Citrus Sinensis ID: 034273

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
Protein Sequence
MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEEEEEEccEEEEEEEEEcccccccEEcccEEEEEEccccccccccEEEEEEEEEEcEEEEcccEEEEEEcccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHHHHHcccccHHHHHHHHHccHHHHHHEHHHHHHHHHHHHcHHHHHccccccccccccccccccccEHHHEEEcccEEEEEEEccc
Coil and Loop (DISEMBL)
msramdedttggkteeeefntgplSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTelpktgkgkkkalpvnkdrFISKMFLRGDSVIIVLRNPK
Flexible Loop (DISEMBL)
msramdedttggkteeeefntgplSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMwtelpktgkgkkkalpvnkdrfiskmflrgdsviivlrnpk
Low Complexity Region (SEG)
MSRAMdedttggkteeeeFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK
Disordered region (IsUnstruct)
************************SVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKT*****KALPVNKDRFISKMFLRGDSVIIVL****
Disordered Region (DISOPRED)
*******************NTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMW******************DRFISKMFLRGDSVIIVLRNP*
Disordered Region (DISEMBL)
*******************NTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTEL*********ALPVNKDRFISKMFLRGDSVIIVLRNPK
Disordered Region (DISPRO)
*********TGGKTEEEEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPK*********PVNKDRFISKMFLRGDSVIIVLRNP*
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK
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	99	2.2.26 [Sep-21-2011]
Q9VI10	119	Probable small nuclear ri	yes	no	0.808	0.672	0.8	7e-28
Q54NC5	112	Probable small nuclear ri	yes	no	0.949	0.839	0.666	2e-27
Q18786	118	Probable small nuclear ri	yes	no	0.848	0.711	0.734	2e-26
P62317	118	Small nuclear ribonucleop	no	no	0.808	0.677	0.777	2e-26
P62316	118	Small nuclear ribonucleop	yes	no	0.808	0.677	0.777	2e-26
Q3SZF8	118	Small nuclear ribonucleop	yes	no	0.808	0.677	0.777	2e-26
O14036	115	Small nuclear ribonucleop	yes	no	0.868	0.747	0.587	9e-25
Q06217	110	Small nuclear ribonucleop	yes	no	0.707	0.636	0.517	7e-19
Q9Y7M4	93	Probable U6 snRNA-associa	no	no	0.686	0.731	0.333	4e-05
P62311	102	U6 snRNA-associated Sm-li	no	no	0.878	0.852	0.294	9e-05

>sp|Q9VI10|SMD2_DROME Probable small nuclear ribonucleoprotein Sm D2 OS=Drosophila melanogaster GN=SmD2 PE=3 SV=1

 Score =  122 bits (306), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 76/90 (84%), Gaps = 10/90 (11%)

Query: 19  FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
           FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTELP+TGKG
Sbjct: 23  FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTELPRTGKG 82

Query: 69  KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
           KKK  PVNKDRFISKMFLRGDSVI+VLRNP
Sbjct: 83  KKKVKPVNKDRFISKMFLRGDSVILVLRNP 112

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

>sp|Q54NC5|SMD2_DICDI Probable small nuclear ribonucleoprotein Sm D2 OS=Dictyostelium discoideum GN=snrpd2 PE=3 SV=1

 Score =  120 bits (302), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 72/108 (66%), Positives = 84/108 (77%), Gaps = 14/108 (12%)

Query: 1   MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNM 50
           MSR M+++T   K ++     GPLS+LM SV NNTQ          LLGRVRAFDRHCNM
Sbjct: 1   MSR-MNDETMEDKPDDS---NGPLSILMDSVNNNTQVLINVRNNKKLLGRVRAFDRHCNM 56

Query: 51  VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
           VLENV+E+WTE+PKT KGKKKA P+NKDRFISKMFLRGDSVI+VL+NP
Sbjct: 57  VLENVKEIWTEVPKTAKGKKKAKPINKDRFISKMFLRGDSVILVLKNP 104

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

Dictyostelium discoideum (taxid: 44689)

>sp|Q18786|SMD2_CAEEL Probable small nuclear ribonucleoprotein Sm D2 OS=Caenorhabditis elegans GN=snr-4 PE=1 SV=1

 Score =  117 bits (294), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 69/94 (73%), Positives = 77/94 (81%), Gaps = 10/94 (10%)

Query: 15  EEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPK 64
           E+EEFN GPLS+L  SVKNN Q          LLGRV+AFDRHCNMVLENV+EMWTE+PK
Sbjct: 20  EDEEFNVGPLSILTNSVKNNHQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPK 79

Query: 65  TGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
           TGKGKKKA  V KDRFISKMFLRGDSVI+V++NP
Sbjct: 80  TGKGKKKAKSVAKDRFISKMFLRGDSVILVVKNP 113

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

Caenorhabditis elegans (taxid: 6239)

>sp|P62317|SMD2_MOUSE Small nuclear ribonucleoprotein Sm D2 OS=Mus musculus GN=Snrpd2 PE=2 SV=1

