Psyllid ID: psy17024

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130--
Protein Sequence
MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRGGPPQRGGRGGWGGPSRGGR
Secondary Structure (PSIPRED)
cccccHHHHHHHHcccEEEEEEccccEEEEEEEEEcccccEEEEEEEEEcccccccccEEEEEEccEEEEEEcccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHcccEEEEEEccccEEEEEEEEEcccccEEEEEEEEEcccccEEEEEEEEEcHHHEEEEEEccHHHccccHccccccccccccccHHHHHHHHHHccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MSIGIPIKLLHEaeghiitcettngdlfrgklveaednmncamadVTVTfrdgkvkpmaniyiRGSKirflilpdmlknapmfkgkqgnkagaagrgksGILRAQAargrgrggppqrggrggwggpsrggr
Flexible Loop (DISEMBL)
MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTvtfrdgkvkpmanIYIRGSKIRFLILPDMLKNAPMFKGKQgnkagaagrgksgILRAQaargrgrggppqrggrggwggpsrggr
Low Complexity Region (SEG)
MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFkgkqgnkagaagrgksgILRAQAArgrgrggppqrggrggwggpsrggr
Disordered region (IsUnstruct)
***GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKN*****************************************************
Disordered Region (DISOPRED)
*SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNA****************************************************
Disordered Region (DISEMBL)
MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFK**************SGILRA****************************
Disordered Region (DISPRO)
*SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFK************************************************
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRGGPPQRGGRGGWGGPSRGGR
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	132	2.2.26 [Sep-21-2011]
O44437	151	Small nuclear ribonucleop	yes	N/A	0.803	0.701	0.719	3e-41
P62323	126	Small nuclear ribonucleop	N/A	N/A	0.810	0.849	0.685	4e-41
P62320	126	Small nuclear ribonucleop	yes	N/A	0.810	0.849	0.685	4e-41
P62318	126	Small nuclear ribonucleop	yes	N/A	0.810	0.849	0.685	4e-41
Q17348	136	Small nuclear ribonucleop	yes	N/A	0.954	0.926	0.580	1e-34
Q9UUC6	97	Small nuclear ribonucleop	yes	N/A	0.727	0.989	0.583	2e-28
P43321	101	Small nuclear ribonucleop	yes	N/A	0.613	0.801	0.555	2e-22
Q9QXA5	137	U6 snRNA-associated Sm-li	no	N/A	0.704	0.678	0.347	6e-12
Q9Y4Z0	139	U6 snRNA-associated Sm-li	no	N/A	0.621	0.589	0.379	1e-08
Q3ZBK6	139	U6 snRNA-associated Sm-li	no	N/A	0.621	0.589	0.379	1e-08

>sp|O44437|SMD3_DROME Small nuclear ribonucleoprotein Sm D3 OS=Drosophila melanogaster GN=SmD3 PE=1 SV=1

 Score =  167 bits (422), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 77/107 (71%), Positives = 90/107 (84%), Gaps = 1/107 (0%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHIITCET  G+++RGKL+EAEDNMNC M  +TVT+RDG+   + N
Sbjct: 1   MSIGVPIKVLHEAEGHIITCETITGEVYRGKLIEAEDNMNCQMTQITVTYRDGRTANLEN 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKGKQGN-KAGAAGRGKSGILRAQA 106
           +YIRGSKIRFLILPDMLKNAPMFK + G    G AGRGK+ ILRAQA
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMFKKQTGKGLGGTAGRGKAAILRAQA 107

Required for pre-mRNA splicing. Required for snRNP biogenesis.
Drosophila melanogaster (taxid: 7227)

>sp|P62323|SMD3_XENLA Small nuclear ribonucleoprotein Sm D3 OS=Xenopus laevis GN=snrpd3 PE=2 SV=1

 Score =  166 bits (420), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 74/108 (68%), Positives = 91/108 (84%), Gaps = 1/108 (0%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct: 1   MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKG-KQGNKAGAAGRGKSGILRAQAA 107
           +YIRGSKIRFLILPDMLKNAPM K  K  N+   AGRGK+ IL+AQ A
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVA 108

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Binds to RNA.

Xenopus laevis (taxid: 8355)

>sp|P62320|SMD3_MOUSE Small nuclear ribonucleoprotein Sm D3 OS=Mus musculus GN=Snrpd3 PE=1 SV=1

 Score =  166 bits (420), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 74/108 (68%), Positives = 91/108 (84%), Gaps = 1/108 (0%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct: 1   MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKG-KQGNKAGAAGRGKSGILRAQAA 107
           +YIRGSKIRFLILPDMLKNAPM K  K  N+   AGRGK+ IL+AQ A
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVA 108

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing (By similarity). Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.

Mus musculus (taxid: 10090)

>sp|P62318|SMD3_HUMAN Small nuclear ribonucleoprotein Sm D3 OS=Homo sapiens GN=SNRPD3 PE=1 SV=1

 Score =  166 bits (420), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 74/108 (68%), Positives = 91/108 (84%), Gaps = 1/108 (0%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct: 1   MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKG-KQGNKAGAAGRGKSGILRAQAA 107
           +YIRGSKIRFLILPDMLKNAPM K  K  N+   AGRGK+ IL+AQ A
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVA 108

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.

Homo sapiens (taxid: 9606)

>sp|Q17348|SMD3_CAEEL Small nuclear ribonucleoprotein Sm D3 OS=Caenorhabditis elegans GN=snr-1 PE=2 SV=2

 Score =  144 bits (364), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 76/131 (58%), Positives = 95/131 (72%), Gaps = 5/131 (3%)

Query: 2   SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANI 61
           S+G+PIK+LHEAEGH++T ET  G+++RGKL EAEDNMNC +A+  VTFRDG+   + N+
Sbjct: 3   SVGVPIKILHEAEGHMVTLETVTGEVYRGKLSEAEDNMNCQLAETVVTFRDGRSHQLDNV 62

Query: 62  YIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRGGPPQRG-G 120
           +IRG+KIRF+ILPDMLKNAPMFK     + GA G G  G+      RGRGRG   +R  G
Sbjct: 63  FIRGNKIRFMILPDMLKNAPMFKNIGRAQKGAIGMGLGGL----DQRGRGRGTAFRRPMG 118

Query: 121 RGGWGGPSRGG 131
           RGG  G SR G
Sbjct: 119 RGGPRGMSRPG 129

Required for pre-mRNA splicing. Required for snRNP biogenesis.

Caenorhabditis elegans (taxid: 6239)

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

 Score =  124 bits (310), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 56/96 (58%), Positives = 70/96 (72%)

Query: 3  IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIY 62
          + + IKLLHE +GHI+T E  NG  +RGKL+EAEDNMNC M D++VT RDG+V  +  +Y
Sbjct: 1  MSLCIKLLHETQGHIVTMELENGSTYRGKLIEAEDNMNCQMRDISVTARDGRVSHLDQVY 60

Query: 63 IRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGK 98
          IRGS IRFLI+PDML+NAPMFK   G       RG+
Sbjct: 61 IRGSHIRFLIVPDMLRNAPMFKVGPGRSVPLPTRGR 96

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|P43321|SMD3_YEAST Small nuclear ribonucleoprotein Sm D3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SMD3 PE=1 SV=1

 Score =  104 bits (260), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 45/81 (55%), Positives = 63/81 (77%)

Query: 4  GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYI 63
          GIP+KLL+EA+GHI++ E T G  +RGKLVE+ED+MN  + DV  T   G V  M  I++
Sbjct: 5  GIPVKLLNEAQGHIVSLELTTGATYRGKLVESEDSMNVQLRDVIATEPQGAVTHMDQIFV 64

Query: 64 RGSKIRFLILPDMLKNAPMFK 84
          RGS+I+F+++PD+LKNAP+FK
Sbjct: 65 RGSQIKFIVVPDLLKNAPLFK 85

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|Q9QXA5|LSM4_MOUSE U6 snRNA-associated Sm-like protein LSm4 OS=Mus musculus GN=Lsm4 PE=2 SV=1

 Score = 69.3 bits (168), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 40/115 (34%), Positives = 60/115 (52%), Gaps = 22/115 (19%)

Query: 5   IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYI 63
           +P+ LL  A+ H +  E  NG+ + G LV  ++ MN  + +V  T RDG K   M   YI
Sbjct: 2   LPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECYI 61

Query: 64  RGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRGGPPQR 118
           RGS I++L +PD + +                     ++R +AA+GRGRGGP Q+
Sbjct: 62  RGSTIKYLRIPDEIID---------------------MVREEAAKGRGRGGPQQK 95

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

Mus musculus (taxid: 10090)

>sp|Q9Y4Z0|LSM4_HUMAN U6 snRNA-associated Sm-like protein LSm4 OS=Homo sapiens GN=LSM4 PE=1 SV=1

 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 49/87 (56%), Gaps = 5/87 (5%)

Query: 5  IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYI 63
          +P+ LL  A+ H +  E  NG+ + G LV  ++ MN  + +V  T RDG K   M   YI
Sbjct: 2  LPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECYI 61

Query: 64 RGSKIRFLILP----DMLKNAPMFKGK 86
          RGS I++L +P    DM+K   + KG+
Sbjct: 62 RGSTIKYLRIPDEIIDMVKEEVVAKGR 88

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

Homo sapiens (taxid: 9606)

>sp|Q3ZBK6|LSM4_BOVIN U6 snRNA-associated Sm-like protein LSm4 OS=Bos taurus GN=LSM4 PE=2 SV=1

 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 49/87 (56%), Gaps = 5/87 (5%)

Query: 5  IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYI 63
          +P+ LL  A+ H +  E  NG+ + G LV  ++ MN  + +V  T RDG K   M   YI
Sbjct: 2  LPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECYI 61

Query: 64 RGSKIRFLILP----DMLKNAPMFKGK 86
          RGS I++L +P    DM+K   + KG+
Sbjct: 62 RGSTIKYLRIPDEIIDMVKEEVVAKGR 88

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

Bos taurus (taxid: 9913)

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	132
91084331	137	PREDICTED: similar to AGAP012380-PA [Tri	0.969	0.934	0.727	3e-48
270008821	152	hypothetical protein TcasGA2_TC015424 [T	0.969	0.842	0.653	2e-45
225714524	138	Small nuclear ribonucleoprotein Sm D3 [L	0.878	0.840	0.714	7e-44
307192020	143	Small nuclear ribonucleoprotein Sm D3 [H	0.886	0.818	0.737	7e-44
156550773	142	PREDICTED: small nuclear ribonucleoprote	0.848	0.788	0.752	3e-43
307192021	142	Small nuclear ribonucleoprotein Sm D3 [H	0.848	0.788	0.752	4e-43
307185014	142	Small nuclear ribonucleoprotein Sm D3 [C	0.848	0.788	0.752	6e-43
332028142	141	Small nuclear ribonucleoprotein Sm D3 [A	0.848	0.794	0.752	8e-43
332028955	142	Small nuclear ribonucleoprotein Sm D3 [A	0.848	0.788	0.752	8e-43
383853962	142	PREDICTED: small nuclear ribonucleoprote	0.848	0.788	0.734	4e-42

>gi|91084331|ref|XP_972583.1| PREDICTED: similar to AGAP012380-PA [Tribolium castaneum]

 Score =  196 bits (498), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 96/132 (72%), Positives = 110/132 (83%), Gaps = 4/132 (3%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M  +TVT+RDG+V  + N
Sbjct: 1   MSIGVPIKVLHEAEGHIVTCETITGEVYRGKLIEAEDNMNCQMTQITVTYRDGRVAQLEN 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRGG-PPQRG 119
           +YIRGSKIRFLILPDMLKNAPMFK +   KAG AGRGKS ILRAQAARGRGRG  P  RG
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMFKKQ--TKAGTAGRGKSAILRAQAARGRGRGANPAVRG 118

Query: 120 GRGG-WGGPSRG 130
           GRGG W  P +G
Sbjct: 119 GRGGAWQAPGQG 130

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270008821|gb|EFA05269.1| hypothetical protein TcasGA2_TC015424 [Tribolium castaneum]

 Score =  186 bits (472), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 96/147 (65%), Positives = 110/147 (74%), Gaps = 19/147 (12%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M  +TVT+RDG+V  + N
Sbjct: 1   MSIGVPIKVLHEAEGHIVTCETITGEVYRGKLIEAEDNMNCQMTQITVTYRDGRVAQLEN 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQ--------------- 105
           +YIRGSKIRFLILPDMLKNAPMFK +   KAG AGRGKS ILRAQ               
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMFKKQ--TKAGTAGRGKSAILRAQGLAVLRVEFWLIVFS 118

Query: 106 AARGRGRGG-PPQRGGRGG-WGGPSRG 130
           AARGRGRG  P  RGGRGG W  P +G
Sbjct: 119 AARGRGRGANPAVRGGRGGAWQAPGQG 145

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225714524|gb|ACO13108.1| Small nuclear ribonucleoprotein Sm D3 [Lepeophtheirus salmonis] gi|290462385|gb|ADD24240.1| Small nuclear ribonucleoprotein Sm D3 [Lepeophtheirus salmonis] gi|290563060|gb|ADD38924.1| Small nuclear ribonucleoprotein Sm D3 [Lepeophtheirus salmonis]

 Score =  181 bits (460), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 85/119 (71%), Positives = 100/119 (84%), Gaps = 3/119 (2%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHI+TCET NG+++RG+L+EAEDNMNC M+ V+VT RDG V  + N
Sbjct: 1   MSIGVPIKVLHEAEGHIVTCETINGEVYRGRLIEAEDNMNCQMSSVSVTHRDGHVSQLEN 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKGK---QGNKAGAAGRGKSGILRAQAARGRGRGGPP 116
           IYIRGSKIRF+ILPDMLKNAPMFK     +G+   +AGRGKS ILR QAARGRGR GPP
Sbjct: 61  IYIRGSKIRFMILPDMLKNAPMFKNMGRGRGSAPASAGRGKSAILREQAARGRGRAGPP 119

Source: Lepeophtheirus salmonis

Species: Lepeophtheirus salmonis

Genus: Lepeophtheirus

Family: Caligidae

Order: Siphonostomatoida

Class: Maxillopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307192020|gb|EFN75404.1| Small nuclear ribonucleoprotein Sm D3 [Harpegnathos saltator]

 Score =  181 bits (460), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 87/118 (73%), Positives = 100/118 (84%), Gaps = 1/118 (0%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHIITCET  G+++RGKL+EAEDNMNC M ++TVT+RDG+V  + N
Sbjct: 1   MSIGVPIKVLHEAEGHIITCETNTGEVYRGKLIEAEDNMNCQMQNITVTYRDGRVAQLEN 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRGGPPQR 118
           +YIRGSKIRFLILPDMLKNAPMFK   G  +G AGRGKS ILRAQ ARGRGRG   QR
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMFKRPGGKGSGTAGRGKSAILRAQ-ARGRGRGQQHQR 117

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156550773|ref|XP_001605596.1| PREDICTED: small nuclear ribonucleoprotein Sm D3-like [Nasonia vitripennis]

 Score =  179 bits (454), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 85/113 (75%), Positives = 98/113 (86%), Gaps = 1/113 (0%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHIITCET  G+++RGKL+EAEDNMNC M ++TVT+RDG+V  + N
Sbjct: 1   MSIGVPIKVLHEAEGHIITCETNTGEVYRGKLIEAEDNMNCQMQNITVTYRDGRVAQLEN 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRG 113
           +YIRGSKIRFLILPDMLKNAPMFK   G  +G AGRGKS ILRAQ ARGRGRG
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMFKRPGGKGSGTAGRGKSAILRAQ-ARGRGRG 112

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307192021|gb|EFN75405.1| Small nuclear ribonucleoprotein Sm D3 [Harpegnathos saltator]

 Score =  179 bits (453), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 85/113 (75%), Positives = 98/113 (86%), Gaps = 1/113 (0%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHIITCET  G+++RGKL+EAEDNMNC M ++TVT+RDG+V  + N
Sbjct: 1   MSIGVPIKVLHEAEGHIITCETNTGEVYRGKLIEAEDNMNCQMQNITVTYRDGRVAQLEN 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRG 113
           +YIRGSKIRFLILPDMLKNAPMFK   G  +G AGRGKS ILRAQ ARGRGRG
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMFKRPGGKGSGTAGRGKSAILRAQ-ARGRGRG 112

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307185014|gb|EFN71243.1| Small nuclear ribonucleoprotein Sm D3 [Camponotus floridanus]

 Score =  178 bits (452), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 85/113 (75%), Positives = 98/113 (86%), Gaps = 1/113 (0%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHIITCET  G+++RGKL+EAEDNMNC M ++TVT+RDG+V  + N
Sbjct: 1   MSIGVPIKVLHEAEGHIITCETNTGEVYRGKLIEAEDNMNCQMQNITVTYRDGQVGQLEN 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRG 113
           +YIRGSKIRFLILPDMLKNAPMFK   G  +G AGRGKS ILRAQ ARGRGRG
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMFKRPGGKGSGTAGRGKSAILRAQ-ARGRGRG 112

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332028142|gb|EGI68193.1| Small nuclear ribonucleoprotein Sm D3 [Acromyrmex echinatior]

 Score =  178 bits (451), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 85/113 (75%), Positives = 98/113 (86%), Gaps = 1/113 (0%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHIITCET  G+++RGKL+EAEDNMNC M ++TVT+RDG+V  + N
Sbjct: 1   MSIGVPIKVLHEAEGHIITCETNTGEVYRGKLIEAEDNMNCQMQNITVTYRDGQVGQLEN 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRG 113
           +YIRGSKIRFLILPDMLKNAPMFK   G  +G AGRGKS ILRAQ ARGRGRG
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMFKRPGGKGSGTAGRGKSAILRAQ-ARGRGRG 112

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332028955|gb|EGI68973.1| Small nuclear ribonucleoprotein Sm D3 [Acromyrmex echinatior]

 Score =  178 bits (451), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 85/113 (75%), Positives = 98/113 (86%), Gaps = 1/113 (0%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHIITCET  G+++RGKL+EAEDNMNC M ++TVT+RDG+V  + N
Sbjct: 1   MSIGVPIKVLHEAEGHIITCETNTGEVYRGKLIEAEDNMNCQMQNITVTYRDGQVGQLEN 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRG 113
           +YIRGSKIRFLILPDMLKNAPMFK   G  +G AGRGKS ILRAQ ARGRGRG
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMFKRPGGKGSGTAGRGKSAILRAQ-ARGRGRG 112

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383853962|ref|XP_003702491.1| PREDICTED: small nuclear ribonucleoprotein Sm D3-like [Megachile rotundata]

 Score =  175 bits (444), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 83/113 (73%), Positives = 97/113 (85%), Gaps = 1/113 (0%)

Query: 1   MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
           MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M ++TVT+RDG+   + N
Sbjct: 1   MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMQNITVTYRDGREVELEN 60

Query: 61  IYIRGSKIRFLILPDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRG 113
           +YIRGSKIRFLILPDMLKNAPMFK   G  +G AGRGKS ILRAQ ARGRGRG
Sbjct: 61  VYIRGSKIRFLILPDMLKNAPMFKRPGGKGSGTAGRGKSAILRAQ-ARGRGRG 112

