCCcEEEEEEEEecccccc
Q psy15782          3 FLMKL--SHETVTIELKNGTQVHGTIQGVDVAMNT   35 (129)
Q Consensus         3 ~L~~l--~~~~V~VeLkng~~~~G~L~~~D~~mNl   35 (129)
                      ||..+  ...+|+|+|.||-.++|++.+||.|.=+
T Consensus         6 fln~lr~~~~~VtifL~nGvkl~G~I~~fD~ftvl   40 (60)
T d1kq1a_           6 ALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVS   40 (60)
T ss_dssp             HHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEE
T ss_pred             HHHHHHHcCCcEEEEEECCcEEEEEEEEEcceEEE
Confidence            55555  3568999999999999999999999844

>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=93.98  E-value=0.13  Score=29.54  Aligned_cols=59  Identities=15%  Similarity=0.236  Sum_probs=37.6

Q ss_pred             hhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782          3 FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI   66 (129)
Q Consensus         3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii   66 (129)
                      .|.+-.+++|-|-.-....+.|+|+.||.-. +.|+||+...    ......++++=+.|.+|.
T Consensus         6 tL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~----GNk~k~llv~idD~nWim   64 (66)
T d1ycya1           6 VLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI----GNRGKQMLIGLEDINWIM   64 (66)
T ss_dssp             HHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT----EEEEEEEEEEGGGEEEEE
T ss_pred             HHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHh----ccccceeEEEeccceeEE
Confidence            4566789999999999999999999999765 5688887652    223334455444444443

>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=89.42  E-value=0.55  Score=25.17  Aligned_cols=31  Identities=16%  Similarity=0.330  Sum_probs=25.7

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEecccccceEe
Q psy15782          7 LSHETVTIELKNGTQVHGTIQGVDVAMNTHLK   38 (129)
Q Consensus         7 l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lk   38 (129)
                      ++|++|.|..-+ .++.|+...+|..=.+.|+
T Consensus         1 f~gk~V~v~~g~-~~i~G~a~gId~~G~Lll~   31 (47)
T d1biaa2           1 FINRPVKLIIGD-KEIFGISRGIDKQGALLLE   31 (47)
T ss_dssp             TTTSEEEEEETT-EEEEEEEEEECTTSCEEEE
T ss_pred             CCCCEEEEEECC-eEEEEEEeeECCCCcEEEE
Confidence            468999997755 6788999999998888666