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 70/90 (77%), Positives = 77/90 (85%), Gaps = 10/90 (11%)

Query: 19  FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
           FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKG
Sbjct: 24  FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 83

Query: 69  KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
           KKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct: 84  KKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113

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

Mus musculus (taxid: 10090)

>sp|P62316|SMD2_HUMAN Small nuclear ribonucleoprotein Sm D2 OS=Homo sapiens GN=SNRPD2 PE=1 SV=1

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 70/90 (77%), Positives = 77/90 (85%), Gaps = 10/90 (11%)

Query: 19  FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
           FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKG
Sbjct: 24  FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 83

Query: 69  KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
           KKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct: 84  KKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113

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

Homo sapiens (taxid: 9606)

>sp|Q3SZF8|SMD2_BOVIN Small nuclear ribonucleoprotein Sm D2 OS=Bos taurus GN=SNRPD2 PE=3 SV=1

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 70/90 (77%), Positives = 77/90 (85%), Gaps = 10/90 (11%)

Query: 19  FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
           FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKG
Sbjct: 24  FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 83

Query: 69  KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
           KKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct: 84  KKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113

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

Bos taurus (taxid: 9913)

>sp|O14036|SMD2_SCHPO Small nuclear ribonucleoprotein Sm D2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smd2 PE=1 SV=1

 Score =  112 bits (279), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 57/97 (58%), Positives = 68/97 (70%), Gaps = 11/97 (11%)

Query: 12  GKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTE 61
            + EE EF+ GPLSVL  +VKN+ Q          LL RV+AFDRH NMVLENV+EMWTE
Sbjct: 18  ARLEEYEFSAGPLSVLQQAVKNHDQVLINCRNNKKLLARVKAFDRHSNMVLENVKEMWTE 77

Query: 62  LPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
             +T  G KK   +NKDRFISKMFLRGD V++V+R P
Sbjct: 78  KKRTASG-KKGKAINKDRFISKMFLRGDGVVLVVRIP 113

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|Q06217|SMD2_YEAST Small nuclear ribonucleoprotein Sm D2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SMD2 PE=1 SV=2

 Score = 92.4 bits (228), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 45/87 (51%), Positives = 64/87 (73%), Gaps = 17/87 (19%)

Query: 22  GPLSVL----------MMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKK 71
           GP+S++          ++S++NN +++ RV+AFDRHCNMVLENV+E+WTE  K GK    
Sbjct: 29  GPMSLINDAMVTRTPVIISLRNNHKIIARVKAFDRHCNMVLENVKELWTE--KKGKN--- 83

Query: 72  ALPVNKDRFISKMFLRGDSVIIVLRNP 98
              +N++RFISK+FLRGDSVI+VL+ P
Sbjct: 84  --VINRERFISKLFLRGDSVIVVLKTP 108

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

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

>sp|Q9Y7M4|LSM3_SCHPO Probable U6 snRNA-associated Sm-like protein LSm3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm3 PE=1 SV=2

 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 26 VLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMF 85
          ++ + ++ + +L GR+ A+D H NMVL +  E+ T        K KAL   +  +   +F
Sbjct: 21 IVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHY-EMLF 79

Query: 86 LRGDSVIIV 94
          +RGDSVI++
Sbjct: 80 VRGDSVILI 88

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

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

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

 Score = 45.8 bits (107), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 30/102 (29%), Positives = 53/102 (51%), Gaps = 15/102 (14%)

Query: 1  MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVL 52
          M+  +D+  T    EE      PL ++ +S+        +N+ +L GR+ A+D+H NM+L
Sbjct: 1  MADDVDQQQTTNTVEE------PLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMIL 54

Query: 53 ENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 94
           +V E  T +    +  ++     K R I  +F+RGD V++V
Sbjct: 55 GDVEETVTTIEIDEETYEEIYKSTK-RNIPMLFVRGDGVVLV 95

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

Mus musculus (taxid: 10090)

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	99
297821194	109	predicted protein [Arabidopsis lyrata su	1.0	0.908	0.853	3e-45
18407411	109	small nuclear ribonucleoprotein D2 [Arab	1.0	0.908	0.844	1e-44
297824871	105	hypothetical protein ARALYDRAFT_483945 [	0.959	0.904	0.857	2e-43
30690747	108	small nuclear ribonucleoprotein D2 [Arab	0.989	0.907	0.844	2e-43
356513032	108	PREDICTED: probable small nuclear ribonu	0.989	0.907	0.844	7e-43
351727138	117	uncharacterized protein LOC100500203 [Gl	0.989	0.837	0.834	1e-42
359806642	108	uncharacterized protein LOC100793233 [Gl	0.989	0.907	0.834	1e-42
192910682	105	small nuclear ribonucleoprotein-like pro	0.959	0.904	0.838	2e-42
357521397	108	Small nuclear ribonucleoprotein-like pro	0.989	0.907	0.834	2e-42
449457536	107	PREDICTED: probable small nuclear ribonu	0.979	0.906	0.834	3e-42