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

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	132
FB|FBgn0023167	151	SmD3 "Small ribonucleoprotein	0.803	0.701	0.644	6.7e-33
ZFIN|ZDB-GENE-030131-5219	171	snrpd3l "small nuclear ribonuc	0.810	0.625	0.611	3.7e-32
UNIPROTKB|Q5ZL58	126	SNRPD3 "Uncharacterized protei	0.810	0.849	0.611	4.7e-32
UNIPROTKB|F1MZ00	126	SNRPD3 "Uncharacterized protei	0.810	0.849	0.611	4.7e-32
UNIPROTKB|P62318	126	SNRPD3 "Small nuclear ribonucl	0.810	0.849	0.611	4.7e-32
UNIPROTKB|F2Z4Y0	126	SNRPD3 "Uncharacterized protei	0.810	0.849	0.611	4.7e-32
UNIPROTKB|P62323	126	snrpd3 "Small nuclear ribonucl	0.810	0.849	0.611	4.7e-32
MGI|MGI:1914582	126	Snrpd3 "small nuclear ribonucl	0.810	0.849	0.611	4.7e-32
ZFIN|ZDB-GENE-040625-55	127	snrpd3 "small nuclear ribonucl	0.810	0.842	0.611	4.7e-32
UNIPROTKB|B4DJP7	120	SNRPD3 "Small nuclear ribonucl	0.621	0.683	0.743	7.7e-32

FB|FBgn0023167 SmD3 "Small ribonucleoprotein particle protein SmD3" [Drosophila melanogaster (taxid:7227)]

 Score = 359 (131.4 bits), Expect = 6.7e-33, P = 6.7e-33
 Identities = 69/107 (64%), Positives = 80/107 (74%)

Query:     1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
             MSIG+PIK+LHEAEGHIITCET  G+++RGKL+EAEDNMNC M  +TVT+RDG+   + N
Sbjct:     1 MSIGVPIKVLHEAEGHIITCETITGEVYRGKLIEAEDNMNCQMTQITVTYRDGRTANLEN 60

Query:    61 IYIRGSKIRFLILPDMLKNAPMFXXXXXXXXXXXXXXX-XXILRAQA 106
             +YIRGSKIRFLILPDMLKNAPMF                  ILRAQA
Sbjct:    61 VYIRGSKIRFLILPDMLKNAPMFKKQTGKGLGGTAGRGKAAILRAQA 107

GO:0007417 "central nervous system development" evidence=IMP

GO:0048542 "lymph gland development" evidence=IMP

GO:0007422 "peripheral nervous system development" evidence=NAS;IMP

GO:0030182 "neuron differentiation" evidence=IMP

GO:0007517 "muscle organ development" evidence=IMP

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISS;NAS;TAS

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

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0005634 "nucleus" evidence=NAS

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0007067 "mitosis" evidence=IMP

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0045495 "pole plasm" evidence=IDA

GO:0045451 "pole plasm oskar mRNA localization" evidence=IMP

ZFIN|ZDB-GENE-030131-5219 snrpd3l "small nuclear ribonucleoprotein D3 polypeptide, like" [Danio rerio (taxid:7955)]

 Score = 352 (129.0 bits), Expect = 3.7e-32, P = 3.7e-32
 Identities = 66/108 (61%), Positives = 81/108 (75%)

Query:     1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
             MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct:    44 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVSQLEQ 103

Query:    61 IYIRGSKIRFLILPDMLKNAPMFXXXXXXXXXXXXXXX-XXILRAQAA 107
             +YIRGSKIRFLILPDMLKNAPM                   IL+AQ A
Sbjct:   104 VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGAGAGRGKAAILKAQVA 151

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q5ZL58 SNRPD3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 66/108 (61%), Positives = 81/108 (75%)

Query:     1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
             MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct:     1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60

Query:    61 IYIRGSKIRFLILPDMLKNAPMFXXXXXXXXXXXXXXX-XXILRAQAA 107
             +YIRGSKIRFLILPDMLKNAPM                   IL+AQ A
Sbjct:    61 VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVA 108

GO:0005683 "U7 snRNP" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0019899 "enzyme binding" evidence=IEA

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

GO:0071208 "histone pre-mRNA DCP binding" evidence=IEA

UNIPROTKB|F1MZ00 SNRPD3 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 66/108 (61%), Positives = 81/108 (75%)

Query:     1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
             MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct:     1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60

Query:    61 IYIRGSKIRFLILPDMLKNAPMFXXXXXXXXXXXXXXX-XXILRAQAA 107
             +YIRGSKIRFLILPDMLKNAPM                   IL+AQ A
Sbjct:    61 VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVA 108

GO:0071208 "histone pre-mRNA DCP binding" evidence=IEA

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

GO:0019899 "enzyme binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0005683 "U7 snRNP" evidence=IEA

UNIPROTKB|P62318 SNRPD3 "Small nuclear ribonucleoprotein Sm D3" [Homo sapiens (taxid:9606)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 66/108 (61%), Positives = 81/108 (75%)

Query:     1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
             MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct:     1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60

Query:    61 IYIRGSKIRFLILPDMLKNAPMFXXXXXXXXXXXXXXX-XXILRAQAA 107
             +YIRGSKIRFLILPDMLKNAPM                   IL+AQ A
Sbjct:    61 VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVA 108

GO:0005515 "protein binding" evidence=IPI

GO:0019899 "enzyme binding" evidence=IPI

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

GO:0071208 "histone pre-mRNA DCP binding" evidence=ISS

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

GO:0005683 "U7 snRNP" evidence=IDA

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

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

GO:0005681 "spliceosomal complex" evidence=TAS

GO:0000387 "spliceosomal snRNP assembly" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006397 "mRNA processing" evidence=TAS

GO:0008334 "histone mRNA metabolic process" 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|F2Z4Y0 SNRPD3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 66/108 (61%), Positives = 81/108 (75%)

Query:     1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
             MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct:     1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60

Query:    61 IYIRGSKIRFLILPDMLKNAPMFXXXXXXXXXXXXXXX-XXILRAQAA 107
             +YIRGSKIRFLILPDMLKNAPM                   IL+AQ A
Sbjct:    61 VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVA 108

GO:0071208 "histone pre-mRNA DCP binding" evidence=IEA

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

GO:0019899 "enzyme binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0005683 "U7 snRNP" evidence=IEA

UNIPROTKB|P62323 snrpd3 "Small nuclear ribonucleoprotein Sm D3" [Xenopus laevis (taxid:8355)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 66/108 (61%), Positives = 81/108 (75%)

Query:     1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
             MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct:     1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60

Query:    61 IYIRGSKIRFLILPDMLKNAPMFXXXXXXXXXXXXXXX-XXILRAQAA 107
             +YIRGSKIRFLILPDMLKNAPM                   IL+AQ A
Sbjct:    61 VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVA 108

GO:0071208 "histone pre-mRNA DCP binding" evidence=ISS

MGI|MGI:1914582 Snrpd3 "small nuclear ribonucleoprotein D3" [Mus musculus (taxid:10090)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 66/108 (61%), Positives = 81/108 (75%)

Query:     1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
             MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct:     1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60

Query:    61 IYIRGSKIRFLILPDMLKNAPMFXXXXXXXXXXXXXXX-XXILRAQAA 107
             +YIRGSKIRFLILPDMLKNAPM                   IL+AQ A
Sbjct:    61 VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVA 108

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005683 "U7 snRNP" evidence=ISO

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:0019899 "enzyme binding" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

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

GO:0071208 "histone pre-mRNA DCP binding" evidence=IDA

ZFIN|ZDB-GENE-040625-55 snrpd3 "small nuclear ribonucleoprotein D3 polypeptide" [Danio rerio (taxid:7955)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 66/108 (61%), Positives = 81/108 (75%)

Query:     1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
             MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDN+NC MA++TVT+RDG+V  +  
Sbjct:     1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNVNCQMANITVTYRDGRVAQLEQ 60

Query:    61 IYIRGSKIRFLILPDMLKNAPMFXXXXXXX-XXXXXXXXXXILRAQAA 107
             +YIRGSKIRFLILPDMLKNAPM                   IL+AQ A
Sbjct:    61 VYIRGSKIRFLILPDMLKNAPMLKSMKNKNPAAGAGRGKAAILKAQVA 108

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|B4DJP7 SNRPD3 "Small nuclear ribonucleoprotein Sm D3" [Homo sapiens (taxid:9606)]

 Score = 349 (127.9 bits), Expect = 7.7e-32, P = 7.7e-32
 Identities = 61/82 (74%), Positives = 75/82 (91%)

Query:     1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
             MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct:     1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60

Query:    61 IYIRGSKIRFLILPDMLKNAPM 82
             +YIRGSKIRFLILPDMLKNAPM
Sbjct:    61 VYIRGSKIRFLILPDMLKNAPM 82

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q17348	SMD3_CAEEL	No assigned EC number	0.5801	0.9545	0.9264	yes	N/A
P62318	SMD3_HUMAN	No assigned EC number	0.6851	0.8106	0.8492	yes	N/A
O44437	SMD3_DROME	No assigned EC number	0.7196	0.8030	0.7019	yes	N/A
Q9UUC6	SMD3_SCHPO	No assigned EC number	0.5833	0.7272	0.9896	yes	N/A
P62323	SMD3_XENLA	No assigned EC number	0.6851	0.8106	0.8492	N/A	N/A
P62320	SMD3_MOUSE	No assigned EC number	0.6851	0.8106	0.8492	yes	N/A
P43321	SMD3_YEAST	No assigned EC number	0.5555	0.6136	0.8019	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	132
cd01721	70	cd01721, Sm_D3, Sm protein D3	2e-45
pfam01423	66	pfam01423, LSM, LSM domain	1e-15
smart00651	67	smart00651, Sm, snRNP Sm proteins	2e-15
cd01733	78	cd01733, LSm10, Like-Sm protein 10	1e-13
cd00600	63	cd00600, Sm_like, Sm and related proteins	7e-13
cd01723	76	cd01723, LSm4, Like-Sm protein 4	4e-12
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	2e-10
cd01724	92	cd01724, Sm_D1, Sm protein D1	5e-07
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	2e-04
pfam12764	102	pfam12764, Gly-rich_Ago1, Glycine-rich region of a	3e-04
cd01726	68	cd01726, LSm6, Like-Sm protein 6	0.003
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.004

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

 Score =  141 bits (359), Expect = 2e-45
 Identities = 49/70 (70%), Positives = 59/70 (84%)

Query: 6  PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRG 65
          PIKLLHEAEGHI+T E   G+++RGKL+EAEDNMNC + DVTVT RDGKV  +  +YIRG
Sbjct: 1  PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGKVSKLEQVYIRG 60

Query: 66 SKIRFLILPD 75
          S+IRF+ILPD
Sbjct: 61 SQIRFIILPD 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|201787 pfam01423, LSM, LSM domain

 Score = 66.0 bits (162), Expect = 1e-15
 Identities = 23/66 (34%), Positives = 32/66 (48%)

Query: 8  KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSK 67
          K L +  G  +T E  NG   RG L   +  MN  + DV  T +DGKV  +  + IRG+ 
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60

Query: 68 IRFLIL 73
          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 = 65.2 bits (160), Expect = 2e-15
 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 8  KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYIRGS 66
          K L +  G  +  E  NG  +RG L   +  MN  + DV  T +DG K + +  ++IRG+
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60

Query: 67 KIRFLIL 73
           I ++IL
Sbjct: 61 NIVYIIL 67

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

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

 Score = 61.4 bits (150), Expect = 1e-13
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 14 EGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL 73
          +G + T E  N    RG +   +  MN  ++D T T R GK       +++G  IR++ +
Sbjct: 18 QGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQHHFDEFFVQGRNIRYVHI 77

Query: 74 P 74
          P
Sbjct: 78 P 78

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|212462 cd00600, Sm_like, Sm and related proteins

 Score = 58.8 bits (143), Expect = 7e-13
 Identities = 22/63 (34%), Positives = 33/63 (52%)

Query: 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIR 69
          L +  G  ++ E  +G +  G LV  +  MN  + DV  T RDGKV+ +  + IRGS I 
Sbjct: 1  LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIV 60

Query: 70 FLI 72
           + 
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 = 57.2 bits (139), Expect = 4e-12
 Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 6  PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYIR 64
          P+ LL  A+GH +  E  NG+ + G LV  ++ MN  + +V  T +DG +   M   YIR
Sbjct: 2  PLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIR 61

Query: 65 GSKIRFLILPD 75
          G+ I++L LPD
Sbjct: 62 GNTIKYLRLPD 72

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

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

 Score = 52.7 bits (127), Expect = 2e-10
 Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 4/73 (5%)

Query: 5  IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVT-FRDG---KVKPMAN 60
          +P+  L +     +  +  NG  +RG LV  +  MN  + DV      DG     +    
Sbjct: 7  LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGE 66

Query: 61 IYIRGSKIRFLIL 73
          + IRG  I  +  
Sbjct: 67 VLIRGDNIVLISP 79

Length = 79

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

 Score = 44.5 bits (106), Expect = 5e-07
 Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 5/89 (5%)

Query: 8  KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSK 67
          KL +E     +T E  NG +  G +   + +MN  + +V +T +      +  + IRG+ 
Sbjct: 8  KLSNET----VTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGNN 63

Query: 68 IRFLILPDMLK-NAPMFKGKQGNKAGAAG 95
          IR++ILPD L  +  +       KA    
Sbjct: 64 IRYIILPDSLNLDTLLVDDTPKAKAKKRA 92

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|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein

 Score = 37.1 bits (86), Expect = 2e-04
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 6  PIKLLHEAEGHIITCETT-NGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIR 64
          P K +    G  I  E   + +  +G+LV  +D MN  + D      + KV+ +  + +R
Sbjct: 1  PNKKVKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLR 60

Query: 65 GSKIRFLILP 74
          G+ I  LI P
Sbjct: 61 GNNI-LLIQP 69

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|221759 pfam12764, Gly-rich_Ago1, Glycine-rich region of argonaut

 Score = 37.3 bits (86), Expect = 3e-04
 Identities = 18/23 (78%), Positives = 19/23 (82%)

Query: 109 GRGRGGPPQRGGRGGWGGPSRGG 131
           GRGRGGPPQ+GGRGG GG   GG
Sbjct: 8   GRGRGGPPQQGGRGGGGGGRGGG 30

This domain is often found at the very N-terminal of argonaut-like proteins. Length = 102

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

 Score = 34.0 bits (79), Expect = 0.003
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 6/68 (8%)

Query: 6  PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN---IY 62
          P K L +  G  +  +  NG  +RG L   +  MN  + D T  + DG++   A     +
Sbjct: 2  PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLED-TEEYVDGQLV--AKYGDAF 58

Query: 63 IRGSKIRF 70
          IRG+ + +
Sbjct: 59 IRGNNVLY 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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 15/50 (30%), Positives = 16/50 (32%)

Query: 83  FKGKQGNKAGAAGRGKSGILRAQAARGRGRGGPPQRGGRGGWGGPSRGGR 132
             G         GRG  G          G  G  +  GRGG GG   GG 
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGG 50

Length = 293

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	132
KOG3172|consensus	119		100.0
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.96
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.95
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.94
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.93
KOG3293|consensus	134		99.93
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.93
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.89
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.89
KOG3428|consensus	109		99.87
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.86
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.84
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.83
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.82
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.82
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.81
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.76
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.75
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.74
KOG3448|consensus	96		99.72
KOG3482|consensus	79		99.71
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.68
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.68
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.61
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.6
KOG1783|consensus	77		99.59
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.55
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.54
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.53
KOG3460|consensus	91		99.46
KOG1775|consensus	84		99.39
KOG1780|consensus	77		99.33
KOG3168|consensus	177		98.66
KOG1774|consensus	88		98.62
KOG1781|consensus	108		98.31
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	98.03
KOG1784|consensus	96		97.86
KOG1782|consensus	129		97.59
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.52
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.5
KOG3459|consensus	114		97.46
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.35
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	96.29
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	95.66
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	95.66
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	95.49
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	95.4
KOG1073|consensus	361		94.59
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	94.4
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	94.2
PRK14638	150	hypothetical protein; Provisional	90.93
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	90.93
PRK02001	152	hypothetical protein; Validated	90.8
COG1923	77	Hfq Uncharacterized host factor I protein [General	90.63
KOG3262|consensus	215		89.39
PRK14639	140	hypothetical protein; Provisional	89.25
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	89.02
PRK14644	136	hypothetical protein; Provisional	88.36
PRK14091	165	RNA-binding protein Hfq; Provisional	87.56
PRK14091	165	RNA-binding protein Hfq; Provisional	87.23
PRK14642	197	hypothetical protein; Provisional	86.78
PRK00092	154	ribosome maturation protein RimP; Reviewed	86.54
PRK14632	172	hypothetical protein; Provisional	85.37
PRK14647	159	hypothetical protein; Provisional	85.21
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	84.72
PRK14636	176	hypothetical protein; Provisional	84.19
PRK14640	152	hypothetical protein; Provisional	84.14
PRK14633	150	hypothetical protein; Provisional	83.99
PRK14643	164	hypothetical protein; Provisional	82.86
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	80.51
PRK14645	154	hypothetical protein; Provisional	80.5

>KOG3172|consensus

Probab=100.00  E-value=1.7e-41  Score=243.28  Aligned_cols=101  Identities=62%  Similarity=1.107  Sum_probs=93.9

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcccccc
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNA   80 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~~a   80 (132)
                      ||+++|++||||++||.|++|+++|++|+|+|+++||+|||+|+|+++|.+||+++++++||||||+|+|++|||+|+||
T Consensus         1 ~s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmLKnA   80 (119)
T KOG3172|consen    1 MSVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDMLKNA   80 (119)
T ss_pred             CccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHhhcC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccCCC-CCccCCchhhh
Q psy17024         81 PMFKGKQGNK-AGAAGRGKSGI  101 (132)
Q Consensus        81 p~lk~~~~~~-~~~~~~g~~~~  101 (132)
                      ||||..+.+. +...+||++++
T Consensus        81 PmFkk~~~~~~g~~~~RG~~~~  102 (119)
T KOG3172|consen   81 PMFKKGKSRSLGGGPGRGRARR  102 (119)
T ss_pred             cccccccCCcCCCCCCcccccc
Confidence            9999766655 55566776643

>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=99.96  E-value=1.8e-28  Score=171.61  Aligned_cols=82  Identities=26%  Similarity=0.526  Sum_probs=78.0

Q ss_pred             HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCccccccccccc
Q psy17024          6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFKG   85 (132)
Q Consensus         6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~~ap~lk~   85 (132)
                      |++||++++|++|+||||||++|+|+|.+||+||||+|+||+++..++...+++++||||++|+||+|||+++..++|.+
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~~~~~l~~   81 (90)
T cd01724           2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLNLDTLLVD   81 (90)
T ss_pred             HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCCcchhhhh
Confidence            78999999999999999999999999999999999999999999888889999999999999999999999998888876


Q ss_pred             cc
Q psy17024         86 KQ   87 (132)
Q Consensus        86 ~~   87 (132)
                      ..
T Consensus        82 ~~   83 (90)
T cd01724          82 ST   83 (90)
T ss_pred             cC
Confidence            53

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.