>gi|297821194|ref|XP_002878480.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297324318|gb|EFH54739.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  185 bits (470), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 93/109 (85%), Positives = 97/109 (88%), Gaps = 10/109 (9%)

Query: 1   MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNM 50
           MS+ M+EDTT GKTEEEEFNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNM
Sbjct: 1   MSKPMEEDTTQGKTEEEEFNTGPLSVLMMSVKNNTQVLINCRNNRKLLGRVRAFDRHCNM 60

Query: 51  VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
           VLENVREMWTE+PKTGKGKKKALPVN+DRFISKMFLRGDSVIIVLRNPK
Sbjct: 61  VLENVREMWTEVPKTGKGKKKALPVNRDRFISKMFLRGDSVIIVLRNPK 109

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18407411|ref|NP_566107.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|145331435|ref|NP_001078076.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|145339793|ref|NP_567134.3| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|20196966|gb|AAM14847.1| putative small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|20197310|gb|AAC63620.2| putative small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|330255773|gb|AEC10867.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|330255776|gb|AEC10870.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|332646879|gb|AEE80400.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana]

 Score =  183 bits (465), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 92/109 (84%), Positives = 96/109 (88%), Gaps = 10/109 (9%)

Query: 1   MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNM 50
           MS+ M+EDT  GKTEEEEFNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNM
Sbjct: 1   MSKPMEEDTNQGKTEEEEFNTGPLSVLMMSVKNNTQVLINCRNNRKLLGRVRAFDRHCNM 60

Query: 51  VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
           VLENVREMWTE+PKTGKGKKKALPVN+DRFISKMFLRGDSVIIVLRNPK
Sbjct: 61  VLENVREMWTEVPKTGKGKKKALPVNRDRFISKMFLRGDSVIIVLRNPK 109

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297824871|ref|XP_002880318.1| hypothetical protein ARALYDRAFT_483945 [Arabidopsis lyrata subsp. lyrata] gi|21554692|gb|AAM63661.1| small nuclear ribonucleoprotein-like protein [Arabidopsis thaliana] gi|21592784|gb|AAM64733.1| small nuclear ribonucleoprotein-like protein [Arabidopsis thaliana] gi|297326157|gb|EFH56577.1| hypothetical protein ARALYDRAFT_483945 [Arabidopsis lyrata subsp. lyrata]

 Score =  179 bits (454), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 90/105 (85%), Positives = 93/105 (88%), Gaps = 10/105 (9%)

Query: 5   MDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLEN 54
           M+EDT  GKTEEEEFNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNMVLEN
Sbjct: 1   MEEDTNQGKTEEEEFNTGPLSVLMMSVKNNTQVLINCRNNRKLLGRVRAFDRHCNMVLEN 60

Query: 55  VREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
           VREMWTE+PKTGKGKKKALPVN+DRFISKMFLRGDSVIIVLRNPK
Sbjct: 61  VREMWTEVPKTGKGKKKALPVNRDRFISKMFLRGDSVIIVLRNPK 105

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30690747|ref|NP_850477.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|42571273|ref|NP_973710.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|145332931|ref|NP_001078331.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|7362764|emb|CAB83134.1| small nuclear ribonucleoprotein-like protein [Arabidopsis thaliana] gi|28466881|gb|AAO44049.1| At2g47640 [Arabidopsis thaliana] gi|110743879|dbj|BAE99774.1| putative small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|330255774|gb|AEC10868.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|330255775|gb|AEC10869.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|332646880|gb|AEE80401.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana]

 Score =  179 bits (453), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 92/109 (84%), Positives = 96/109 (88%), Gaps = 11/109 (10%)

Query: 1   MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNM 50
           MS+ M+EDT  GKTEEEEFNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNM
Sbjct: 1   MSKPMEEDT-NGKTEEEEFNTGPLSVLMMSVKNNTQVLINCRNNRKLLGRVRAFDRHCNM 59

Query: 51  VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
           VLENVREMWTE+PKTGKGKKKALPVN+DRFISKMFLRGDSVIIVLRNPK
Sbjct: 60  VLENVREMWTEVPKTGKGKKKALPVNRDRFISKMFLRGDSVIIVLRNPK 108

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513032|ref|XP_003525218.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D2-like [Glycine max]

 Score =  177 bits (449), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 92/109 (84%), Positives = 94/109 (86%), Gaps = 11/109 (10%)

Query: 1   MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNM 50
           MSR M+EDT G K EEEEFNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNM
Sbjct: 1   MSRPMEEDTVG-KNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNM 59

Query: 51  VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
           VLENVREMWTE+PKTGKGKKKA PVNKDRFISKMFLRGDSVIIVLRNPK
Sbjct: 60  VLENVREMWTEVPKTGKGKKKAQPVNKDRFISKMFLRGDSVIIVLRNPK 108

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727138|ref|NP_001238430.1| uncharacterized protein LOC100500203 [Glycine max] gi|255629692|gb|ACU15195.1| unknown [Glycine max]

 Score =  176 bits (447), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 91/109 (83%), Positives = 94/109 (86%), Gaps = 11/109 (10%)

Query: 1   MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNM 50
           MSR M+EDT  GK EEEEFNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNM
Sbjct: 1   MSRPMEEDT-AGKNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNM 59

Query: 51  VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
           VLENVREMWTE+PKTGKGKKK+ PVNKDRFISKMFLRGDSVIIVLRNPK
Sbjct: 60  VLENVREMWTEVPKTGKGKKKSQPVNKDRFISKMFLRGDSVIIVLRNPK 108

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359806642|ref|NP_001241022.1| uncharacterized protein LOC100793233 [Glycine max] gi|255633912|gb|ACU17317.1| unknown [Glycine max]

 Score =  176 bits (446), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 91/109 (83%), Positives = 93/109 (85%), Gaps = 11/109 (10%)

Query: 1   MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNM 50
           MSR M+ED   GK EEEEFNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNM
Sbjct: 1   MSRPMEEDA-AGKNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNM 59

Query: 51  VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
           VLENVREMWTE+PKTGKGKKKA PVNKDRFISKMFLRGDSVIIVLRNPK
Sbjct: 60  VLENVREMWTEVPKTGKGKKKAQPVNKDRFISKMFLRGDSVIIVLRNPK 108

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|192910682|gb|ACF06449.1| small nuclear ribonucleoprotein-like protein [Elaeis guineensis]

 Score =  176 bits (446), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 88/105 (83%), Positives = 91/105 (86%), Gaps = 10/105 (9%)

Query: 5   MDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLEN 54
           M++D   GK EEEEFNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNMVLEN
Sbjct: 1   MEDDANAGKKEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 60

Query: 55  VREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
           VREMWTE+PKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK
Sbjct: 61  VREMWTEVPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 105

Source: Elaeis guineensis

Species: Elaeis guineensis

Genus: Elaeis

Family: Arecaceae

Order: Arecales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357521397|ref|XP_003630987.1| Small nuclear ribonucleoprotein-like protein [Medicago truncatula] gi|355525009|gb|AET05463.1| Small nuclear ribonucleoprotein-like protein [Medicago truncatula] gi|388506390|gb|AFK41261.1| unknown [Medicago truncatula]

 Score =  176 bits (445), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 91/109 (83%), Positives = 93/109 (85%), Gaps = 11/109 (10%)

Query: 1   MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNM 50
           MSR M+ED  G K EEEEFNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNM
Sbjct: 1   MSRPMEEDAVG-KNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNM 59

Query: 51  VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
           VLENVREMWTE+PKTGKGKKKA PVNKDRFISKMFLRGDSVIIVLRNPK
Sbjct: 60  VLENVREMWTEVPKTGKGKKKAQPVNKDRFISKMFLRGDSVIIVLRNPK 108

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457536|ref|XP_004146504.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D2-like [Cucumis sativus] gi|449499984|ref|XP_004160970.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D2-like [Cucumis sativus]

 Score =  175 bits (444), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 91/109 (83%), Positives = 94/109 (86%), Gaps = 12/109 (11%)

Query: 1   MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNM 50
           MSR M+EDT+  K EEEEFNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNM
Sbjct: 1   MSRPMEEDTS--KNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNM 58

Query: 51  VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
           VLENVREMWTE+PKTGKGKKKA PVNKDRFISKMFLRGDSVIIVLRNPK
Sbjct: 59  VLENVREMWTEVPKTGKGKKKAQPVNKDRFISKMFLRGDSVIIVLRNPK 107

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	99
TAIR|locus:2043323	109	AT2G47640 "AT2G47640" [Arabido	1.0	0.908	0.752	3.5e-36
TAIR|locus:2081685	109	AT3G62840 "AT3G62840" [Arabido	1.0	0.908	0.752	3.5e-36
FB|FBgn0261789	119	SmD2 "Small ribonucleoprotein	0.808	0.672	0.8	1.8e-32
UNIPROTKB|G3X6Z3	117	SNRPD2 "Small nuclear ribonucl	0.808	0.683	0.777	6e-32
UNIPROTKB|Q3SZF8	118	SNRPD2 "Small nuclear ribonucl	0.808	0.677	0.777	6e-32
UNIPROTKB|F1PSI7	118	SNRPD2 "Uncharacterized protei	0.808	0.677	0.777	6e-32
UNIPROTKB|P62316	118	SNRPD2 "Small nuclear ribonucl	0.808	0.677	0.777	6e-32
MGI|MGI:98345	118	Snrpd2 "small nuclear ribonucl	0.808	0.677	0.777	6e-32
RGD|1593018	118	Snrpd2 "small nuclear ribonucl	0.808	0.677	0.777	6e-32
ZFIN|ZDB-GENE-040914-10	118	snrpd2 "small nuclear ribonucl	0.808	0.677	0.777	6e-32

TAIR|locus:2043323 AT2G47640 "AT2G47640" [Arabidopsis thaliana (taxid:3702)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 82/109 (75%), Positives = 85/109 (77%)