>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=99.95  E-value=3.4e-28  Score=162.72  Aligned_cols=70  Identities=70%  Similarity=1.191  Sum_probs=68.6

Q ss_pred             HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024          6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      |++||++++|++|+||||||.+|+|+|.+||+|||++|+||+++.++++..+++++||||++|+||+|||
T Consensus         1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd   70 (70)
T cd01721           1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence            8999999999999999999999999999999999999999999999999899999999999999999998

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.

>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=99.94  E-value=2.6e-26  Score=155.64  Aligned_cols=73  Identities=36%  Similarity=0.679  Sum_probs=69.5

Q ss_pred             cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc-eeecceEEEecCeEEEEecCccc
Q psy17024          5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK-VKPMANIYIRGSKIRFLILPDML   77 (132)
Q Consensus         5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~lPd~l   77 (132)
                      +|++||++++|++|+||||||.+|+|+|.+||+|||++|+||+++..+|+ ...++++||||++|+||++||++
T Consensus         1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~   74 (76)
T cd01723           1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI   74 (76)
T ss_pred             CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence            59999999999999999999999999999999999999999999988886 46789999999999999999986

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.

>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=99.93  E-value=6.4e-26  Score=154.97  Aligned_cols=71  Identities=30%  Similarity=0.514  Sum_probs=68.3

Q ss_pred             ccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecC
Q psy17024          4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILP   74 (132)
Q Consensus         4 ~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lP   74 (132)
                      ..+++||++++|++|+||||||.+|+|+|.+||+|||++|+||+++.+++...+++++||||++|+||+||
T Consensus         8 ~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733           8 NTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             chHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence            46789999999999999999999999999999999999999999998888888999999999999999998

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=99.93  E-value=4e-26  Score=167.22  Aligned_cols=75  Identities=35%  Similarity=0.656  Sum_probs=71.7

Q ss_pred             cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc-eeecceEEEecCeEEEEecCccccc
Q psy17024          5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK-VKPMANIYIRGSKIRFLILPDMLKN   79 (132)
Q Consensus         5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~lPd~l~~   79 (132)
                      +||.||+.+.++++.||||||++|.|.|+.||.+||++|++|++|.+||. ++.+++|||||++|+|+.|||.+-+
T Consensus         2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~iid   77 (134)
T KOG3293|consen    2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEIID   77 (134)
T ss_pred             cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHHH
Confidence            79999999999999999999999999999999999999999999999985 8899999999999999999998743

>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=99.93  E-value=2.1e-25  Score=153.10  Aligned_cols=76  Identities=24%  Similarity=0.388  Sum_probs=69.3

Q ss_pred             cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc--eeecceEEEecCeEEEEecCcccccc
Q psy17024          5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK--VKPMANIYIRGSKIRFLILPDMLKNA   80 (132)
Q Consensus         5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~--~~~l~~vfIRGs~Ir~I~lPd~l~~a   80 (132)
                      +|+.||++++|++|+||||||++|+|+|.+||+||||+|+||+++.+++.  ...++++||||++|+||++||++-+.
T Consensus         1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~~   78 (81)
T cd01725           1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVDT   78 (81)
T ss_pred             ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcCc
Confidence            58999999999999999999999999999999999999999999976653  56789999999999999999987443

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=99.90  E-value=1e-23  Score=139.59  Aligned_cols=67  Identities=19%  Similarity=0.351  Sum_probs=63.4

Q ss_pred             HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      |++||+++++++|+||||||++|+|+|.+||+|||++|+||+++..+++...++++||||++|+||.
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence            8999999999999999999999999999999999999999999876666889999999999999984

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=99.89  E-value=9.1e-23  Score=135.52  Aligned_cols=68  Identities=18%  Similarity=0.339  Sum_probs=63.1

Q ss_pred             cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      .|+++|++++|++|+||||||++|+|+|.++|+|||++|+||+++...++...++++||||++|+||.
T Consensus         1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence            49999999999999999999999999999999999999999998864446789999999999999984

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=99.89  E-value=1.5e-22  Score=135.92  Aligned_cols=71  Identities=21%  Similarity=0.377  Sum_probs=66.1

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      |+ ..|+++|+++++++|+|+||||++|+|+|.+||+|||++|+||+++..+.....++.+||||++|.||.
T Consensus         1 ~~-~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~   71 (72)
T PRK00737          1 MA-QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVS   71 (72)
T ss_pred             CC-cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEc
Confidence            66 689999999999999999999999999999999999999999999865555779999999999999985

>KOG3428|consensus

Probab=99.87  E-value=1.5e-21  Score=140.25  Aligned_cols=82  Identities=24%  Similarity=0.450  Sum_probs=76.9

Q ss_pred             HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcccccccccccc
Q psy17024          7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFKGK   86 (132)
Q Consensus         7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~~ap~lk~~   86 (132)
                      +.||+++.+++|+||||||++++|+|.++|.+||.+|.+|.++.+. ++.+++.++|||++|||+++||.+...+++.+.
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            7899999999999999999999999999999999999999999764 789999999999999999999999999988876


Q ss_pred             cCC
Q psy17024         87 QGN   89 (132)
Q Consensus        87 ~~~   89 (132)
                      .+.
T Consensus        83 ~~~   85 (109)
T KOG3428|consen   83 APR   85 (109)
T ss_pred             hhh
Confidence            654

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

Probab=99.86  E-value=2.1e-21  Score=128.59  Aligned_cols=67  Identities=21%  Similarity=0.407  Sum_probs=64.0

Q ss_pred             HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      |+++|+++++++|+|+|+||++|+|+|.+||+|||++|+||+++..++....++.+||||++|.||.
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~   67 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFIS   67 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEc
Confidence            8999999999999999999999999999999999999999999987777889999999999999985

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=99.84  E-value=2.6e-20  Score=121.61  Aligned_cols=65  Identities=32%  Similarity=0.556  Sum_probs=61.8

Q ss_pred             HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC-CceeecceEEEecCeEEEEec
Q psy17024          9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD-GKVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus         9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d-g~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      +|+++++++|+|+|+||++|.|+|.++|+|||++|+||+++..+ .+..+++.+||||++|+||++
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence            79999999999999999999999999999999999999999877 678999999999999999974

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=99.83  E-value=3e-20  Score=121.47  Aligned_cols=66  Identities=35%  Similarity=0.652  Sum_probs=62.7

Q ss_pred             HHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC-ceeecceEEEecCeEEEEec
Q psy17024          8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus         8 ~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      .+|++++|++|+|+|+||.+|+|+|.+||+|||++|+||+++..+. +...++.+||||++|+||++
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            4799999999999999999999999999999999999999998777 78999999999999999975

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 ....

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

Probab=99.82  E-value=1e-19  Score=123.62  Aligned_cols=70  Identities=26%  Similarity=0.434  Sum_probs=62.2

Q ss_pred             cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEec-CCce---eecceEEEecCeEEEEe
Q psy17024          3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFR-DGKV---KPMANIYIRGSKIRFLI   72 (132)
Q Consensus         3 ~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~-dg~~---~~l~~vfIRGs~Ir~I~   72 (132)
                      ...|+++|+++++++|.|+||||++|+|+|.+||+|||++|+||+++.. ++..   ...+.+||||++|.||.
T Consensus         5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~   78 (79)
T COG1958           5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLIS   78 (79)
T ss_pred             cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEe
Confidence            4568999999999999999999999999999999999999999999874 4433   34459999999999986

>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=99.82  E-value=1.5e-19  Score=122.98  Aligned_cols=69  Identities=25%  Similarity=0.393  Sum_probs=63.6

Q ss_pred             ccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe---cCCceeecceEEEecCeEEEEe
Q psy17024          4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF---RDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         4 ~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~---~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      .+|+++|+++++++|.|+|++|++|.|+|.+||.|||++|+||+++.   .+++..+++.+||||++|.+|+
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~   73 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLV   73 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEE
Confidence            47999999999999999999999999999999999999999998875   3334678999999999999987

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.

>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=99.81  E-value=1.8e-19  Score=116.08  Aligned_cols=63  Identities=29%  Similarity=0.555  Sum_probs=60.1

Q ss_pred             HHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024         10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus        10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      |++++|++|+|+|+||++|.|+|.++|+|||++|+||+++..+.+..+++.+||||++|+||+
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            578999999999999999999999999999999999999988888999999999999999984

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=99.76  E-value=3.5e-18  Score=115.00  Aligned_cols=69  Identities=17%  Similarity=0.176  Sum_probs=62.8

Q ss_pred             HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024          7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      -..|+++++++|.|+|++|.+|.|+|.+||+|||++|+||+++..+.....++.++|||++|.+|..-|
T Consensus         2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~   70 (72)
T cd01719           2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALE   70 (72)
T ss_pred             chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEccc
Confidence            457899999999999999999999999999999999999999875556789999999999999998644

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.

>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=99.75  E-value=1e-17  Score=114.97  Aligned_cols=68  Identities=16%  Similarity=0.349  Sum_probs=61.1

Q ss_pred             cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC-------------CceeecceEEEecCeEEEE
Q psy17024          5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD-------------GKVKPMANIYIRGSKIRFL   71 (132)
Q Consensus         5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d-------------g~~~~l~~vfIRGs~Ir~I   71 (132)
                      .|+++|+.+.+++|+|+|++|.+|.|+|.+||.|||++|+||+++...             .....++.+||||++|.+|
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i   80 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV   80 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence            399999999999999999999999999999999999999999997532             1245889999999999997


Q ss_pred             e
Q psy17024         72 I   72 (132)
Q Consensus        72 ~   72 (132)
                      .
T Consensus        81 ~   81 (82)
T cd01730          81 S   81 (82)
T ss_pred             C
Confidence            5

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=99.74  E-value=1.3e-17  Score=116.27  Aligned_cols=68  Identities=16%  Similarity=0.355  Sum_probs=60.4

Q ss_pred             cHHHHHHhhC--CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC-------------ceeecceEEEecCeEE
Q psy17024          5 IPIKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-------------KVKPMANIYIRGSKIR   69 (132)
Q Consensus         5 ~Pl~lL~~~~--g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg-------------~~~~l~~vfIRGs~Ir   69 (132)
                      -|+++|+++.  +++|.|+|+++..|.|+|.+||.|||++|+||+++....             +...++.|||||++|.
T Consensus         2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv   81 (87)
T cd01720           2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI   81 (87)
T ss_pred             ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence            4999999996  899999999999999999999999999999999975331             1346899999999999


Q ss_pred             EEe
Q psy17024         70 FLI   72 (132)
Q Consensus        70 ~I~   72 (132)
                      ||.
T Consensus        82 ~Is   84 (87)
T cd01720          82 LVL   84 (87)
T ss_pred             EEe
Confidence            976

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.

>KOG3448|consensus

Probab=99.72  E-value=2.1e-17  Score=115.37  Aligned_cols=80  Identities=23%  Similarity=0.365  Sum_probs=71.2

Q ss_pred             HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc--eeecceEEEecCeEEEEecCccccccccc
Q psy17024          6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK--VKPMANIYIRGSKIRFLILPDMLKNAPMF   83 (132)
Q Consensus         6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~--~~~l~~vfIRGs~Ir~I~lPd~l~~ap~l   83 (132)
                      -.+|++.++|+.|+|||||+-.+.|+|.++|+|+|+.|.|+++++++.-  -..+..+|||||.||||.+|..-.+...+
T Consensus         3 FysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vdtqll   82 (96)
T KOG3448|consen    3 FYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVDTQLL   82 (96)
T ss_pred             hHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHHHHHHH
Confidence            4689999999999999999999999999999999999999999987653  46788999999999999999877666665


Q ss_pred             cc
Q psy17024         84 KG   85 (132)
Q Consensus        84 k~   85 (132)
                      .+
T Consensus        83 ~d   84 (96)
T KOG3448|consen   83 QD   84 (96)
T ss_pred             HH
Confidence            53

>KOG3482|consensus

Probab=99.71  E-value=1.6e-17  Score=112.25  Aligned_cols=67  Identities=22%  Similarity=0.409  Sum_probs=61.9

Q ss_pred             cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc-eeecceEEEecCeEEEEe
Q psy17024          5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK-VKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~   72 (132)
                      .|-.||+.+.|++|.|+||.|.+|+|+|+++|.|||++|.++++.. ||. .-++.+++||.+||.||.
T Consensus         8 NPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~i-dG~~~g~lGEilIRCNNvlyi~   75 (79)
T KOG3482|consen    8 NPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYI-DGVSTGNLGEILIRCNNVLYIR   75 (79)
T ss_pred             CchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhh-cccccccceeEEEEeccEEEEe
Confidence            5789999999999999999999999999999999999999998864 554 679999999999999994

>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=99.68  E-value=2.8e-16  Score=107.89  Aligned_cols=70  Identities=17%  Similarity=0.265  Sum_probs=62.4

Q ss_pred             cccHHHHHHhhCCC--EEEEEEc--CCCEEEEEEEeeCCccceEEeeEEEEec-CCceeecceEEEecCeEEEEe
Q psy17024          3 IGIPIKLLHEAEGH--IITCETT--NGDLFRGKLVEAEDNMNCAMADVTVTFR-DGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         3 ~~~Pl~lL~~~~g~--~V~VELK--nG~~y~G~L~~~D~~MNi~L~dv~~t~~-dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      +..|+++|+.+..+  +|+|.|+  +|.+|.|+|.+||+|||++|+||++... ......++.++|||++|.+|+
T Consensus         4 ~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~   78 (79)
T cd01718           4 MVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQ   78 (79)
T ss_pred             ccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEc
Confidence            46799999999999  7888887  8999999999999999999999999864 335678999999999999986

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.

>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=99.68  E-value=3.8e-16  Score=107.22  Aligned_cols=66  Identities=20%  Similarity=0.271  Sum_probs=59.0

Q ss_pred             HHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC--------ceeecceEEEecCeEEEEecCc
Q psy17024         10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG--------KVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus        10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg--------~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      |+++++++|.|.|++|.+|.|+|.+||.|||++|+||++...+.        ....++.++|||++|.+|...|
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            88999999999999999999999999999999999999976431        3577999999999999987543

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.

>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=99.61  E-value=4.1e-15  Score=101.19  Aligned_cols=65  Identities=14%  Similarity=0.260  Sum_probs=57.5

Q ss_pred             HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC----------CceeecceEEEecCeEEEEec
Q psy17024          9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD----------GKVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus         9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d----------g~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      =|+++++++|.|.|++|..|.|+|.++|.|||++|+||+++..+          .+..+++.+||||++|.+|.+
T Consensus         4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            37889999999999999999999999999999999999996421          135689999999999999875

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.

>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=99.60  E-value=8.6e-15  Score=99.22  Aligned_cols=68  Identities=18%  Similarity=0.144  Sum_probs=59.3

Q ss_pred             HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC---ceeecceEEEecCeEEEEec
Q psy17024          6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG---KVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus         6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg---~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      ++.-|.++++++|.|.|++|++|.|+|.+||.|||++|+||.++..++   ....++.++|||++|.++.+
T Consensus         3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728           3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence            355688999999999999999999999999999999999998875433   24678999999999999864

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.

>KOG1783|consensus

Probab=99.59  E-value=3e-16  Score=106.03  Aligned_cols=72  Identities=21%  Similarity=0.395  Sum_probs=66.0

Q ss_pred             cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc-eeecceEEEecCeEEEEecCc
Q psy17024          3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK-VKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         3 ~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      -..|-+||.+.+|++|.|+|.+|..|+|+|.++|.||||.|+.+++.. ||+ +..+..+||||++|.||...+
T Consensus         4 ~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~-ngql~n~ygdaFirGnnVlyIs~~~   76 (77)
T KOG1783|consen    4 GSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV-NGQLKNKYGDAFIRGNNVLYISTQK   76 (77)
T ss_pred             ccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh-cCcccccccceeeccccEEEEEecc
Confidence            357999999999999999999999999999999999999999998875 665 789999999999999998753

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

Probab=99.55  E-value=4.8e-14  Score=94.95  Aligned_cols=67  Identities=19%  Similarity=0.242  Sum_probs=58.6

Q ss_pred             HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEec---CC-ceeecceEEEecCeEEEEecCc
Q psy17024          9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFR---DG-KVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~---dg-~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      -|.++++++|.|.|++|..|.|+|.++|.|||++|++|++...   ++ ....++.++|||++|.+|..-|
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            4788999999999999999999999999999999999988743   22 3567999999999999988544

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=99.54  E-value=6.4e-14  Score=95.16  Aligned_cols=66  Identities=14%  Similarity=0.195  Sum_probs=60.1

Q ss_pred             HHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC------CceeecceEEEecCeEEEEec
Q psy17024          8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD------GKVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus         8 ~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d------g~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      +-|+++++++|.|.|++|..|.|+|.++|.+||+.|+||.++..+      .....++.++|||++|..|.+
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            568899999999999999999999999999999999999998643      347899999999999999875

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=99.53  E-value=5.1e-14  Score=98.70  Aligned_cols=71  Identities=15%  Similarity=0.284  Sum_probs=59.0

Q ss_pred             cccHHHHHHhhCCC--EEEEEEcC--CCEEEEEEEeeCCccceEEeeEEEEecCC-ceeecceEEEecCeEEEEec
Q psy17024          3 IGIPIKLLHEAEGH--IITCETTN--GDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus         3 ~~~Pl~lL~~~~g~--~V~VELKn--G~~y~G~L~~~D~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      +..|+++|+++...  +|.|.|++  +.+|.|+|.+||.|||++|+||+++..++ ....++.++|||++|.+|..
T Consensus        12 ~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~   87 (89)
T PTZ00138         12 MTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA   87 (89)
T ss_pred             ecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEc
Confidence            46799999999665  45555556  58999999999999999999999986433 46789999999999999863

>KOG3460|consensus

Probab=99.46  E-value=4.3e-14  Score=97.80  Aligned_cols=75  Identities=17%  Similarity=0.322  Sum_probs=65.2

Q ss_pred             CcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe--cCC-----------ceeecceEEEecCeE
Q psy17024          2 SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF--RDG-----------KVKPMANIYIRGSKI   68 (132)
Q Consensus         2 s~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~--~dg-----------~~~~l~~vfIRGs~I   68 (132)
                      ++..|++||+-+.+..|.|+|+++++++|+|.+||+|+|++|.||.+|-  .+.           ....++.+||||++|
T Consensus         2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~V   81 (91)
T KOG3460|consen    2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGV   81 (91)
T ss_pred             cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeE
Confidence            4678999999999999999999999999999999999999999987653  222           146788999999999


Q ss_pred             EEEecCcc
Q psy17024         69 RFLILPDM   76 (132)
Q Consensus        69 r~I~lPd~   76 (132)
                      .+|.-|-.
T Consensus        82 ilvspp~~   89 (91)
T KOG3460|consen   82 ILVSPPLR   89 (91)
T ss_pred             EEEcCccc
Confidence            99987754

>KOG1775|consensus

Probab=99.39  E-value=2.9e-13  Score=92.41  Aligned_cols=71  Identities=27%  Similarity=0.428  Sum_probs=64.4

Q ss_pred             CcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe--cCCc-eeecceEEEecCeEEEEe
Q psy17024          2 SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF--RDGK-VKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         2 s~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~--~dg~-~~~l~~vfIRGs~Ir~I~   72 (132)
                      |.-+|++|+.+++|+.|.|-+|++.++.|||++||+|.|++|+||++..  ++++ ..+++++++.|++|..+.
T Consensus         4 ~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLv   77 (84)
T KOG1775|consen    4 STLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLV   77 (84)
T ss_pred             hhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEe
Confidence            3568999999999999999999999999999999999999999999863  5554 689999999999998765