Query:     1 MSRAMXXXXXXXXXXXXXFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNM 50
             MS+ M             FNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNM
Sbjct:     1 MSKPMEEDTNQGKTEEEEFNTGPLSVLMMSVKNNTQVLINCRNNRKLLGRVRAFDRHCNM 60

Query:    51 VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
             VLENVREMWTE+PKTGKGKKKALPVN+DRFISKMFLRGDSVIIVLRNPK
Sbjct:    61 VLENVREMWTEVPKTGKGKKKALPVNRDRFISKMFLRGDSVIIVLRNPK 109

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0005730 "nucleolus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0001510 "RNA methylation" evidence=RCA

TAIR|locus:2081685 AT3G62840 "AT3G62840" [Arabidopsis thaliana (taxid:3702)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 82/109 (75%), Positives = 85/109 (77%)

Query:     1 MSRAMXXXXXXXXXXXXXFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNM 50
             MS+ M             FNTGPLSVLMMSVKNNTQ          LLGRVRAFDRHCNM
Sbjct:     1 MSKPMEEDTNQGKTEEEEFNTGPLSVLMMSVKNNTQVLINCRNNRKLLGRVRAFDRHCNM 60

Query:    51 VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 99
             VLENVREMWTE+PKTGKGKKKALPVN+DRFISKMFLRGDSVIIVLRNPK
Sbjct:    61 VLENVREMWTEVPKTGKGKKKALPVNRDRFISKMFLRGDSVIIVLRNPK 109

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0005829 "cytosol" evidence=RCA

FB|FBgn0261789 SmD2 "Small ribonucleoprotein particle protein SmD2" [Drosophila melanogaster (taxid:7227)]

 Score = 355 (130.0 bits), Expect = 1.8e-32, P = 1.8e-32
 Identities = 72/90 (80%), Positives = 76/90 (84%)

Query:    19 FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
             FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTELP+TGKG
Sbjct:    23 FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTELPRTGKG 82

Query:    69 KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
             KKK  PVNKDRFISKMFLRGDSVI+VLRNP
Sbjct:    83 KKKVKPVNKDRFISKMFLRGDSVILVLRNP 112

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

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

GO:0005681 "spliceosomal complex" evidence=ISS

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:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|G3X6Z3 SNRPD2 "Small nuclear ribonucleoprotein Sm D2" [Bos taurus (taxid:9913)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 70/90 (77%), Positives = 77/90 (85%)

Query:    19 FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
             FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKG
Sbjct:    23 FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 82

Query:    69 KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
             KKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct:    83 KKKSKPVNKDRYISKMFLRGDSVIVVLRNP 112

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

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

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

GO:0008380 "RNA splicing" evidence=IEA

UNIPROTKB|Q3SZF8 SNRPD2 "Small nuclear ribonucleoprotein Sm D2" [Bos taurus (taxid:9913)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 70/90 (77%), Positives = 77/90 (85%)

Query:    19 FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
             FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKG
Sbjct:    24 FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 83

Query:    69 KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
             KKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct:    84 KKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113

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

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

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

UNIPROTKB|F1PSI7 SNRPD2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 70/90 (77%), Positives = 77/90 (85%)

Query:    19 FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
             FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKG
Sbjct:    24 FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 83

Query:    69 KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
             KKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct:    84 KKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113

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

GO:0008380 "RNA splicing" evidence=IEA

UNIPROTKB|P62316 SNRPD2 "Small nuclear ribonucleoprotein Sm D2" [Homo sapiens (taxid:9606)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 70/90 (77%), Positives = 77/90 (85%)

Query:    19 FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
             FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKG
Sbjct:    24 FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 83

Query:    69 KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
             KKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct:    84 KKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113

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

GO:0005515 "protein binding" evidence=IPI

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

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

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

GO:0000245 "spliceosomal complex assembly" 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: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

MGI|MGI:98345 Snrpd2 "small nuclear ribonucleoprotein D2" [Mus musculus (taxid:10090)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 70/90 (77%), Positives = 77/90 (85%)

Query:    19 FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
             FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKG
Sbjct:    24 FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 83

Query:    69 KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
             KKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct:    84 KKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

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

RGD|1593018 Snrpd2 "small nuclear ribonucleoprotein D2 polypeptide" [Rattus norvegicus (taxid:10116)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 70/90 (77%), Positives = 77/90 (85%)

Query:    19 FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
             FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKG
Sbjct:    24 FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 83

Query:    69 KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
             KKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct:    84 KKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

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

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

ZFIN|ZDB-GENE-040914-10 snrpd2 "small nuclear ribonucleoprotein D2 polypeptide" [Danio rerio (taxid:7955)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 70/90 (77%), Positives = 77/90 (85%)

Query:    19 FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
             FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKG
Sbjct:    24 FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 83

Query:    69 KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
             KKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct:    84 KKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113

GO:0008380 "RNA splicing" evidence=IEA

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

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)
Q06217	SMD2_YEAST	No assigned EC number	0.5172	0.7070	0.6363	yes	no
P62316	SMD2_HUMAN	No assigned EC number	0.7777	0.8080	0.6779	yes	no
Q18786	SMD2_CAEEL	No assigned EC number	0.7340	0.8484	0.7118	yes	no
Q9VI10	SMD2_DROME	No assigned EC number	0.8	0.8080	0.6722	yes	no
Q3SZF8	SMD2_BOVIN	No assigned EC number	0.7777	0.8080	0.6779	yes	no
Q54NC5	SMD2_DICDI	No assigned EC number	0.6666	0.9494	0.8392	yes	no
O14036	SMD2_SCHPO	No assigned EC number	0.5876	0.8686	0.7478	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	Al_scaffold_0005_3236	annotation not avaliable (109 aa)
		(Arabidopsis lyrata)
Predicted Functional Partners:
	fgenesh2_kg.1__265__AT1G03330.1	annotation not avaliable (93 aa)				•	•	•	•		0.848
	scaffold_801217.1	annotation not avaliable (88 aa)				•	•		•		0.729
	scaffold_701187.1	annotation not avaliable (88 aa)				•	•	•	•		0.600
	scaffold_304344.1	annotation not avaliable (88 aa)				•	•	•	•		0.599
	fgenesh2_kg.3__1190__AT3G11500.1	annotation not avaliable (79 aa)				•	•	•	•		0.593
	scaffold_400381.1	annotation not avaliable (80 aa)				•	•	•	•		0.587
	scaffold_701198.1	annotation not avaliable (88 aa)				•	•	•	•		0.579
	scaffold_303615.1	annotation not avaliable (88 aa)				•	•	•	•		0.579
	fgenesh2_kg.8__2445__AT5G64270.1	annotation not avaliable (1264 aa)					•	•	•		0.518
	scaffold_100009.1	annotation not avaliable (150 aa)				•		•			0.513

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	99
cd01720	89	cd01720, Sm_D2, Sm protein D2	5e-48
cd01730	82	cd01730, LSm3, Like-Sm protein 3	2e-12
smart00651	67	smart00651, Sm, snRNP Sm proteins	2e-11
pfam01423	66	pfam01423, LSM, LSM domain	3e-10
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	3e-08
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	3e-06
cd00600	63	cd00600, Sm_like, Sm and related proteins	3e-06
cd01739	63	cd01739, LSm11_M, Like-Sm protein 11, middle domai	0.002

>gnl|CDD|212467 cd01720, Sm_D2, Sm protein D2

 Score =  147 bits (373), Expect = 5e-48
 Identities = 69/90 (76%), Positives = 74/90 (82%), Gaps = 11/90 (12%)

Query: 19 FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
          FNTGPLS+L  SVKNNTQ          LL RV+AFDRHCNMVLENV+EMWTE+PKTGKG
Sbjct: 1  FNTGPLSLLTQSVKNNTQVLINCRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKG 60

Query: 69 KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
          KK   PVNKDRFISKMFLRGDSVI+VLRNP
Sbjct: 61 KKSK-PVNKDRFISKMFLRGDSVILVLRNP 89

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 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. Length = 89

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

 Score = 56.9 bits (138), Expect = 2e-12
 Identities = 22/64 (34%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 31 VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 90
          ++ + +L GR+ A+D+H NM+L +V E  T +    +  ++     K R I  +F+RGD 
Sbjct: 18 LRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTK-RNIPMLFVRGDG 76

Query: 91 VIIV 94
          VI+V
Sbjct: 77 VILV 80

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

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

 Score = 54.0 bits (131), Expect = 2e-11
 Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 13/63 (20%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          KN  +  G ++ FD+  N+VLE+V E   +               K R +  +F+RG+++
Sbjct: 16 KNGREYRGTLKGFDQFMNLVLEDVEETVKD-------------GEKKRKLGLVFIRGNNI 62

Query: 92 IIV 94
          + +
Sbjct: 63 VYI 65

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

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

 Score = 51.0 bits (123), Expect = 3e-10
 Identities = 14/63 (22%), Positives = 31/63 (49%), Gaps = 14/63 (22%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          KN  +L G ++ FD+  N+VL++V E   +               K   +  + +RG+++
Sbjct: 16 KNGRELRGTLKGFDQFMNLVLDDVEETIKD--------------GKVNKLGLVLIRGNNI 61

Query: 92 IIV 94
          +++
Sbjct: 62 VLI 64

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

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

 Score = 46.5 bits (111), Expect = 3e-08
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 18/78 (23%)

Query: 23 PLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALP 74
          PLS L   +        KN  +  G +  FD++ N+VL++V E+ +       G+K    
Sbjct: 8  PLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH-----DGEK---- 58

Query: 75 VNKDRFISKMFLRGDSVI 92
           N  R   ++ +RGD+++
Sbjct: 59 -NVRRLGGEVLIRGDNIV 75

Length = 79

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

 Score = 41.0 bits (97), Expect = 3e-06
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 22/80 (27%)

Query: 23 PLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALP 74
          PL VL  S+        K   ++ G ++ FD+H N+VLEN  E   E    G+  +K   
Sbjct: 2  PLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENA-EEIIE----GESVRK--- 53