>KOG1780|consensus

Probab=99.33  E-value=3.6e-12  Score=86.44  Aligned_cols=70  Identities=24%  Similarity=0.297  Sum_probs=63.9

Q ss_pred             CC-cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          1 MS-IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         1 ms-~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      || .+.|  =|+++.++++.++|..+..+.|.|..||.|||++|+++++...++....+..++|||++|..+-
T Consensus         1 Msksg~P--eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~e   71 (77)
T KOG1780|consen    1 MSKSGHP--ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVE   71 (77)
T ss_pred             CCcccCc--hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEe
Confidence            54 3477  6899999999999999999999999999999999999999988888899999999999998764

>KOG3168|consensus

Probab=98.66  E-value=2.9e-08  Score=76.64  Aligned_cols=83  Identities=18%  Similarity=0.307  Sum_probs=68.1

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe---------cCC-ceeecceEEEecCeEEE
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF---------RDG-KVKPMANIYIRGSKIRF   70 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~---------~dg-~~~~l~~vfIRGs~Ir~   70 (132)
                      |+++-+.++|+. +++.+.|.++++.+|.|++.+||.|||++|.||++.-         .|+ +..-|..|.+||.+|..
T Consensus         1 M~~a~sskml~~-iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs   79 (177)
T KOG3168|consen    1 MTVAKSSKMLQH-INYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVS   79 (177)
T ss_pred             CCccchhHHHHh-hcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEE
Confidence            788888888865 7899999999999999999999999999999987642         122 25678999999999999


Q ss_pred             EecCcccccccccc
Q psy17024         71 LILPDMLKNAPMFK   84 (132)
Q Consensus        71 I~lPd~l~~ap~lk   84 (132)
                      ..+.+-..-++-|.
T Consensus        80 ~tVegppp~s~s~~   93 (177)
T KOG3168|consen   80 MTVEGPPPPSDSFR   93 (177)
T ss_pred             EeccCCCCCccccc
Confidence            99876665554444

>KOG1774|consensus

Probab=98.62  E-value=4.5e-08  Score=67.73  Aligned_cols=69  Identities=20%  Similarity=0.299  Sum_probs=54.1

Q ss_pred             ccHHHHHHhhC--CCEEEEEEcC--CCEEEEEEEeeCCccceEEeeEEEEecCCc-eeecceEEEecCeEEEEe
Q psy17024          4 GIPIKLLHEAE--GHIITCETTN--GDLFRGKLVEAEDNMNCAMADVTVTFRDGK-VKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         4 ~~Pl~lL~~~~--g~~V~VELKn--G~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~   72 (132)
                      ..|+.++..++  -.+|.|=|..  +..+.|.+++||+|||++|++|++.+...+ -..++.++++|++|..|.
T Consensus        11 v~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~   84 (88)
T KOG1774|consen   11 VQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQ   84 (88)
T ss_pred             cCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEe
Confidence            45666666553  3456666665  789999999999999999999998764433 348999999999999876

>KOG1781|consensus

Probab=98.31  E-value=1e-07  Score=68.05  Aligned_cols=70  Identities=19%  Similarity=0.207  Sum_probs=60.7

Q ss_pred             HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC--------ceeecceEEEecCeEEEEecCcccc
Q psy17024          9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG--------KVKPMANIYIRGSKIRFLILPDMLK   78 (132)
Q Consensus         9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg--------~~~~l~~vfIRGs~Ir~I~lPd~l~   78 (132)
                      =|.+.+++.|.|++..|.++.|+|.++|..||++|+|+.+..+|-        +..+++.+.+||..+..|.--|-.+
T Consensus        21 DLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e   98 (108)
T KOG1781|consen   21 DLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE   98 (108)
T ss_pred             hHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence            367889999999999999999999999999999999998875543        2478999999999999988766554

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

Probab=98.03  E-value=1.9e-05  Score=52.98  Aligned_cols=45  Identities=18%  Similarity=0.337  Sum_probs=36.6

Q ss_pred             HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCC---ccceEEeeEEEEec
Q psy17024          7 IKLLHEAEGHIITCETTNGDLFRGKLVEAED---NMNCAMADVTVTFR   51 (132)
Q Consensus         7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~---~MNi~L~dv~~t~~   51 (132)
                      +-++..++|++|+|.+|||..|+|.|.+++.   .+.+.|+.+.....
T Consensus         4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~   51 (77)
T PF14438_consen    4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPK   51 (77)
T ss_dssp             HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS
T ss_pred             HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccc
Confidence            3467889999999999999999999999998   89999999888653

>KOG1784|consensus

Probab=97.86  E-value=1.9e-05  Score=55.70  Aligned_cols=77  Identities=14%  Similarity=0.164  Sum_probs=61.1

Q ss_pred             HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe---cCC-ceeecceEEEecCeEEEEecCcccccccccc
Q psy17024          9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF---RDG-KVKPMANIYIRGSKIRFLILPDMLKNAPMFK   84 (132)
Q Consensus         9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~---~dg-~~~~l~~vfIRGs~Ir~I~lPd~l~~ap~lk   84 (132)
                      -|..+.++.|.|-+.+|+.+-|.|.+||..-|+.|+++-+-.   ..+ ....++...|||.||..|-.-|+- ..|+++
T Consensus         4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe-~d~~ld   82 (96)
T KOG1784|consen    4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEE-LDSRLD   82 (96)
T ss_pred             hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchh-hhhhhh
Confidence            477889999999999999999999999999999999986532   122 356788899999999998875543 334555


Q ss_pred             cc
Q psy17024         85 GK   86 (132)
Q Consensus        85 ~~   86 (132)
                      ..
T Consensus        83 ~t   84 (96)
T KOG1784|consen   83 LT   84 (96)
T ss_pred             hh
Confidence            44

>KOG1782|consensus

Probab=97.59  E-value=1.6e-05  Score=58.84  Aligned_cols=66  Identities=23%  Similarity=0.196  Sum_probs=54.9

Q ss_pred             HHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEE-ecCCc--eeecceEEEecCeEEEEecCc
Q psy17024         10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVT-FRDGK--VKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus        10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t-~~dg~--~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      |-+.+.+.+.|-|++|....|.|.+||+|-|++|++|.+- ..+.+  ....+-..|||.||..+-.-|
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            6677899999999999999999999999999999998773 33332  345677899999999987644

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

Probab=97.52  E-value=7.7e-05  Score=49.72  Aligned_cols=39  Identities=26%  Similarity=0.306  Sum_probs=32.1

Q ss_pred             CCCEEEEEEcC----CCEEEEEEEeeCCccceEEeeEEEEecC
Q psy17024         14 EGHIITCETTN----GDLFRGKLVEAEDNMNCAMADVTVTFRD   52 (132)
Q Consensus        14 ~g~~V~VELKn----G~~y~G~L~~~D~~MNi~L~dv~~t~~d   52 (132)
                      ..++|.|-++.    .-.++|.|++||.|||+.|.||+++...
T Consensus         7 er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~   49 (66)
T cd01739           7 ERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK   49 (66)
T ss_pred             CCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence            45677777765    3478899999999999999999998754

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=97.50  E-value=0.00048  Score=48.90  Aligned_cols=65  Identities=18%  Similarity=0.206  Sum_probs=54.9

Q ss_pred             hhCCCEEEEEEcCCCEEEEEEEeeCC-ccceEEeeEEEEecCCc---------eeecceEEEecCeEEEEecCcc
Q psy17024         12 EAEGHIITCETTNGDLFRGKLVEAED-NMNCAMADVTVTFRDGK---------VKPMANIYIRGSKIRFLILPDM   76 (132)
Q Consensus        12 ~~~g~~V~VELKnG~~y~G~L~~~D~-~MNi~L~dv~~t~~dg~---------~~~l~~vfIRGs~Ir~I~lPd~   76 (132)
                      .++|+.|.+..|++..|.|+|..+|. .-.|.|+||....-+++         ...++.+..||+.|.-+.+-+.
T Consensus         5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~   79 (96)
T PF12701_consen    5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEP   79 (96)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred             cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcC
Confidence            57899999999999999999999996 88999999988654443         3468899999999999887543

>KOG3459|consensus

Probab=97.46  E-value=2.6e-05  Score=56.68  Aligned_cols=68  Identities=15%  Similarity=0.358  Sum_probs=55.3

Q ss_pred             cHHHHHHhhC--CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe----c--CCc-------eeecceEEEecCeEE
Q psy17024          5 IPIKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF----R--DGK-------VKPMANIYIRGSKIR   69 (132)
Q Consensus         5 ~Pl~lL~~~~--g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~----~--dg~-------~~~l~~vfIRGs~Ir   69 (132)
                      -|+++|..+.  ..+|.|-+.|...+-|.+.++|-|+|++|+|+.+..    .  +|+       ...++.+||||++|.
T Consensus        24 Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI  103 (114)
T KOG3459|consen   24 GPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVI  103 (114)
T ss_pred             CchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEE
Confidence            4788888874  568999999999999999999999999999987743    1  222       346889999999876


Q ss_pred             EEe
Q psy17024         70 FLI   72 (132)
Q Consensus        70 ~I~   72 (132)
                      .+.
T Consensus       104 ~v~  106 (114)
T KOG3459|consen  104 LVL  106 (114)
T ss_pred             EEE
Confidence            654

>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=96.35  E-value=0.021  Score=38.91  Aligned_cols=59  Identities=20%  Similarity=0.218  Sum_probs=47.2

Q ss_pred             hhCCCEEEEEEcCCCEEEEEEEeeCC-ccceEEeeEEEEecCCc----------eeecceEEEecCeEEE
Q psy17024         12 EAEGHIITCETTNGDLFRGKLVEAED-NMNCAMADVTVTFRDGK----------VKPMANIYIRGSKIRF   70 (132)
Q Consensus        12 ~~~g~~V~VELKnG~~y~G~L~~~D~-~MNi~L~dv~~t~~dg~----------~~~l~~vfIRGs~Ir~   70 (132)
                      +++|+.|++-.|++..|.|+|.++|. .--+.|+||....-+|+          ..-++.+.-||+.|.-
T Consensus         3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD   72 (74)
T cd01736           3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD   72 (74)
T ss_pred             cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence            57899999999999999999999995 55788999988765543          2346677778887753

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=96.29  E-value=0.026  Score=38.97  Aligned_cols=64  Identities=11%  Similarity=0.134  Sum_probs=50.8

Q ss_pred             HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeC-CccceEEeeEEEEecCCceeecceEEEecCeEEEEecC
Q psy17024          6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAE-DNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILP   74 (132)
Q Consensus         6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D-~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lP   74 (132)
                      -|.+|..+.|++|.+.|....++.|+..++| +-.|+.++|..  .+=|   ..++..||.+-|..+.+.
T Consensus        15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~--TPlG---v~~eAlLR~~DVi~~~f~   79 (80)
T PF11095_consen   15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ--TPLG---VQPEALLRCSDVISISFD   79 (80)
T ss_dssp             HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE--TTTT---EEEEEEEEGGGEEEEEE-
T ss_pred             HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC--CCcc---cChhheeecCCEEEEEec
Confidence            4788999999999999999999999999999 57799998853  3444   347899999999988764

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.

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

Probab=95.66  E-value=0.072  Score=32.66  Aligned_cols=31  Identities=16%  Similarity=0.157  Sum_probs=28.2

Q ss_pred             CCCEEEEEEcCCCEEEEEEEeeCCccceEEee
Q psy17024         14 EGHIITCETTNGDLFRGKLVEAEDNMNCAMAD   45 (132)
Q Consensus        14 ~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~d   45 (132)
                      .|++|+|++ ++..++|+...+|++=.+.++.
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            589999999 7778899999999999999876

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

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

Probab=95.66  E-value=0.036  Score=36.46  Aligned_cols=35  Identities=20%  Similarity=0.189  Sum_probs=29.0

Q ss_pred             HHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024          9 LLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAM   43 (132)
Q Consensus         9 lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L   43 (132)
                      ||+++  ...+|+|-|.||..++|++.++|+|+=+.-
T Consensus         3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~   39 (61)
T cd01716           3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLE   39 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEE
Confidence            45554  677999999999999999999999975443

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.

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

Probab=95.49  E-value=0.12  Score=34.52  Aligned_cols=52  Identities=27%  Similarity=0.586  Sum_probs=39.5

Q ss_pred             HHHHHhhCCCEEEEEEcCCCEEEEEEEeeC-CccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          7 IKLLHEAEGHIITCETTNGDLFRGKLVEAE-DNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D-~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      .+.|++++|+.|+|++-.|+. +|+|.++. ||.  .|+.      ++     ..+|||=.+|.+|.
T Consensus        13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~------~~-----~~~~IR~~~IV~v~   65 (66)
T PF10842_consen   13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEE------NG-----TPFFIRIAQIVWVM   65 (66)
T ss_pred             HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEe------CC-----cEEEEEeeeEEEEc
Confidence            678999999999999977766 99999987 454  2221      12     35789888888764

>TIGR02383 Hfq RNA chaperone Hfq

Probab=95.40  E-value=0.05  Score=35.78  Aligned_cols=36  Identities=17%  Similarity=0.134  Sum_probs=29.4

Q ss_pred             HHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024          8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAM   43 (132)
Q Consensus         8 ~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L   43 (132)
                      .||.++  ...+|+|-|.||..++|++.++|+|+=+.-
T Consensus         6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~   43 (61)
T TIGR02383         6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLE   43 (61)
T ss_pred             HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence            345554  678999999999999999999999975543

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.

>KOG1073|consensus

Probab=94.59  E-value=0.078  Score=45.66  Aligned_cols=66  Identities=23%  Similarity=0.295  Sum_probs=54.6

Q ss_pred             HhhCCCEEEEEEcCCCEEEEEEEeeC-CccceEEeeEEEEecCCc---------e-eecceEEEecCeEEEEecCcc
Q psy17024         11 HEAEGHIITCETTNGDLFRGKLVEAE-DNMNCAMADVTVTFRDGK---------V-KPMANIYIRGSKIRFLILPDM   76 (132)
Q Consensus        11 ~~~~g~~V~VELKnG~~y~G~L~~~D-~~MNi~L~dv~~t~~dg~---------~-~~l~~vfIRGs~Ir~I~lPd~   76 (132)
                      ...+|+.|.+.-|++..|+|.|..+| +.-=|-|++|.....+++         . .-++.|+-||+.|+-+++-|.
T Consensus         5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~   81 (361)
T KOG1073|consen    5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQET   81 (361)
T ss_pred             cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccC
Confidence            35789999999999999999999999 577899999977654442         1 267889999999998887653

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=94.40  E-value=0.12  Score=35.62  Aligned_cols=54  Identities=17%  Similarity=0.174  Sum_probs=37.9

Q ss_pred             HHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024          8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus         8 ~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      .||..+  ...+|+|-|.||..++|++.++|+|+=+...       +++     +-+|-=..|..|..
T Consensus        10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~-------~gk-----qqLIYKHAISTI~p   65 (79)
T PRK00395         10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRN-------TGK-----SQLVYKHAISTVVP   65 (79)
T ss_pred             HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEE-------CCc-----EEEEEEeeeEEEec
Confidence            345544  6789999999999999999999999755433       332     22455556666654

>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=94.20  E-value=0.3  Score=32.02  Aligned_cols=31  Identities=16%  Similarity=0.324  Sum_probs=27.8

Q ss_pred             hCCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024         13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAM   43 (132)
Q Consensus        13 ~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L   43 (132)
                      ++|+.|.+++-.|++++|.|..||..-++.+
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lI   34 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLI   34 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEE
Confidence            5799999999999999999999998876654

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.

>PRK14638 hypothetical protein; Provisional

Probab=90.93  E-value=0.49  Score=35.77  Aligned_cols=29  Identities=21%  Similarity=0.332  Sum_probs=26.4

Q ss_pred             HHhhCCCEEEEEEcCCCEEEEEEEeeCCc
Q psy17024         10 LHEAEGHIITCETTNGDLFRGKLVEAEDN   38 (132)
Q Consensus        10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~   38 (132)
                      +..++|+.|.|+|+++..++|+|.++|+.
T Consensus        95 f~r~~G~~v~V~~~~~k~~~G~L~~~~~~  123 (150)
T PRK14638         95 YVRFTGKLAKIVTKDGKTFIGRIESFVDG  123 (150)
T ss_pred             HHHhCCCEEEEEECCCcEEEEEEEEEeCC
Confidence            45689999999999999999999999974

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

Probab=90.93  E-value=1.5  Score=34.01  Aligned_cols=61  Identities=11%  Similarity=0.215  Sum_probs=42.4

Q ss_pred             HHHhhCCCEEEEEEcCCCEEEEEEEeeCC-ccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcc
Q psy17024          9 LLHEAEGHIITCETTNGDLFRGKLVEAED-NMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDM   76 (132)
Q Consensus         9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~-~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~   76 (132)
                      .+..++++.|.|.+.+ .+|.|-|..+|. .-|++|-+..   .|++.   .--+|-|.+|+.|.+-+.
T Consensus        11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~---e~~~~---sv~~I~ghaVk~vevl~~   72 (166)
T PF06372_consen   11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQ---EDGKR---SVKVIMGHAVKSVEVLSE   72 (166)
T ss_dssp             HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE----TTS-E---EEEEE-GGGEEEEEEEE-
T ss_pred             HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcc---cCCce---eEEEEEccceEEEEEccC
Confidence            3567899999999999 999999999996 6788886543   24432   347899999999887543

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.

>PRK02001 hypothetical protein; Validated

Probab=90.80  E-value=0.7  Score=35.20  Aligned_cols=29  Identities=28%  Similarity=0.437  Sum_probs=26.5

Q ss_pred             HHhhCCCEEEEEEcCCCEEEEEEEeeCCc
Q psy17024         10 LHEAEGHIITCETTNGDLFRGKLVEAEDN   38 (132)
Q Consensus        10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~   38 (132)
                      +..++|+.|.|.|+++..|.|+|.++|+.
T Consensus        85 f~r~~G~~v~V~l~~~~~~~G~L~~~~~~  113 (152)
T PRK02001         85 YKKNIGRELEVLTKNGKKIEGELKSADEN  113 (152)
T ss_pred             HHHhCCCEEEEEECCCCEEEEEEEEEeCC
Confidence            45689999999999999999999999975

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

Probab=90.63  E-value=0.53  Score=32.32  Aligned_cols=32  Identities=19%  Similarity=0.200  Sum_probs=27.2

Q ss_pred             HHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCcc
Q psy17024          8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNM   39 (132)
Q Consensus         8 ~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~M   39 (132)
                      .||..+  ...+|+|-|.||...+|.+.+||.|.
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            345543  78899999999999999999999885

>KOG3262|consensus

Probab=89.39  E-value=1.5  Score=35.10  Aligned_cols=58  Identities=29%  Similarity=0.350  Sum_probs=30.0

Q ss_pred             HHHHHhhCCCEEEEEEcC-------------CCEEEEEEEeeCCccceEEeeEEEEecCC----ceeecceEEEecCe
Q psy17024          7 IKLLHEAEGHIITCETTN-------------GDLFRGKLVEAEDNMNCAMADVTVTFRDG----KVKPMANIYIRGSK   67 (132)
Q Consensus         7 l~lL~~~~g~~V~VELKn-------------G~~y~G~L~~~D~~MNi~L~dv~~t~~dg----~~~~l~~vfIRGs~   67 (132)
                      -+|||.+++..|+= |.+             +.+..|++.++=.-+|=++-  +++..|+    ....-+++||-..+
T Consensus        57 g~flh~Cegd~Vck-~~~~kIPyfNAPIylenk~qIGKVDEIfG~i~d~~f--sIK~~dgv~assfk~g~k~fi~p~K  131 (215)
T KOG3262|consen   57 GKFLHMCEGDLVCK-LTNKKIPYFNAPIYLENKEQIGKVDEIFGPINDVHF--SIKPSDGVQASSFKPGDKLFIDPDK  131 (215)
T ss_pred             hhhhhhcCCceEEe-eccccCCCCCCceeecchhhhcchhhhcccccccEE--EEecCCCceeecccCCCeEEecccc
Confidence            36889999887753 222             33445777776444443332  2222222    13344566665554

>PRK14639 hypothetical protein; Provisional

Probab=89.25  E-value=0.79  Score=34.27  Aligned_cols=34  Identities=24%  Similarity=0.513  Sum_probs=28.6

Q ss_pred             HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024          9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAM   43 (132)
Q Consensus         9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L   43 (132)
                      =++.++|+.|.|+|++...+.|+|.++|+. ++.|
T Consensus        82 ~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l  115 (140)
T PRK14639         82 HFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL  115 (140)
T ss_pred             HHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            356789999999999999999999999984 4444

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

Probab=89.02  E-value=1.3  Score=29.91  Aligned_cols=29  Identities=24%  Similarity=0.528  Sum_probs=24.7

Q ss_pred             HHhhCCCEEEEEEc---CC-CEEEEEEEeeCCc
Q psy17024         10 LHEAEGHIITCETT---NG-DLFRGKLVEAEDN   38 (132)
Q Consensus        10 L~~~~g~~V~VELK---nG-~~y~G~L~~~D~~   38 (132)
                      +..++|+.|.|+|+   ++ ..+.|+|.++|+.
T Consensus        20 ~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~   52 (83)
T cd01734          20 FERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD   52 (83)
T ss_pred             HHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence            45679999999998   55 5899999999984

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=88.36  E-value=0.76  Score=34.30  Aligned_cols=41  Identities=20%  Similarity=0.377  Sum_probs=31.5

Q ss_pred             cccHHHH--HHhhCCCEEEEEEcCC----CEEEEEEEeeCCccceEEe
Q psy17024          3 IGIPIKL--LHEAEGHIITCETTNG----DLFRGKLVEAEDNMNCAMA   44 (132)
Q Consensus         3 ~~~Pl~l--L~~~~g~~V~VELKnG----~~y~G~L~~~D~~MNi~L~   44 (132)
                      +..||+-  +..++|+.|.|+|++.    ..+.|+|.++|+. ++.|+
T Consensus        71 ldRpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         71 FDMDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             CCCCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            3445444  6678999999999987    8999999999984 34443

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=87.56  E-value=1.4  Score=34.25  Aligned_cols=36  Identities=11%  Similarity=-0.004  Sum_probs=29.6

Q ss_pred             HHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024          8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAM   43 (132)
Q Consensus         8 ~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L   43 (132)
                      .||.++  ...+|+|-|.||..++|++.+||+|.=+..
T Consensus        15 ~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~   52 (165)
T PRK14091         15 IFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLR   52 (165)
T ss_pred             HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEE
Confidence            466665  577899999999999999999999865443

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=87.23  E-value=1.5  Score=34.04  Aligned_cols=36  Identities=17%  Similarity=0.171  Sum_probs=29.1

Q ss_pred             HHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024          8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAM   43 (132)
Q Consensus         8 ~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L   43 (132)
                      .||..+  ...+|+|-|.||..++|.+.+||+|.=+..
T Consensus        95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~  132 (165)
T PRK14091         95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLE  132 (165)
T ss_pred             HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEE
Confidence            344444  678999999999999999999999975443

>PRK14642 hypothetical protein; Provisional

Probab=86.78  E-value=1.6  Score=34.68  Aligned_cols=36  Identities=31%  Similarity=0.502  Sum_probs=28.4

Q ss_pred             cccHHHH---HHhhCCCEEEEEEc-------------CCCEEEEEEEeeCCc
Q psy17024          3 IGIPIKL---LHEAEGHIITCETT-------------NGDLFRGKLVEAEDN   38 (132)
Q Consensus         3 ~~~Pl~l---L~~~~g~~V~VELK-------------nG~~y~G~L~~~D~~   38 (132)
                      +..||+-   +..++|+.|.|.|+             +...|+|+|.++|+.
T Consensus        85 ldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~  136 (197)
T PRK14642         85 IDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG  136 (197)
T ss_pred             CCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence            3445443   44579999999999             679999999999984

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=86.54  E-value=3.4  Score=31.00  Aligned_cols=30  Identities=13%  Similarity=0.246  Sum_probs=25.5

Q ss_pred             HHHhhCCCEEEEEE----cCCCEEEEEEEeeCCc
Q psy17024          9 LLHEAEGHIITCET----TNGDLFRGKLVEAEDN   38 (132)
Q Consensus         9 lL~~~~g~~V~VEL----KnG~~y~G~L~~~D~~   38 (132)
                      =+..++|+.|.|+|    .+...++|+|.++|+.
T Consensus        92 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~  125 (154)
T PRK00092         92 DFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE  125 (154)
T ss_pred             HHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence            35678999999998    4577999999999984

>PRK14632 hypothetical protein; Provisional

Probab=85.37  E-value=2.1  Score=33.04  Aligned_cols=33  Identities=21%  Similarity=0.377  Sum_probs=26.9

Q ss_pred             HHhhCCCEEEEEEcC-------CCEEEEEEEeeCCccceEE
Q psy17024         10 LHEAEGHIITCETTN-------GDLFRGKLVEAEDNMNCAM   43 (132)
Q Consensus        10 L~~~~g~~V~VELKn-------G~~y~G~L~~~D~~MNi~L   43 (132)
                      +..++|+.|.|+|++       ...+.|+|.++|+. ++.|
T Consensus        93 f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l  132 (172)
T PRK14632         93 MSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVL  132 (172)
T ss_pred             HHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEE
Confidence            457899999999986       56999999999974 4444

>PRK14647 hypothetical protein; Provisional

Probab=85.21  E-value=3.7  Score=31.15  Aligned_cols=30  Identities=20%  Similarity=0.284  Sum_probs=25.0

Q ss_pred             HHHhhCCCEEEEEEcC---------CCEEEEEEEeeCCc
Q psy17024          9 LLHEAEGHIITCETTN---------GDLFRGKLVEAEDN   38 (132)
Q Consensus         9 lL~~~~g~~V~VELKn---------G~~y~G~L~~~D~~   38 (132)
                      =+..++|+.|.|+|+.         ...|.|+|.++|+.
T Consensus        93 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~  131 (159)
T PRK14647         93 DYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG  131 (159)
T ss_pred             HHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC
Confidence            3556899999999963         47999999999973

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.72  E-value=2.7  Score=32.13  Aligned_cols=30  Identities=17%  Similarity=0.323  Sum_probs=26.7

Q ss_pred             HHhhCCCEEEEEE----cCCCEEEEEEEeeCCcc
Q psy17024         10 LHEAEGHIITCET----TNGDLFRGKLVEAEDNM   39 (132)
Q Consensus        10 L~~~~g~~V~VEL----KnG~~y~G~L~~~D~~M   39 (132)
                      +..+.|+.|.|+|    .+.+.+.|+|.++|..+
T Consensus        94 f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~  127 (153)
T COG0779          94 FARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET  127 (153)
T ss_pred             HHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence            4557999999999    67899999999999887

>PRK14636 hypothetical protein; Provisional

Probab=84.19  E-value=3.4  Score=32.10  Aligned_cols=30  Identities=23%  Similarity=0.415  Sum_probs=25.3

Q ss_pred             HHHhhCCCEEEEEEc---CC-CEEEEEEEeeCCc
Q psy17024          9 LLHEAEGHIITCETT---NG-DLFRGKLVEAEDN   38 (132)
Q Consensus         9 lL~~~~g~~V~VELK---nG-~~y~G~L~~~D~~   38 (132)
                      =+..++|+.|.|+|+   +| ..++|+|.++|+.
T Consensus        92 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~  125 (176)
T PRK14636         92 DFADWAGHEARIALSEPLDGRKQFRGELKGIDGD  125 (176)
T ss_pred             HHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC
Confidence            355789999999998   55 6999999999884

>PRK14640 hypothetical protein; Provisional

Probab=84.14  E-value=2.1  Score=32.30  Aligned_cols=30  Identities=13%  Similarity=0.247  Sum_probs=25.6

Q ss_pred             HHHhhCCCEEEEEE----cCCCEEEEEEEeeCCc
Q psy17024          9 LLHEAEGHIITCET----TNGDLFRGKLVEAEDN   38 (132)
Q Consensus         9 lL~~~~g~~V~VEL----KnG~~y~G~L~~~D~~   38 (132)
                      =++.++|+.|.|+|    .+...++|+|.++|+.
T Consensus        91 ~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~  124 (152)
T PRK14640         91 QFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD  124 (152)
T ss_pred             HHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            35578999999999    4668999999999985

>PRK14633 hypothetical protein; Provisional

Probab=83.99  E-value=2.9  Score=31.55  Aligned_cols=34  Identities=24%  Similarity=0.299  Sum_probs=27.0

Q ss_pred             HHHhhCCCEEEEEEc----CCCEEEEEEEeeCCccceEE
Q psy17024          9 LLHEAEGHIITCETT----NGDLFRGKLVEAEDNMNCAM   43 (132)
Q Consensus         9 lL~~~~g~~V~VELK----nG~~y~G~L~~~D~~MNi~L   43 (132)
                      =+..++|+.|.|+|+    +...++|+|.++|+. ++.|
T Consensus        88 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l  125 (150)
T PRK14633         88 QAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL  125 (150)
T ss_pred             HHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence            345689999999995    568999999999985 4444

>PRK14643 hypothetical protein; Provisional

Probab=82.86  E-value=3.1  Score=31.94  Aligned_cols=30  Identities=20%  Similarity=0.164  Sum_probs=25.7

Q ss_pred             HHHhhCCCEEEEEEcC----CCEEEEEEEeeCCc
Q psy17024          9 LLHEAEGHIITCETTN----GDLFRGKLVEAEDN   38 (132)
Q Consensus         9 lL~~~~g~~V~VELKn----G~~y~G~L~~~D~~   38 (132)
                      =+..++|+.|.|.|+.    ...++|+|.++|+.
T Consensus        98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         98 ELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             HHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            3567899999999976    58999999999975

>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=80.51  E-value=4.6  Score=29.64  Aligned_cols=35  Identities=23%  Similarity=0.440  Sum_probs=24.5

Q ss_pred             cccHH---HHHHhhCCCEEEEEEc----CCCEEEEEEEeeCC
Q psy17024          3 IGIPI---KLLHEAEGHIITCETT----NGDLFRGKLVEAED   37 (132)
Q Consensus         3 ~~~Pl---~lL~~~~g~~V~VELK----nG~~y~G~L~~~D~   37 (132)
                      +..||   .-+..++|+.|.|.++    +...+.|+|.++|+
T Consensus        72 ~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~  113 (141)
T PF02576_consen   72 IDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE  113 (141)
T ss_dssp             SSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred             CCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence            34455   4567789999999995    45689999999998

; PDB: 1IB8_A.

>PRK14645 hypothetical protein; Provisional

Probab=80.50  E-value=3.1  Score=31.64  Aligned_cols=29  Identities=14%  Similarity=0.289  Sum_probs=24.9

Q ss_pred             HHHhhCCCEEEEEEcCCCEEEEEEEeeCCc
Q psy17024          9 LLHEAEGHIITCETTNGDLFRGKLVEAEDN   38 (132)
Q Consensus         9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~   38 (132)
                      =+..++|+.|.|.+ ++..+.|+|.++|+.
T Consensus        96 df~r~~G~~v~v~~-~~k~~~G~L~~~~d~  124 (154)
T PRK14645         96 HFERFAGLKAKVRG-PGENFTGRIKAVSGD  124 (154)
T ss_pred             HHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence            35567999999986 789999999999985

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	132
3pgw_Z	126	Crystal Structure Of Human U1 Snrnp Length = 126		4e-36
3cw1_D	126	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		2e-35
1d3b_A	75	Crystal Structure Of The D3b Subcomplex Of The Huma		1e-30
4emh_A	105	Crystal Structure Of Splsm4 Length = 105		3e-05
1b34_A	119	Crystal Structure Of The D1d2 Sub-Complex From The		1e-04

>pdb|3PGW|Z Chain Z, Crystal Structure Of Human U1 Snrnp Length = 126

Iteration: 1
 Score =  146 bits (368), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 61/83 (73%), Positives = 75/83 (90%)
Query: 1  MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
          MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct: 1  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60
Query: 61 IYIRGSKIRFLILPDMLKNAPMF 83
          +YIRGSKIRFLILPDMLKNAPM 
Sbjct: 61 VYIRGSKIRFLILPDMLKNAPML 83

>pdb|3CW1|D Chain D, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 126

Iteration: 1
 Score =  144 bits (362), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 60/83 (72%), Positives = 74/83 (89%)
Query: 1  MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
          MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct: 1  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60
Query: 61 IYIRGSKIRFLILPDMLKNAPMF 83
          +YIRG KIRFLILPDMLKNAPM 
Sbjct: 61 VYIRGCKIRFLILPDMLKNAPML 83

>pdb|1D3B|A Chain A, Crystal Structure Of The D3b Subcomplex Of The Human Core Snrnp Domain At 2.0a Resolution Length = 75

Iteration: 1
 Score =  127 bits (320), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 53/75 (70%), Positives = 67/75 (89%)
Query: 1  MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
          MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  
Sbjct: 1  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60
Query: 61 IYIRGSKIRFLILPD 75
          +YIRG KIRFLILPD
Sbjct: 61 VYIRGCKIRFLILPD 75

>pdb|4EMH|A Chain A, Crystal Structure Of Splsm4 Length = 105

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 5  IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYI 63
          +P+ LL+  +G  I  E  NG+ F G L   ++  N  + +V  T  DG K   +   YI
Sbjct: 16 LPLTLLNATQGRPILVELKNGETFNGHLENCDNYXNLTLREVIRTXPDGDKFFRLPECYI 75
Query: 64 RGSKIRFLILPD 75
          RG+ I++L + D
Sbjct: 76 RGNNIKYLRIQD 87

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 7  IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGS 66
          +KL HE     +T E  NG    G +   + +MN  +  V +T ++ +   +  + IRG+
Sbjct: 8  MKLSHET----VTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGN 63
Query: 67 KIRFLILPDML 77
           IR+ ILPD L
Sbjct: 64 NIRYFILPDSL 74

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	132
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	100.0
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.97
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.96
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.96
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.9
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.9
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.9
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.9
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.89
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.88
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.88
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.87
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.86
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.86
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.85
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.84
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.82
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.8
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.8
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.79
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.78
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.76
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.72
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.71
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	98.67
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.05
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	96.66
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.58
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	96.51
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	96.34
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	96.28
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	95.97
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	95.9
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	95.73
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	95.64
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	95.29
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	94.99
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	94.47
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	93.63
1ycy_A	71	Conserved hypothetical protein; structural genomic	92.56
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	91.07
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	82.88
3by7_A	100	Uncharacterized protein; metagenomics, structural	82.15

>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=100.00  E-value=5e-38  Score=230.80  Aligned_cols=113  Identities=66%  Similarity=1.164  Sum_probs=83.2

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcccccc
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNA   80 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~~a   80 (132)
                      ||+++|++||++++|++|+||||||++|+|+|.+||+||||+|+||+++.++++..++++|||||++|+||++||+++++
T Consensus         1 ~~~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd~l~~~   80 (126)
T 2y9a_D            1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNA   80 (126)
T ss_dssp             ---CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCSSCSSS
T ss_pred             CCcccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEccccccch
Confidence            89999999999999999999999999999999999999999999999998898899999999999999999999999999


Q ss_pred             cccccccCC-CCCccCCchhhhhhhhhccCCCCCC
Q psy17024         81 PMFKGKQGN-KAGAAGRGKSGILRAQAARGRGRGG  114 (132)
Q Consensus        81 p~lk~~~~~-~~~~~~~g~~~~~r~~~~rg~grgg  114 (132)
                      |+|++...+ ++.++++|++++.|+++ ++||||.
T Consensus        81 ~~l~~~~~k~~~~~~~~g~~~~~~~~~-~~~~~~~  114 (126)
T 2y9a_D           81 PMLKSMKNKNQGSGAGRGKAAILKAQV-AARGRGR  114 (126)
T ss_dssp             SHHHHHHHHHC------------------------
T ss_pred             HHhhhhhhcccccccCcCchhhhhccc-ccCCCCC
Confidence            999976543 25567899999988874 3444443

>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=4.8e-31  Score=191.37  Aligned_cols=85  Identities=24%  Similarity=0.429  Sum_probs=78.0

Q ss_pred             cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcccccccccc
Q psy17024          5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFK   84 (132)
Q Consensus         5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~~ap~lk   84 (132)
                      .|++||+++++++|+|||+||.+|+|+|.+||+||||+|+||+++..+++..+++++||||++|+||++||+|+.+|+|+
T Consensus         2 ~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~~lg~v~IRG~nI~~I~~pd~l~~d~~l~   81 (119)
T 1b34_A            2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLV   81 (119)
T ss_dssp             CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTCCHHHHTC
T ss_pred             ChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEEEcCCeEEEEEeccccccchhHh
Confidence            69999999999999999999999999999999999999999999988888899999999999999999999999999998


Q ss_pred             cccCC
Q psy17024         85 GKQGN   89 (132)
Q Consensus        85 ~~~~~   89 (132)
                      +..++
T Consensus        82 ~~~pK   86 (119)
T 1b34_A           82 DVEPK   86 (119)
T ss_dssp             -----
T ss_pred             hhccc
Confidence            76555

>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=99.96  E-value=1.3e-29  Score=170.39  Aligned_cols=75  Identities=71%  Similarity=1.292  Sum_probs=70.9

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      ||++.|++||++++|++|+||||||++|+|+|.+||+|||++|+||+++.++++..+++++||||++|+||++||
T Consensus         1 ~~~~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             ---CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             CCccCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEEEeCCEEEEEEcCC
Confidence            899999999999999999999999999999999999999999999999998888999999999999999999997

>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=99.96  E-value=5.4e-29  Score=177.64  Aligned_cols=86  Identities=30%  Similarity=0.520  Sum_probs=57.4