Query: 75 VNKDRFISKMFLRGDSVIIV 94
                +  + +RGD+V+ +
Sbjct: 54 ------LGTVLVRGDNVVFI 67

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

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

 Score = 40.7 bits (96), Expect = 3e-06
 Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 14/63 (22%)

Query: 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 89
           +K+   L G + AFD++ N+VL++V E   +               K R +  + +RG 
Sbjct: 12 ELKDGRVLTGTLVAFDKYMNLVLDDVVETGRD--------------GKVRVLGLVLIRGS 57

Query: 90 SVI 92
          +++
Sbjct: 58 NIV 60

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|212485 cd01739, LSm11_M, Like-Sm protein 11, middle domain

 Score = 33.4 bits (77), Expect = 0.002
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 39 GRVRAFDRHCNMVLENVREMWTE 61
          G + AFD+H N+ L +V E WT 
Sbjct: 27 GYLVAFDKHWNLALVDVDETWTR 49

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. LSm11 is an SmD2-like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-membered 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. Length = 63

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	99
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.81
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.8
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.8
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.79
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.79
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.75
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.74
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.74
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.73
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.72
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	99.71
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	99.71
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.7
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.7
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.68
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.66
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.65
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.6
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.59
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.57
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.51
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.47
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.45
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.43
KOG3168	177	consensus U1 snRNP component [Transcription]	99.4
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.4
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.39
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	99.35
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.33
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	99.18
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.12
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	99.05
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.88
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	98.48
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	98.09
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	97.71
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	96.8
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	90.41
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	89.32
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	88.84
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	87.02
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	85.24

>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=99.91  E-value=1.6e-24  Score=142.05  Aligned_cols=77  Identities=84%  Similarity=1.347  Sum_probs=62.0

Q ss_pred             CCChhhhhhhh----------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 034273           21 TGPLSVLMMSV----------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS   90 (99)
Q Consensus        21 ~~Pl~vL~~~l----------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn   90 (99)
                      +||+++|+.++          ++|+.+.|+|+|||+||||+|+||+|++...++++.+. +..+..++|++|.+||||||
T Consensus         1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~-~~~~~~~~r~lg~v~iRGd~   79 (87)
T cd01720           1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGK-KAKPVNKDRFISKMFLRGDS   79 (87)
T ss_pred             CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccc-cccceeeeeEcccEEEeCCE
Confidence            48999998884          78999999999999999999999999987654432211 11123456889999999999


Q ss_pred             EEEEEeCC
Q 034273           91 VIIVLRNP   98 (99)
Q Consensus        91 Vv~V~~~p   98 (99)
                      |++|+++|
T Consensus        80 Vv~Is~~~   87 (87)
T cd01720          80 VILVLRNP   87 (87)
T ss_pred             EEEEecCC
Confidence            99999987

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.

>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=99.87  E-value=3.8e-22  Score=128.89  Aligned_cols=74  Identities=34%  Similarity=0.579  Sum_probs=56.0

Q ss_pred             CChhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 034273           22 GPLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII   93 (99)
Q Consensus        22 ~Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~   93 (99)
                      .|+++|+.+        +++||++.|+|+|||+||||+|+||+|++....++.+.. ........|.+|.+|||||||++
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~-~~~~~~~~r~lg~~~iRGd~Vv~   79 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETY-EEIVKTTKRNIPMLFVRGDSVIL   79 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeeccccccccc-ccccceeEEEcCeEEEeCCEEEE
Confidence            367777665        489999999999999999999999999987543322110 00112246889999999999999


Q ss_pred             EEe
Q 034273           94 VLR   96 (99)
Q Consensus        94 V~~   96 (99)
                      |+|
T Consensus        80 i~~   82 (82)
T cd01730          80 VSP   82 (82)
T ss_pred             ECC
Confidence            985

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.

>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=99.84  E-value=1.3e-20  Score=120.60  Aligned_cols=66  Identities=26%  Similarity=0.492  Sum_probs=54.6

Q ss_pred             CCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273           21 TGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI   92 (99)
Q Consensus        21 ~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv   92 (99)
                      ..|+++|.+++        ++|+++.|+|+|||+||||+|+||+|++.. ++.   .       ..+++|.+|||||||+
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~-~~~---~-------~~~~lg~v~iRG~nV~   70 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEIT-PEG---R-------KITKLDQILLNGNNIC   70 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEc-CCC---c-------eeeEcCeEEEeCCeEE
Confidence            36888887765        899999999999999999999999999842 111   1       1367999999999999


Q ss_pred             EEEeC
Q 034273           93 IVLRN   97 (99)
Q Consensus        93 ~V~~~   97 (99)
                      +|+|.
T Consensus        71 ~i~p~   75 (76)
T cd01732          71 MLVPG   75 (76)
T ss_pred             EEECC
Confidence            99974

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

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.81  E-value=1.1e-19  Score=114.74  Aligned_cols=63  Identities=32%  Similarity=0.535  Sum_probs=52.9