Q ss_pred             ccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC-ceeecceEEEecCeEEEEecCcccccccc
Q psy17024          4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYIRGSKIRFLILPDMLKNAPM   82 (132)
Q Consensus         4 ~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~Ir~I~lPd~l~~ap~   82 (132)
                      ..|++||++++|++|+||||||++|+|+|.+||+|||++|+||+++..++ +..+++.+||||++|+||++||++.++|+
T Consensus        15 ~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG~nI~~I~~pd~l~d~p~   94 (105)
T 4emh_A           15 MLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNIKYLRIQDEVLSQVA   94 (105)
T ss_dssp             -----------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECGGGEEEEEC---------
T ss_pred             CcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeCCeEEEEecCHHHhhhhh
Confidence            47999999999999999999999999999999999999999999998888 48899999999999999999999999999


Q ss_pred             cccccCC
Q psy17024         83 FKGKQGN   89 (132)
Q Consensus        83 lk~~~~~   89 (132)
                      |++.+++
T Consensus        95 ~~~~~~~  101 (105)
T 4emh_A           95 KQQAQQR  101 (105)
T ss_dssp             -------
T ss_pred             hhhhccc
Confidence            9987554

>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=99.90  E-value=7e-24  Score=142.00  Aligned_cols=75  Identities=21%  Similarity=0.311  Sum_probs=69.4

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcc
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDM   76 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~   76 (132)
                      || ..|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..+++..+++.+||||++|+||++||.
T Consensus         1 m~-~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~   75 (77)
T 1i4k_A            1 MP-PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSPAPG   75 (77)
T ss_dssp             ---CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEECC-
T ss_pred             CC-ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCcEeECCEEEECCCEEEEEEeCCC
Confidence            54 4799999999999999999999999999999999999999999999887778999999999999999999985

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

Probab=99.90  E-value=7.5e-24  Score=141.39  Aligned_cols=75  Identities=23%  Similarity=0.353  Sum_probs=68.3

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcc
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDM   76 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~   76 (132)
                      || ..|+++|+++++++|+|+||||++|+|+|.+||+|||++|+||+++..+++..+++.+||||++|+||..||+
T Consensus         1 m~-~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~e   75 (75)
T 1h64_1            1 MA-ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTEE   75 (75)
T ss_dssp             ---CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             CC-chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEEECCCEEEEEEeCCC
Confidence            54 4799999999999999999999999999999999999999999999877778999999999999999999874

>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=99.90  E-value=8.9e-24  Score=145.32  Aligned_cols=78  Identities=18%  Similarity=0.232  Sum_probs=67.9

Q ss_pred             CC-cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcccc
Q psy17024          1 MS-IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLK   78 (132)
Q Consensus         1 ms-~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~   78 (132)
                      || ...|++||+++++++|+|+||||++|+|+|.+||+|||++|+||+++....+..+++.+||||++|+||++||.-.
T Consensus         1 ms~~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~IRG~nI~~i~~~d~~~   79 (86)
T 3s6n_F            1 MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEEE   79 (86)
T ss_dssp             --CCCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEEECGGGEEEEEECC---
T ss_pred             CCcCcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEEEeCCeEEEEEeCCccc
Confidence            53 6789999999999999999999999999999999999999999998753335789999999999999999998654

>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=99.90  E-value=1.3e-23  Score=140.94  Aligned_cols=73  Identities=22%  Similarity=0.383  Sum_probs=68.3

Q ss_pred             ccHHHHHHhhCCCEEEEEEcCC-CEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcc
Q psy17024          4 GIPIKLLHEAEGHIITCETTNG-DLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDM   76 (132)
Q Consensus         4 ~~Pl~lL~~~~g~~V~VELKnG-~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~   76 (132)
                      -.|+.+|+++++++|+|+|||| ++|+|+|.+||+|||++|+||+++..+++..+++.+||||++|+||++||+
T Consensus         4 ~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~nI~~i~~~de   77 (77)
T 1ljo_A            4 VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQEE   77 (77)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             cchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEEEeCCeEEEEEeCCC
Confidence            5899999999999999999999 999999999999999999999999877678999999999999999999984

>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=99.89  E-value=3.2e-23  Score=138.71  Aligned_cols=74  Identities=20%  Similarity=0.339  Sum_probs=67.5

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      || ..|+++|+++++++|+|+||||++|+|+|.+||+|||++|+||+++..+.+..+++.+||||++|+||...|
T Consensus         1 m~-~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 4emk_B            1 MD-SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVLYVSALD   74 (75)
T ss_dssp             CC-SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEEEEGGGSSEEEEC-
T ss_pred             CC-CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEEEcCCeEEEEEecC
Confidence            55 689999999999999999999999999999999999999999999865546789999999999999998654

>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=99.88  E-value=1.3e-22  Score=137.47  Aligned_cols=73  Identities=22%  Similarity=0.315  Sum_probs=68.5

Q ss_pred             ccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcc
Q psy17024          4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDM   76 (132)
Q Consensus         4 ~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~   76 (132)
                      ..|+.+|+++++++|+|+|+||++|+|+|.+||+|||++|+||+++..+++..+++.+||||++|+||+.||.
T Consensus         8 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   80 (81)
T 1th7_A            8 ETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             HHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEEC--
T ss_pred             cchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEEECCCEEEEEEecCC
Confidence            4799999999999999999999999999999999999999999999888788999999999999999999874

>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=99.88  E-value=1.1e-22  Score=142.00  Aligned_cols=73  Identities=15%  Similarity=0.221  Sum_probs=63.0

Q ss_pred             cccHHHHHHhhCCCEEEEEEcCC-CEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024          3 IGIPIKLLHEAEGHIITCETTNG-DLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         3 ~~~Pl~lL~~~~g~~V~VELKnG-~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      ...|+++|++++|++|+|+|||| ++|+|+|.+||+|||++|+||+++..+++..+++.+||||++|+||..||
T Consensus        19 ~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~IRG~nI~~I~~~~   92 (93)
T 1n9r_A           19 PVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELP   92 (93)
T ss_dssp             -------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECC
T ss_pred             cCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEEEcCCeEEEEEeCC
Confidence            46799999999999999999999 99999999999999999999999976666889999999999999999886

>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=99.87  E-value=3.1e-22  Score=135.63  Aligned_cols=72  Identities=18%  Similarity=0.274  Sum_probs=67.6

Q ss_pred             cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024          3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         3 ~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      ...|+.+|+++++++|+|+|+||++|+|+|.+||+|||++|+||+++ .+.+..+++.+||||++|+||+.||
T Consensus         9 ~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~~~~lg~v~iRG~~I~~i~~~d   80 (81)
T 1i8f_A            9 FATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTMVVRGENVLFISPVP   80 (81)
T ss_dssp             -CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETTEEEEEEEEEECGGGEEEEEECC
T ss_pred             ccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCCcccCCCEEEECCCEEEEEEeCC
Confidence            45899999999999999999999999999999999999999999999 5566889999999999999999887

>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=99.86  E-value=9.5e-22  Score=133.93  Aligned_cols=70  Identities=19%  Similarity=0.296  Sum_probs=66.9

Q ss_pred             cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         3 ~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      ...|+.+|+++++++|+|+|+||++|+|+|.+||+|||++|+||+++..+++..+++.+||||++|+||+
T Consensus        13 ~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~IRG~~I~~i~   82 (83)
T 1mgq_A           13 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYIS   82 (83)
T ss_dssp             TTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEE
T ss_pred             CcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEEECCCEEEEEE
Confidence            5689999999999999999999999999999999999999999999987777899999999999999986

>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=99.86  E-value=1.7e-21  Score=136.34  Aligned_cols=72  Identities=22%  Similarity=0.311  Sum_probs=66.0

Q ss_pred             cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe-cCCceeecceEEEecCeEEEEecC
Q psy17024          3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF-RDGKVKPMANIYIRGSKIRFLILP   74 (132)
Q Consensus         3 ~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~-~dg~~~~l~~vfIRGs~Ir~I~lP   74 (132)
                      ...|++||+++++++|+|+||||++|+|+|.+||+|||++|+||+++. .+++...++.+||||++|.||...
T Consensus        18 ~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG~nI~~i~p~   90 (94)
T 4emk_A           18 TILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGNGMCMLIPG   90 (94)
T ss_dssp             --CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECSTTEEEEEEC
T ss_pred             cccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcCCEEEEEEeC
Confidence            578999999999999999999999999999999999999999999998 556688999999999999999843

>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=99.85  E-value=1.9e-21  Score=130.46  Aligned_cols=75  Identities=19%  Similarity=0.200  Sum_probs=53.8

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcc
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDM   76 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~   76 (132)
                      ||-. |..+|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..+++...++.+||||++|.||...|.
T Consensus         1 ms~~-~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            1 MSKA-HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             --------------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEEECSSSEEEEEC---
T ss_pred             CCCc-chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEEECCCeEEEEEeccC
Confidence            5533 77899999999999999999999999999999999999999999877788999999999999999998764

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

Probab=99.84  E-value=9.3e-21  Score=131.97  Aligned_cols=73  Identities=15%  Similarity=0.324  Sum_probs=64.2

Q ss_pred             CcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC----C---------ceeecceEEEecCeE
Q psy17024          2 SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD----G---------KVKPMANIYIRGSKI   68 (132)
Q Consensus         2 s~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d----g---------~~~~l~~vfIRGs~I   68 (132)
                      ++..|++||+++++++|+|+|++|.+|+|+|.+||+|||++|+||+++..+    +         ....++.+||||++|
T Consensus         6 ~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nV   85 (93)
T 4emg_A            6 AVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSV   85 (93)
T ss_dssp             ---CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGE
T ss_pred             ccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeE
Confidence            478999999999999999999999999999999999999999999998642    3         357899999999999


Q ss_pred             EEEecC
Q psy17024         69 RFLILP   74 (132)
Q Consensus        69 r~I~lP   74 (132)
                      .+|..|
T Consensus        86 v~I~p~   91 (93)
T 4emg_A           86 ILIAPP   91 (93)
T ss_dssp             EEEECC
T ss_pred             EEEEec
Confidence            999865

>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=99.82  E-value=1.8e-20  Score=138.00  Aligned_cols=76  Identities=16%  Similarity=0.298  Sum_probs=70.3

Q ss_pred             HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcccccccccccc
Q psy17024          7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFKGK   86 (132)
Q Consensus         7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~~ap~lk~~   86 (132)
                      +.+|++++|++|+|+||||++|+|+|.+||+|||++|+||+++.  +  .+++.+||||++|+||++||...++++|++.
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~--~--~~lg~v~IRG~nI~~I~~~d~~~d~~~f~~~   77 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA--G--EKFNRVFIMYRYIVHIDSTERRIDMREFAKQ   77 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT--C--CEEEEEEECGGGEEEEEECCCCCCHHHHHHH
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc--C--CEeceEEEeCCeEEEEEcCCcccCHHHHHHH
Confidence            47899999999999999999999999999999999999999873  3  5789999999999999999999999888754

>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=99.80  E-value=1.8e-19  Score=125.89  Aligned_cols=79  Identities=15%  Similarity=0.281  Sum_probs=67.2

Q ss_pred             cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC------C-ceeecceEEEecCeEEEEecCc
Q psy17024          3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD------G-KVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         3 ~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d------g-~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      +..|+.+|+++++++|+|+|++|.+|.|+|.+||.|||++|+||+++..+      + ....++.+||||++|.+|..+|
T Consensus         8 ~~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d   87 (96)
T 3bw1_A            8 METPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPS   87 (96)
T ss_dssp             CCCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC
T ss_pred             hhhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecC
Confidence            46799999999999999999999999999999999999999999998643      2 3578999999999999999988


Q ss_pred             cccccc
Q psy17024         76 MLKNAP   81 (132)
Q Consensus        76 ~l~~ap   81 (132)
                      ...++.
T Consensus        88 ~~~d~~   93 (96)
T 3bw1_A           88 EDDDGA   93 (96)
T ss_dssp             -----C
T ss_pred             cccccc
Confidence            765543

>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=99.80  E-value=7e-20  Score=132.81  Aligned_cols=74  Identities=22%  Similarity=0.314  Sum_probs=66.1

Q ss_pred             cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC---------C-c-----eeecceEEEecCe
Q psy17024          3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD---------G-K-----VKPMANIYIRGSK   67 (132)
Q Consensus         3 ~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d---------g-~-----~~~l~~vfIRGs~   67 (132)
                      ...|++||+++++++|+|+|++|++|.|+|.+||+|||++|+||+++..+         + .     ...++.+||||++
T Consensus        26 ~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~n  105 (121)
T 2fwk_A           26 IILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNN  105 (121)
T ss_dssp             CCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGG
T ss_pred             ccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCE
Confidence            46899999999999999999999999999999999999999999998743         4 2     5789999999999


Q ss_pred             EEEEecCcc
Q psy17024         68 IRFLILPDM   76 (132)
Q Consensus        68 Ir~I~lPd~   76 (132)
                      |.||...+.
T Consensus       106 Vv~I~~~~~  114 (121)
T 2fwk_A          106 VAMLVPGGD  114 (121)
T ss_dssp             EEEEESSSC
T ss_pred             EEEEEecCC
Confidence            999998654

>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=99.79  E-value=1.2e-19  Score=124.90  Aligned_cols=75  Identities=13%  Similarity=0.262  Sum_probs=62.3

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEec---------C-CceeecceEEEecCeEEE
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFR---------D-GKVKPMANIYIRGSKIRF   70 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~---------d-g~~~~l~~vfIRGs~Ir~   70 (132)
                      |++ .|..+|+++++++|+|+|+||.+|.|+|.+||+|||++|+||+++..         + .....++.+||||++|.+
T Consensus         1 m~~-~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~   79 (91)
T 1d3b_B            1 MTV-GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVS   79 (91)
T ss_dssp             -------CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEE
T ss_pred             CCC-ChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEE
Confidence            443 36788999999999999999999999999999999999999999641         1 236789999999999999


Q ss_pred             EecCcc
Q psy17024         71 LILPDM   76 (132)
Q Consensus        71 I~lPd~   76 (132)
                      |.+++.
T Consensus        80 i~~~~~   85 (91)
T 1d3b_B           80 MTVEGP   85 (91)
T ss_dssp             EEEEEC
T ss_pred             EEcCCC
Confidence            999864

>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=99.78  E-value=2.8e-19  Score=124.52  Aligned_cols=73  Identities=16%  Similarity=0.231  Sum_probs=66.3

Q ss_pred             cccHHHHHHhhCCCEEEEEE----cCCCEEEEEEEeeCCccceEEeeEEEEecC-CceeecceEEEecCeEEEEecCc
Q psy17024          3 IGIPIKLLHEAEGHIITCET----TNGDLFRGKLVEAEDNMNCAMADVTVTFRD-GKVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         3 ~~~Pl~lL~~~~g~~V~VEL----KnG~~y~G~L~~~D~~MNi~L~dv~~t~~d-g~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      +..|++||+++++++|+|++    ++|.+|+|+|.+||+|||++|+||+++..+ .+...++.+||||++|.||..+|
T Consensus        14 m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~nV~~i~~~~   91 (92)
T 3s6n_E           14 MVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSVS   91 (92)
T ss_dssp             CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGGGEEEEEEC-
T ss_pred             ccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCCEEEEEEeCC
Confidence            45799999999999999999    999999999999999999999999998744 35788999999999999998654

>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=99.76  E-value=1.6e-18  Score=125.14  Aligned_cols=74  Identities=14%  Similarity=0.328  Sum_probs=63.1

Q ss_pred             cccHHHHHHhhC--CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC----Cc----------eeecceEEEecC
Q psy17024          3 IGIPIKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD----GK----------VKPMANIYIRGS   66 (132)
Q Consensus         3 ~~~Pl~lL~~~~--g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d----g~----------~~~l~~vfIRGs   66 (132)
                      ...|++||++++  +++|+|+|+||.+|.|+|.+||+|||++|+||+++...    ++          ..+++.+||||+
T Consensus        25 ~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~  104 (118)
T 1b34_B           25 NTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGD  104 (118)
T ss_dssp             -CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGG
T ss_pred             ccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCC
Confidence            357999999999  59999999999999999999999999999999987522    11          235999999999


Q ss_pred             eEEEEecCcc
Q psy17024         67 KIRFLILPDM   76 (132)
Q Consensus        67 ~Ir~I~lPd~   76 (132)
                      +|.||..++.
T Consensus       105 nVv~I~~~~~  114 (118)
T 1b34_B          105 SVIVVLRNPL  114 (118)
T ss_dssp             GEEEEEECCC
T ss_pred             EEEEEEeCch
Confidence            9999998765

>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=99.72  E-value=1.9e-17  Score=119.09  Aligned_cols=74  Identities=22%  Similarity=0.305  Sum_probs=56.7

Q ss_pred             cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC-------CceeecceEEEecCeEEEEecCccc
Q psy17024          5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD-------GKVKPMANIYIRGSKIRFLILPDML   77 (132)
Q Consensus         5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d-------g~~~~l~~vfIRGs~Ir~I~lPd~l   77 (132)
                      -|+..|.++++++|.|+|++|.+|.|+|.+||.|||++|+||+++..+       .....++.+||||++|.+|..+|.-
T Consensus        23 e~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~  102 (113)
T 4emk_C           23 ESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDGS  102 (113)
T ss_dssp             ---------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC--
T ss_pred             chHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCcc
Confidence            367889999999999999999999999999999999999999998654       2468899999999999999988744


Q ss_pred             c
Q psy17024         78 K   78 (132)
Q Consensus        78 ~   78 (132)
                      +
T Consensus       103 e  103 (113)
T 4emk_C          103 E  103 (113)
T ss_dssp             -
T ss_pred             c
Confidence            3

>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=7.4e-17  Score=128.48  Aligned_cols=76  Identities=14%  Similarity=0.295  Sum_probs=65.9

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEec----C------CceeecceEEEecCeEEE
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFR----D------GKVKPMANIYIRGSKIRF   70 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~----d------g~~~~l~~vfIRGs~Ir~   70 (132)
                      |+++ +-..|+++++++|+|+|+||++|.|+|.+||+||||+|+||+|+..    +      .+..+++.+||||+||.+
T Consensus         1 ~~v~-k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~   79 (231)
T 3pgw_B            1 MTVG-KSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVS   79 (231)
T ss_pred             CCcC-chHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEE
Confidence            5543 5678899999999999999999999999999999999999999752    1      246899999999999999


Q ss_pred             EecCccc
Q psy17024         71 LILPDML   77 (132)
Q Consensus        71 I~lPd~l   77 (132)
                      |.+.+--
T Consensus        80 Isve~pP   86 (231)
T 3pgw_B           80 MTVEGPP   86 (231)
T ss_pred             EEecCCC
Confidence            9987543

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

Probab=98.67  E-value=7.5e-08  Score=66.23  Aligned_cols=66  Identities=11%  Similarity=0.150  Sum_probs=55.4

Q ss_pred             cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeC-CccceEEeeEEEEecCCceeecceEEEecCeEEEEecCccc
Q psy17024          5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAE-DNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDML   77 (132)
Q Consensus         5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D-~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l   77 (132)
                      .|+ -|+.++||.|.|.|.||++|+|.|.++| ...|++|.|+   ..+   .++..++|.|+.|..|.+-+.-
T Consensus         8 ~p~-el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~---~~~---~~~~~~iI~G~aI~eI~v~~~~   74 (86)
T 1y96_A            8 GPL-EWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF---LED---GSMSVTGIMGHAVQTVETMNEG   74 (86)
T ss_dssp             CHH-HHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE---CTT---SCEEEEEECGGGEEEEEEEECC
T ss_pred             CHH-HHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec---ccC---CeEEEEEEecceEEEEEEecch
Confidence            355 5789999999999999999999999999 8999999998   223   3447899999999998874443

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

Probab=97.05  E-value=0.0032  Score=43.21  Aligned_cols=63  Identities=17%  Similarity=0.243  Sum_probs=53.5

Q ss_pred             hCCCEEEEEEcCCCEEEEEEEeeC-CccceEEeeEEEEecCCc---------eeecceEEEecCeEEEEecCc
Q psy17024         13 AEGHIITCETTNGDLFRGKLVEAE-DNMNCAMADVTVTFRDGK---------VKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus        13 ~~g~~V~VELKnG~~y~G~L~~~D-~~MNi~L~dv~~t~~dg~---------~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      .+|+.|++-.|++..|.|+|..+| +.--+.|+||....-+++         ..-++.+.-||+.|+-+.+-+
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 577899999998765553         245788999999999987643

>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=96.66  E-value=0.0032  Score=43.82  Aligned_cols=67  Identities=21%  Similarity=0.191  Sum_probs=54.5

Q ss_pred             HHHhhCCCEEEEEEcCCCEEEEEEEeeC-CccceEEeeEEEEecCCc---------eeecceEEEecCeEEEEecCc
Q psy17024          9 LLHEAEGHIITCETTNGDLFRGKLVEAE-DNMNCAMADVTVTFRDGK---------VKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         9 lL~~~~g~~V~VELKnG~~y~G~L~~~D-~~MNi~L~dv~~t~~dg~---------~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      --..++|+.|++-.|++..|.|+|..+| +.--+.|+||....-+++         ..-++.+..||+-|+-+.+-+
T Consensus        13 ~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e   89 (95)
T 2fb7_A           13 GGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   89 (95)
T ss_dssp             ---CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESC
T ss_pred             ccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEec
Confidence            3456799999999999999999999999 577899999988765543         245789999999999988744

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

Probab=96.58  E-value=0.0061  Score=44.25  Aligned_cols=53  Identities=15%  Similarity=0.108  Sum_probs=41.0

Q ss_pred             HHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEE--eeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024         10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAM--ADVTVTFRDGKVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus        10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L--~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      +.+++|..|.|+|++|..|+|+|..||. -++.|  ++|+...          ..|+.+.|.-+.+
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd~-k~LtL~~~~a~~s~----------~~I~asdI~DLkV   61 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFDS-SNSILQLRLANDST----------KSIVTKDIKDLRI   61 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEET-TTTEEEEEETTTEE----------EEEEGGGEEEEEE
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeecC-CeeEEecccccccc----------ceeecccccceee
Confidence            3578999999999999999999999984 35555  9884321          2788888876554

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

Probab=96.51  E-value=0.0072  Score=41.13  Aligned_cols=59  Identities=12%  Similarity=0.264  Sum_probs=50.2

Q ss_pred             hhCCCEEEEEEcCCC-EEEEEEEeeCC-ccceEEeeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024         12 EAEGHIITCETTNGD-LFRGKLVEAED-NMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus        12 ~~~g~~V~VELKnG~-~y~G~L~~~D~-~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      +.+|+.|+|+.+++. +|.|.|..+|. .-|+.|.+|.   ++|-+.+..+|.++++-|.-+-+
T Consensus         6 ~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f---~NG~~~~s~eVtls~~DI~~L~i   66 (84)
T 2vc8_A            6 DWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF---HNGVKCLVPEVTFRAGDITELKI   66 (84)
T ss_dssp             TTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE---ETTEECSSSEEEEEGGGCSEEEE
T ss_pred             cccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh---hCCCCCCCcEEEEEecChhheEE
Confidence            568999999999999 99999999996 5689999994   68876677789999987765554

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

Probab=96.34  E-value=0.024  Score=38.60  Aligned_cols=63  Identities=17%  Similarity=0.179  Sum_probs=53.3

Q ss_pred             HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeC-CccceEEeeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024          6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAE-DNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus         6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D-~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      -|.+|..+.|++|.+.|+...++.|+..++| +..|+..+|..  .+=|   .+++..+|.+-|..+.+
T Consensus        20 fLr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~--TPiG---v~~eAlLR~~Dii~~sF   83 (85)
T 1y96_B           20 YLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQ--TPIG---VQAEALLRCSDIISYTF   83 (85)
T ss_dssp             HHHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEC--CTTC---CEEEEEEEGGGEEEEEE
T ss_pred             HHHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcC--CCcc---cchhhhhhcCCEEEEEe
Confidence            3788999999999999999999999999999 57799988852  2333   46789999999998876

>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A*

Probab=96.28  E-value=0.0058  Score=40.57  Aligned_cols=56  Identities=9%  Similarity=0.061  Sum_probs=42.6

Q ss_pred             HHHHHhhC--CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024          7 IKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         7 l~lL~~~~--g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      -.||+.+.  ..+|+|.|.||..++|++..+|.|+=+.-        ++     ...+|-=..|.+|..-.
T Consensus        11 d~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL~--------~~-----~~~LIYKhAIsTI~p~~   68 (74)
T 2ylb_A           11 DPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK--------NT-----VSQMVYKHAISTVVPSR   68 (74)
T ss_dssp             HHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEE--------SS-----SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE--------CC-----ceEEEEeeeEEEEeEcc
Confidence            45777764  88999999999999999999999974432        11     24577777888877433

>1kq1_A HFQ, HOST factor for Q beta; hexamer, RNA binding protein, translational regulator, SM motif; 1.55A {Staphylococcus aureus} SCOP: b.38.1.2 PDB: 1kq2_A

Probab=95.97  E-value=0.016  Score=38.76  Aligned_cols=55  Identities=20%  Similarity=0.147  Sum_probs=41.5

Q ss_pred             HHHHHhhC--CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024          7 IKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus         7 l~lL~~~~--g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      -.||+.+.  ..+|+|.|.||..++|++.++|.|+=+.-.       +++     +.+|-=..|.+|..
T Consensus         9 d~fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~~-------~g~-----~qLIYKhAISTI~p   65 (77)
T 1kq1_A            9 DKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNS-------QGK-----QHLIYKHAISTYTV   65 (77)
T ss_dssp             HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEE-------TTE-----EEEEEGGGEEEEEC
T ss_pred             HHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEEE-------CCe-----eEEEEeeeEEEEeE
Confidence            35677775  899999999999999999999999754432       343     34566677777764

>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=95.90  E-value=0.011  Score=40.06  Aligned_cols=58  Identities=10%  Similarity=0.062  Sum_probs=42.7

Q ss_pred             HHHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCccc
Q psy17024          7 IKLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDML   77 (132)
Q Consensus         7 l~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l   77 (132)
                      -.||+.+  ...+|+|-|.||..++|++.+||.|+=+.- +       +     .+.+|-=..|..|..-..+
T Consensus         9 d~fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~-~-------~-----~qqLVYKHAISTI~p~~~v   68 (82)
T 1u1s_A            9 DPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK-N-------T-----VSQMVYKHAISTVVPSRPV   68 (82)
T ss_dssp             HHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE-S-------S-----SCEEEEGGGEEEEEESSCC
T ss_pred             HHHHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEe-c-------C-----ceEEEEeeeeEEEeecccc
Confidence            3567766  488999999999999999999999974432 1       2     2456777788887754433

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

Probab=95.73  E-value=0.019  Score=38.53  Aligned_cols=56  Identities=18%  Similarity=0.188  Sum_probs=41.4

Q ss_pred             HHHHhhC--CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024          8 KLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         8 ~lL~~~~--g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      .+|+.+.  ..+|+|-|.||..++|++.+||.|+=+.-       .+++     +.+|-=..|..|..-.
T Consensus        14 ~fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~-------~~g~-----qqlIYKhAISTI~p~~   71 (78)
T 3ahu_A           14 QFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLE-------SEGK-----QQLIYKHAISTFAPQK   71 (78)
T ss_dssp             HHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEE-------SSSC-----EEEEEGGGEEEEEESS
T ss_pred             HHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEEE-------ECCe-----eEEEEcceEEEEeecc
Confidence            4666664  89999999999999999999999975443       2443     2356666777776444

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

Probab=95.64  E-value=0.011  Score=41.74  Aligned_cols=58  Identities=9%  Similarity=0.056  Sum_probs=43.2

Q ss_pred             HHHHHhhC--CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCccc
Q psy17024          7 IKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDML   77 (132)
Q Consensus         7 l~lL~~~~--g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l   77 (132)
                      -.||+.+.  ..+|+|.|.||..++|++.++|.|+=|.-        ++     .+.+|-=..|.+|..-..+
T Consensus        11 d~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~--------~~-----kqqLIYKHAISTI~p~~~v   70 (104)
T 2y90_A           11 DPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK--------NT-----VSQMVYKHAISTVVPSRPV   70 (104)
T ss_dssp             HHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE--------SS-----SEEEEEGGGEEEEEESSCC
T ss_pred             HHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE--------CC-----ceEEEEeeeeEEEeecccc
Confidence            35677764  45999999999999999999999975443        12     2466777888988854433

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

Probab=95.29  E-value=0.031  Score=37.51  Aligned_cols=56  Identities=11%  Similarity=0.090  Sum_probs=41.7

Q ss_pred             HHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcc
Q psy17024          8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDM   76 (132)
Q Consensus         8 ~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~   76 (132)
                      .||..+  ...+|+|.|.||..++|++.++|.|+=|. +       +++     +.+|-=..|.+|..-..
T Consensus        11 ~fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL-~-------~g~-----~qLIYKhAISTI~P~~~   68 (79)
T 3sb2_A           11 PFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL-R-------NTV-----TQMVYKHAISTVVPARA   68 (79)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE-E-------SSS-----EEEEEGGGEEEEEESSC
T ss_pred             HHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE-E-------CCc-----eEEEEeeeEEEEeecCc
Confidence            456655  56789999999999999999999997553 2       343     34677778888775433

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

Probab=94.99  E-value=0.054  Score=35.67  Aligned_cols=29  Identities=10%  Similarity=0.203  Sum_probs=26.3

Q ss_pred             CCCEEEEEEcCCCEEEEEEEeeCCccceE
Q psy17024         14 EGHIITCETTNGDLFRGKLVEAEDNMNCA   42 (132)
Q Consensus        14 ~g~~V~VELKnG~~y~G~L~~~D~~MNi~   42 (132)
                      ...+|+|-|.||..++|++.++|.|+=+.
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll   52 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSNYEIMV   52 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            67899999999999999999999997544

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

Probab=94.47  E-value=0.12  Score=33.98  Aligned_cols=41  Identities=12%  Similarity=0.213  Sum_probs=34.5

Q ss_pred             cccH-HHHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024          3 IGIP-IKLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAM   43 (132)
Q Consensus         3 ~~~P-l~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L   43 (132)
                      .++| +.+||+.  ...+|+|+|-||..+.|.|.-.|.++=|..
T Consensus         6 t~lPsvR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L~   49 (70)
T 3hfo_A            6 SGLPSVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLV   49 (70)
T ss_dssp             CSCHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             CCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEEE
Confidence            4566 7788887  578999999999999999999999886554

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

Probab=93.63  E-value=0.24  Score=32.58  Aligned_cols=42  Identities=17%  Similarity=0.396  Sum_probs=34.2

Q ss_pred             cccH-HHHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEEe
Q psy17024          3 IGIP-IKLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAMA   44 (132)
Q Consensus         3 ~~~P-l~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~   44 (132)
                      .++| +.+||+.  ...+|+|+|-||..+.|+|.-.|.++=|...
T Consensus         8 t~lPsvR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L~~   52 (72)
T 3hfn_A            8 TSLPSIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIAD   52 (72)
T ss_dssp             -CHHHHHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEEEC
T ss_pred             CCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEEEc
Confidence            3556 7888887  5678999999999999999999998865543

>1ycy_A Conserved hypothetical protein; structural genomics, southeast collaboratory for structural genomics, secsg, protein structure initiative; 2.80A {Pyrococcus furiosus} SCOP: b.38.1.4

Probab=92.56  E-value=0.77  Score=29.79  Aligned_cols=62  Identities=23%  Similarity=0.392  Sum_probs=42.8

Q ss_pred             HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024          7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus         7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      -+.|.+-.|++|-|-.-....++|+|..||+-. +.|+||+-..  |  .+-.++.|+=+-|.+|.|
T Consensus         8 dktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~--G--Nk~k~liv~idDinWimL   69 (71)
T 1ycy_A            8 EKVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI--G--NRGKQMLIGLEDINWIML   69 (71)
T ss_dssp             HHHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT--E--EEEEEEEEEGGGEEEEEE
T ss_pred             HHHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHh--c--cccceeEEEeccceEEEe
Confidence            467889999999999999999999999999864 7789987543  2  223356666566665554

>2rm4_A CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-BODY component, SM-like protein,, protein binding; NMR {Drosophila melanogaster}

Probab=91.07  E-value=1.5  Score=30.50  Aligned_cols=59  Identities=17%  Similarity=0.231  Sum_probs=49.6

Q ss_pred             hhCCCEEEEEEcCCC-EEEEEEEeeCCccceEEeeEEEEecCCc--eeecceEEEecCeEEEEecC
Q psy17024         12 EAEGHIITCETTNGD-LFRGKLVEAEDNMNCAMADVTVTFRDGK--VKPMANIYIRGSKIRFLILP   74 (132)
Q Consensus        12 ~~~g~~V~VELKnG~-~y~G~L~~~D~~MNi~L~dv~~t~~dg~--~~~l~~vfIRGs~Ir~I~lP   74 (132)
                      +.+|+.|+|...+.- +|.|.+..+|. -++.|.++.   ++|-  ..+..+|.++..-|.-+-|-
T Consensus         9 dwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaF---rNGiplk~~~~EVtLsa~DI~~L~II   70 (103)
T 2rm4_A            9 DWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAF---RNGVPLRKQNAEVVLKCTDIRSIDLI   70 (103)
T ss_dssp             GGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEE---ETTEECSCSSSCEEEETTTEEEEEEE
T ss_pred             ceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhh---hcCcCcCCCCceEEEEecchhheeee
Confidence            578999999999998 99999999995 448888875   5886  67788999999988877663

>1ib8_A Conserved protein SP14.3; nucleic acid binding protein, ribosomal protein, essential gene, structural genomics; NMR {Streptococcus pneumoniae} SCOP: b.38.2.1 d.52.4.1

Probab=82.88  E-value=1.7  Score=32.09  Aligned_cols=29  Identities=24%  Similarity=0.405  Sum_probs=24.6

Q ss_pred             HHhhCCCEEEEEEc----CCCEEEEEEEeeCCc
Q psy17024         10 LHEAEGHIITCETT----NGDLFRGKLVEAEDN   38 (132)
Q Consensus        10 L~~~~g~~V~VELK----nG~~y~G~L~~~D~~   38 (132)
                      +..++|+.|.|+|+    +...++|+|.++|+.
T Consensus        99 f~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T 1ib8_A           99 VAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED  131 (164)
T ss_dssp             HHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             HHHhCCcEEEEEEecccCCceEEEEEEEEEeCC
Confidence            44679999999994    458999999999975

>3by7_A Uncharacterized protein; metagenomics, structural genomics, joint center for structur genomics, JCSG, protein structure initiative; 2.60A {Uncultured marine organism}

Probab=82.15  E-value=6.9  Score=27.03  Aligned_cols=54  Identities=20%  Similarity=0.254  Sum_probs=42.0

Q ss_pred             EEEEcCCCEEEEEEEeeCCccceEEeeEEEEec----CCc-----------eeecceEEEecCeEEEEecC
Q psy17024         19 TCETTNGDLFRGKLVEAEDNMNCAMADVTVTFR----DGK-----------VKPMANIYIRGSKIRFLILP   74 (132)
Q Consensus        19 ~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~----dg~-----------~~~l~~vfIRGs~Ir~I~lP   74 (132)
                      .|+|++|+.+-+.+..-|+.  +.++|..+...    +|+           .+.-+++.||-+.|.++.-+
T Consensus         7 iiRlvSGEEIia~v~et~~~--i~i~nPv~V~~~~~e~gk~~gigF~pW~plsde~~~ii~~~~ViT~~e~   75 (100)
T 3by7_A            7 IMRLVTGEDIIGNISESQGL--ITIKKAFVIIPMQATPGKPVQLVLSPWQPYTDDKEIVIDDSKVITITSP   75 (100)
T ss_dssp             EEEETTSCEEEEEEEEETTE--EEEEEEEEEEEEC-----CCEEEEEESCTTBCCSEEEEEGGGEEEEECB
T ss_pred             EEEecCccceeEEEEecCce--EEEECCEEEEEeecCCCcceeEeeecccccCcCceEEEchhhEEEEEeC
Confidence            68999999999999987774  89999776542    221           34578899999999998865

---

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	132
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	2e-27
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	2e-26
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-19
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-18
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	3e-18
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	8e-18
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	2e-17
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	1e-14
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	3e-14
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	2e-12
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	5e-04

>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 = 94.5 bits (235), Expect = 2e-27
 Identities = 50/72 (69%), Positives = 64/72 (88%)

Query: 4  GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYI 63
          G+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG+V  +  +YI
Sbjct: 1  GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYI 60

Query: 64 RGSKIRFLILPD 75
          RG KIRFLILPD
Sbjct: 61 RGCKIRFLILPD 72

>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 = 92.5 bits (230), Expect = 2e-26
 Identities = 20/76 (26%), Positives = 37/76 (48%)

Query: 7  IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGS 66
          ++ L +     +T E  NG    G +   + +MN  +  V +T ++ +   +  + IRG+
Sbjct: 3  VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGN 62

Query: 67 KIRFLILPDMLKNAPM 82
           IR+ ILPD L    +
Sbjct: 63 NIRYFILPDSLPLDTL 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 = 74.7 bits (184), Expect = 1e-19
 Identities = 13/72 (18%), Positives = 28/72 (38%)

Query: 1  MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
          +++  P+  L  +    +  +      FRG L   + +MN  + D          + +  
Sbjct: 2  VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGT 61

Query: 61 IYIRGSKIRFLI 72
          + IRG  I ++ 
Sbjct: 62 VLIRGDNIVYIS 73

>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 = 71.7 bits (176), Expect = 2e-18
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 2  SIGIPIKLLHEAEGHIITCETTNGDL-FRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN 60
          ++ +P +++    G II  E    +    GKL   +D MN  + +      + KV+ +  
Sbjct: 2  AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGE 61

Query: 61 IYIRGSKIRFLI 72
          I +RG+ +  + 
Sbjct: 62 IVLRGNNVVLIQ 73

>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 71.3 bits (175), Expect = 3e-18
 Identities = 16/66 (24%), Positives = 29/66 (43%)

Query: 6  PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRG 65
            K+L E+  +++  +       RG L   + +MN  ++D      DG  K +  I IRG
Sbjct: 8  AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRG 67

Query: 66 SKIRFL 71
            +  +
Sbjct: 68 DNVILI 73

>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 = 70.1 bits (172), Expect = 8e-18
 Identities = 16/66 (24%), Positives = 30/66 (45%)

Query: 6  PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRG 65
          P+ ++H +    +      G  FRG+L+  + ++N  +AD  +      VK    I IRG
Sbjct: 3  PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRG 62

Query: 66 SKIRFL 71
            +  +
Sbjct: 63 DNVLAI 68

>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 = 69.3 bits (170), Expect = 2e-17
 Identities = 15/66 (22%), Positives = 29/66 (43%)

Query: 6  PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRG 65
          P+ +L+ +    +      G  FRG L   + +MN  + D         V+ + ++ IRG
Sbjct: 4  PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRG 63

Query: 66 SKIRFL 71
            + F+
Sbjct: 64 DTVVFV 69

>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 = 63.6 bits (155), Expect = 1e-14
 Identities = 10/69 (14%), Positives = 28/69 (40%), Gaps = 4/69 (5%)

Query: 9  LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKI 68
           L+   G  +    +NG++++G L   ++ +N  +A+ +    +        ++I    I
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEK----FNRVFIMYRYI 59

Query: 69 RFLILPDML 77
            +   +  
Sbjct: 60 VHIDSTERR 68

>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 60.9 bits (148), Expect = 3e-14
 Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIR 69
          L ++ G  +  +  +    RG L   + ++N  + D      DG V     + +RG  + 
Sbjct: 7  LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTMVVRGENVL 65

Query: 70 FLILP 74
          F+   
Sbjct: 66 FISPV 70

>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 = 56.3 bits (136), Expect = 2e-12
 Identities = 12/68 (17%), Positives = 26/68 (38%), Gaps = 2/68 (2%)

Query: 10 LHEAEGHIITCETTNGDL-FRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKI 68
          L     H +  +       +RG LV  ++  N  + +            +  I+IR + +
Sbjct: 1  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNV 60

Query: 69 RFL-ILPD 75
           ++  LP+
Sbjct: 61 LYIRELPN 68

>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 = 34.8 bits (80), Expect = 5e-04
 Identities = 13/76 (17%), Positives = 30/76 (39%)

Query: 2  SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANI 61
          +I +P+ L+ +  G+ I         F G L   ++ +N  + DV         + ++  
Sbjct: 2  NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGG 61

Query: 62 YIRGSKIRFLILPDML 77
            +  ++    L  +L
Sbjct: 62 NKKLKRVMVNRLETIL 77

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	132
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.96
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.96
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.91
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.9
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.89
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.89
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.87
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.87
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.85
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.82
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.77
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.67
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.57
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	97.1
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	94.5
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	94.26
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	93.13
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	93.1
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	84.38
d2d6fa1	72	Glutamyl-tRNA(Gln) amidotransferase subunit D, Gat	83.75
d1ewna_	214	3-methyladenine DNA glycosylase (AAG, ANPG, MPG) {	81.02

>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=99.96  E-value=3e-29  Score=165.93  Aligned_cols=72  Identities=69%  Similarity=1.298  Sum_probs=70.5

Q ss_pred             ccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024          4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus         4 ~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      ++|++||++++|+.|+||||||++|+|+|.+||+|||++|+||+++.++++..+++.+||||++|+||++||
T Consensus         1 g~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           1 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             CCchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCeEEEECCEEEEEEcCC
Confidence            689999999999999999999999999999999999999999999999999999999999999999999998

>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=99.96  E-value=2.7e-29  Score=169.52  Aligned_cols=77  Identities=26%  Similarity=0.502  Sum_probs=75.0

Q ss_pred             HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCccccccccc
Q psy17024          7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMF   83 (132)
Q Consensus         7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~~ap~l   83 (132)
                      ++||++++|++|+||||||++|+|+|.++|+|||++|+||+++.++++..+++++||||++|+||++||+++.+|+|
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~lPd~l~~~~~L   79 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLL   79 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTCCHHHHT
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEECCCCccccccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999998876

>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=99.91  E-value=1.3e-24  Score=143.85  Aligned_cols=72  Identities=18%  Similarity=0.299  Sum_probs=69.5

Q ss_pred             CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      |++..|+++|+++++++|+|+||||.+|+|+|.+||+|||++|+||+++..+++..+++.+||||++|+||+
T Consensus         2 ~~~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~IRG~~I~~I~   73 (74)
T d1mgqa_           2 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYIS   73 (74)
T ss_dssp             CCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEE
T ss_pred             CcccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEEEeCCEEEEEe
Confidence            688999999999999999999999999999999999999999999999988888899999999999999986

>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=99.90  E-value=3.7e-24  Score=142.45  Aligned_cols=71  Identities=23%  Similarity=0.419  Sum_probs=67.9

Q ss_pred             CcccHHHHHHhhCCCEEEEEEcCC-CEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          2 SIGIPIKLLHEAEGHIITCETTNG-DLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         2 s~~~Pl~lL~~~~g~~V~VELKnG-~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      |+.+|+++|+++++++|+|||||| .+|.|+|.+||+|||++|+||+++..+++..+++.+||||++|+||+
T Consensus         2 ~~~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~I~   73 (75)
T d1ljoa_           2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQ   73 (75)
T ss_dssp             CCCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEE
T ss_pred             CccccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCcEeEcceEEEeCCEEEEEE
Confidence            678999999999999999999987 58999999999999999999999988888999999999999999997

>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=99.89  E-value=1.2e-23  Score=137.87  Aligned_cols=68  Identities=24%  Similarity=0.374  Sum_probs=65.6

Q ss_pred             cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      .|+++|++++|+.|+|+||||.+|+|+|.+||+|||++|+||+++.++++..+++.+||||++|+||+
T Consensus         2 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~l~~~~IRG~~I~~Is   69 (71)
T d1h641_           2 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAIS   69 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEE
T ss_pred             CchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCcEeEcCcEEEECCeEEEEe
Confidence            69999999999999999999999999999999999999999999988778899999999999999986

>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=99.89  E-value=1.9e-23  Score=137.50  Aligned_cols=69  Identities=22%  Similarity=0.345  Sum_probs=66.2

Q ss_pred             ccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         4 ~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      ..|+++|+++++++|+|+||||.+|+|+|.+||+|||++|+||+++..+++..+++.+||||++|.||+
T Consensus         2 ~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~Is   70 (72)
T d1i4k1_           2 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVS   70 (72)
T ss_dssp             CCHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEEEEECGGGEEEEE
T ss_pred             CChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcceEEEeCCeEEEEE
Confidence            369999999999999999999999999999999999999999999988888899999999999999986

>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=99.87  E-value=8.3e-23  Score=133.58  Aligned_cols=66  Identities=18%  Similarity=0.352  Sum_probs=61.0

Q ss_pred             HHhhCCCEEEEEEcC-CCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe-cCc
Q psy17024         10 LHEAEGHIITCETTN-GDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI-LPD   75 (132)
Q Consensus        10 L~~~~g~~V~VELKn-G~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~-lPd   75 (132)
                      |+++++++|+|+||+ +.+|+|+|.+||+|||++|+||+++..++...+++.+||||++|+||. +||
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            578999999999995 567999999999999999999999987777889999999999999996 887

>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=99.87  E-value=2.1e-22  Score=133.75  Aligned_cols=69  Identities=23%  Similarity=0.354  Sum_probs=66.4

Q ss_pred             ccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         4 ~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      ..|.++|++++|++|+|+||||.+|+|+|.+||+|||++|+||+++..+++...++.+||||++|+||.
T Consensus         6 ~~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~~~v~iRG~~I~~I~   74 (76)
T d1th7a1           6 ETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILIS   74 (76)
T ss_dssp             HHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEE
T ss_pred             ccHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCcccCcceEEEECCEEEEEE
Confidence            358999999999999999999999999999999999999999999999999999999999999999986

>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=99.85  E-value=2.7e-21  Score=127.16  Aligned_cols=68  Identities=19%  Similarity=0.312  Sum_probs=62.8

Q ss_pred             cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024          5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus         5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      .+..+|++++|++|+|+||||.+|.|+|.+||+|||++|+||+++. +++...++.+||||++|.||..
T Consensus         2 t~~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~-~~~~~~~g~v~iRG~~I~~I~~   69 (71)
T d1i8fa_           2 TLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII-DGNVYKRGTMVVRGENVLFISP   69 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEECGGGEEEEEE
T ss_pred             cHhHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEE-CCCEEEcceEEEeCCeEEEEeC
Confidence            3568999999999999999999999999999999999999999885 5577889999999999999984

>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=99.82  E-value=8.1e-21  Score=137.78  Aligned_cols=68  Identities=15%  Similarity=0.276  Sum_probs=62.0

Q ss_pred             HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcccc
Q psy17024          7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLK   78 (132)
Q Consensus         7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~   78 (132)
                      ++.|++++|++|+||||||++|+|+|.+||+||||+|+||+++..+    .++++||||++|+||.+||+.-
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~~~----k~~~v~IRG~~I~~I~~~e~~i   69 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGE----KFNRVFIMYRYIVHIDSTERRI   69 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETTCC----EEEEEEECGGGEEEEEECSCCC
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECCCC----cccEEEEeCCeEEEEEcchhhc
Confidence            5789999999999999999999999999999999999999886433    5788999999999999998754

>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=99.77  E-value=2.3e-19  Score=122.53  Aligned_cols=71  Identities=21%  Similarity=0.342  Sum_probs=63.0

Q ss_pred             CcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC---------------ceeecceEEEecC
Q psy17024          2 SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG---------------KVKPMANIYIRGS   66 (132)
Q Consensus         2 s~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg---------------~~~~l~~vfIRGs   66 (132)
                      ++.+|+++|+++++++|.|+|++|..|.|+|.+||.|||++|+||+++..+.               ...+++.+||||+
T Consensus         2 ~~~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~   81 (92)
T d2fwka1           2 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGN   81 (92)
T ss_dssp             CCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGG
T ss_pred             CccChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCC
Confidence            5789999999999999999999999999999999999999999999874211               1346889999999


Q ss_pred             eEEEEe
Q psy17024         67 KIRFLI   72 (132)
Q Consensus        67 ~Ir~I~   72 (132)
                      +|.||.
T Consensus        82 ~Vv~I~   87 (92)
T d2fwka1          82 NVAMLV   87 (92)
T ss_dssp             GEEEEE
T ss_pred             EEEEEE
Confidence            999987

>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=99.67  E-value=1e-16  Score=109.92  Aligned_cols=70  Identities=13%  Similarity=0.326  Sum_probs=60.5

Q ss_pred             HHHHHHhhC--CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC--------------ceeecceEEEecCeEE
Q psy17024          6 PIKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG--------------KVKPMANIYIRGSKIR   69 (132)
Q Consensus         6 Pl~lL~~~~--g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg--------------~~~~l~~vfIRGs~Ir   69 (132)
                      |+.+|+++.  +++|.|.|+++..|.|+|.+||.|||++|+||+++....              +..+++.+||||++|.
T Consensus         3 Pl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnVv   82 (93)
T d1b34b_           3 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVI   82 (93)
T ss_dssp             HHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEE
T ss_pred             cHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEEE
Confidence            999999997  999999999999999999999999999999999974311              1357899999999999


Q ss_pred             EEecCc
Q psy17024         70 FLILPD   75 (132)
Q Consensus        70 ~I~lPd   75 (132)
                      +|..|.
T Consensus        83 ~I~~~p   88 (93)
T d1b34b_          83 VVLRNP   88 (93)
T ss_dssp             EEEECC
T ss_pred             EEEcCh
Confidence            997654

>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=99.57  E-value=2.4e-15  Score=100.27  Aligned_cols=64  Identities=14%  Similarity=0.317  Sum_probs=55.9

Q ss_pred             HHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEec----C-C-----ceeecceEEEecCeEEEEec
Q psy17024         10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFR----D-G-----KVKPMANIYIRGSKIRFLIL   73 (132)
Q Consensus        10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~----d-g-----~~~~l~~vfIRGs~Ir~I~l   73 (132)
                      |.+.++++|.|.|++|..|.|+|.++|.|||++|+||+++..    + .     ....++.++|||++|.+|.+
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            568899999999999999999999999999999999998631    1 1     14678999999999999975

>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=97.10  E-value=0.002  Score=41.95  Aligned_cols=63  Identities=22%  Similarity=0.239  Sum_probs=53.1

Q ss_pred             hCCCEEEEEEcCCCEEEEEEEeeCC-ccceEEeeEEEEecCCc---------eeecceEEEecCeEEEEecCc
Q psy17024         13 AEGHIITCETTNGDLFRGKLVEAED-NMNCAMADVTVTFRDGK---------VKPMANIYIRGSKIRFLILPD   75 (132)
Q Consensus        13 ~~g~~V~VELKnG~~y~G~L~~~D~-~MNi~L~dv~~t~~dg~---------~~~l~~vfIRGs~Ir~I~lPd   75 (132)
                      .+|+.|++-.|++..|.|+|.++|. .--+.|+||....-+|+         ..-++.+.-||+.|+-+.+-|
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            4799999999999999999999995 55699999998764443         346789999999999888755

>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.50  E-value=0.046  Score=33.43  Aligned_cols=35  Identities=17%  Similarity=0.103  Sum_probs=28.6

Q ss_pred             HHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024          9 LLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAM   43 (132)
Q Consensus         9 lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L   43 (132)
                      ||.++  ...+|+|-|.||-.++|++.++|+|.=+..
T Consensus         6 fln~lr~~~~~VtifL~nGvkl~G~I~~fD~ftvlL~   42 (60)
T d1kq1a_           6 ALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLN   42 (60)
T ss_dssp             HHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHcCCcEEEEEECCcEEEEEEEEEcceEEEEE
Confidence            44443  578999999999999999999999875543

>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=94.26  E-value=0.042  Score=34.21  Aligned_cols=32  Identities=16%  Similarity=0.165  Sum_probs=27.3

Q ss_pred             HHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccc
Q psy17024          9 LLHEA--EGHIITCETTNGDLFRGKLVEAEDNMN   40 (132)
Q Consensus         9 lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MN   40 (132)
                      ||.++  ...+|+|-|.||..++|++.++|+|.=
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            45554  678999999999999999999999954

>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=93.13  E-value=0.27  Score=30.03  Aligned_cols=61  Identities=21%  Similarity=0.377  Sum_probs=41.2

Q ss_pred             HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024          7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI   72 (132)
Q Consensus         7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~   72 (132)
                      -+.|.+-.|+.|-|-.-....++|+|..||... +.|+||+-..  |  .+-.++.|+=+-|.+|.
T Consensus         4 dktL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~--G--Nk~k~llv~idD~nWim   64 (66)
T d1ycya1           4 EKVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI--G--NRGKQMLIGLEDINWIM   64 (66)
T ss_dssp             HHHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT--E--EEEEEEEEEGGGEEEEE
T ss_pred             HHHHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHh--c--cccceeEEEeccceeEE
Confidence            367889999999999999999999999999864 7789987543  2  22235555555555543

>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=93.10  E-value=0.19  Score=28.54  Aligned_cols=46  Identities=9%  Similarity=-0.094  Sum_probs=33.9

Q ss_pred             hCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC-ceeecceEEEe
Q psy17024         13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYIR   64 (132)
Q Consensus        13 ~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg-~~~~l~~vfIR   64 (132)
                      +.|++|+|..-+ +++.|+-..+|+.=.+.|+.     .++ +...-.+|.||
T Consensus         1 f~gk~V~v~~g~-~~i~G~a~gId~~G~Lll~t-----~~g~~~~~sGEVSlR   47 (47)
T d1biaa2           1 FINRPVKLIIGD-KEIFGISRGIDKQGALLLEQ-----DGIIKPWMGGEISLR   47 (47)
T ss_dssp             TTTSEEEEEETT-EEEEEEEEEECTTSCEEEEE-----TTEEEEESSCEEEEC
T ss_pred             CCCCEEEEEECC-eEEEEEEeeECCCCcEEEEE-----CCCEEEEEEEEEEeC
Confidence            468999997655 78999999999999998874     233 23445566654

>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]}

class: All beta proteins
fold: Sm-like fold
superfamily: YhbC-like, C-terminal domain
family: YhbC-like, C-terminal domain
domain: Hypothetical protein SP14.3 (SP0552)
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=84.38  E-value=0.55  Score=28.51  Aligned_cols=29  Identities=24%  Similarity=0.402  Sum_probs=25.0

Q ss_pred             HHhhCCCEEEEEEcC---C-CEEEEEEEeeCCc
Q psy17024         10 LHEAEGHIITCETTN---G-DLFRGKLVEAEDN   38 (132)
Q Consensus        10 L~~~~g~~V~VELKn---G-~~y~G~L~~~D~~   38 (132)
                      +..++|+.|.|+|+.   | ..++|+|.++|+.
T Consensus         9 f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~   41 (74)
T d1ib8a1           9 VAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED   41 (74)
T ss_dssp             HHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             HHHhCCCEEEEEEecccCCceEEEEEEEeecCC
Confidence            567899999999974   4 6999999999985

>d2d6fa1 b.38.3.1 (A:2-73) Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD {Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: Sm-like fold
superfamily: GatD N-terminal domain-like
family: GatD N-terminal domain-like
domain: Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD
species: Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=83.75  E-value=0.71  Score=28.78  Aligned_cols=39  Identities=18%  Similarity=0.382  Sum_probs=29.3

Q ss_pred             HHHHHHhh---CCCEEEEEEcCCCEEEEEEEe----e-CCccceEEee
Q psy17024          6 PIKLLHEA---EGHIITCETTNGDLFRGKLVE----A-EDNMNCAMAD   45 (132)
Q Consensus         6 Pl~lL~~~---~g~~V~VELKnG~~y~G~L~~----~-D~~MNi~L~d   45 (132)
                      -.+||.+.   +|..|.|+ +++.+|+|+|.-    . |++.=+.|+|
T Consensus         6 ~~~fL~~~~i~vGD~V~i~-~~~~~~eGilmP~~e~sd~~~iVlKL~n   52 (72)
T d2d6fa1           6 ARKFLESASIDVGDMVLVE-KPDVTYEGMVLDRADDADDRHIVLKLEN   52 (72)
T ss_dssp             HHHHHHTTTCCTTCEEEEE-CSSCEEEEEECCCCTTSCSSEEEEECTT
T ss_pred             HHHHHHHcCCCCCCEEEEE-ECCcEEEEEEcCCcccCCCCEEEEEecC
Confidence            35677775   79999998 688999999993    3 3566666653

>d1ewna_ b.46.1.2 (A:) 3-methyladenine DNA glycosylase (AAG, ANPG, MPG) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: FMT C-terminal domain-like
superfamily: FMT C-terminal domain-like
family: 3-methyladenine DNA glycosylase (AAG, ANPG, MPG)
domain: 3-methyladenine DNA glycosylase (AAG, ANPG, MPG)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.02  E-value=0.91  Score=33.41  Aligned_cols=35  Identities=23%  Similarity=0.468  Sum_probs=31.8

Q ss_pred             HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccc
Q psy17024          6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMN   40 (132)
Q Consensus         6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MN   40 (132)
                      ++.+=++++|+.++.++.+|..+.|.|+++|.|+-
T Consensus        14 ~~~vA~~LLG~~Lv~~~~~g~~~~g~IvEtEAY~G   48 (214)
T d1ewna_          14 AVPLARAFLGQVLVRRLPNGTELRGRIVETQAYLG   48 (214)
T ss_dssp             HHHHHHHHTTCEEEEECTTSCEEEEEEEEEEEECS
T ss_pred             HHHHHHHhCCCEEEEEcCCCCEEEEEEEEEeccCC
Confidence            56777899999999999999999999999999973