Q ss_pred             cCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 034273           20 NTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV   91 (99)
Q Consensus        20 ~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV   91 (99)
                      ...|+.+|..++        ++|+.+.|+|+|||+||||+|+||.|++..       .       ..+.+|.+||||+||
T Consensus         2 ~~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------~-------~~~~lg~v~iRG~~V   67 (72)
T PRK00737          2 AQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG-------E-------VVRKLGKVVIRGDNV   67 (72)
T ss_pred             CcchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC-------C-------eEeEcCcEEEeCCEE
Confidence            357888887765        899999999999999999999999997531       1       136799999999999


Q ss_pred             EEEEe
Q 034273           92 IIVLR   96 (99)
Q Consensus        92 v~V~~   96 (99)
                      ++|+|
T Consensus        68 ~~i~~   72 (72)
T PRK00737         68 VYVSP   72 (72)
T ss_pred             EEEcC
Confidence            99975

>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=99.80  E-value=2.1e-19  Score=116.10  Aligned_cols=65  Identities=18%  Similarity=0.472  Sum_probs=54.2

Q ss_pred             ccCCChhhhhhhh------------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEE
Q 034273           19 FNTGPLSVLMMSV------------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFL   86 (99)
Q Consensus        19 ~~~~Pl~vL~~~l------------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~I   86 (99)
                      .+..|+.+|...+            ++|++++|+|.|||+||||+|+||+|+...      +.       ..+.+|.++|
T Consensus         3 ~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~------~~-------~~~~lG~ili   69 (79)
T cd01718           3 VMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK------TK-------TRKPLGRILL   69 (79)
T ss_pred             cccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC------Cc-------eEeEcCcEEE
Confidence            4678888887765            388999999999999999999999998742      11       1367999999


Q ss_pred             eCCcEEEEEe
Q 034273           87 RGDSVIIVLR   96 (99)
Q Consensus        87 RGdnVv~V~~   96 (99)
                      |||||++|+|
T Consensus        70 RGnnV~~I~p   79 (79)
T cd01718          70 KGDNITLIQN   79 (79)
T ss_pred             eCCEEEEEcC
Confidence            9999999985

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.

>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=99.80  E-value=1.4e-19  Score=115.96  Aligned_cols=71  Identities=25%  Similarity=0.440  Sum_probs=53.6

Q ss_pred             ccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           19 FNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        19 ~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      +.+.++.+   .+++||.+.|+|+|||+||||+|+||+|++...++.+..    ......|++|++||||+||++|+-
T Consensus         8 ~l~~~V~V---~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~----~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           8 LINYRLRV---TLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKN----SEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             HcCCEEEE---EECCCcEEEEEEEEEcCccCEEcCCEEEEEecccccccc----ccCcceeEeeeEEEcCCEEEEEEE
Confidence            34444444   678999999999999999999999999998654321100    012245889999999999999974

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.

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

Probab=99.79  E-value=3e-19  Score=111.37  Aligned_cols=53  Identities=28%  Similarity=0.562  Sum_probs=46.0

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      .+++|+.+.|+|.|||+||||+|+||+|++..      +        ..+.+|.+||||+||++|+|
T Consensus        16 ~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~------~--------~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731          16 KLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG------E--------PVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             EECCCCEEEEEEEEECCcceEEEeeEEEEecC------C--------eEeEcCcEEEeCCEEEEEcC
Confidence            45899999999999999999999999998642      1        13679999999999999986

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.

>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=99.79  E-value=2.4e-19  Score=115.79  Aligned_cols=71  Identities=18%  Similarity=0.334  Sum_probs=53.4

Q ss_pred             cccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273           18 EFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN   97 (99)
Q Consensus        18 ~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~   97 (99)
                      .+.+.++.+   .+++||++.|+|+|||+||||+|+||+|+........      ......+.+|.++|||+||++|++.
T Consensus         9 ~~i~k~V~V---~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~------~~~~~~~~lG~v~iRG~nV~~i~~~   79 (81)
T cd01729           9 KYVDKKIRV---KFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPY------KLTDKTRQLGLVVCRGTSVVLISPV   79 (81)
T ss_pred             HhcCCeEEE---EECCCcEEEEEEEEEcCcccEEecCEEEEEccCCccc------ccccceeEccEEEEcCCEEEEEecC
Confidence            344555544   5689999999999999999999999999975322110      0011347899999999999999875

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.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.75  E-value=6.2e-18  Score=111.39  Aligned_cols=69  Identities=22%  Similarity=0.507  Sum_probs=56.5

Q ss_pred             cccccCCChhhhhhhh------------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeece
Q 034273           16 EEEFNTGPLSVLMMSV------------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISK   83 (99)
Q Consensus        16 ~~~~~~~Pl~vL~~~l------------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~   83 (99)
                      ....+..|+.++...+            +++++++|+|+|||+||||+|+||+|++..      + .      ..+.+|.
T Consensus         8 ~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~------~-~------~~~~lG~   74 (89)
T PTZ00138          8 LQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK------K-N------TRKDLGR   74 (89)
T ss_pred             cceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC------C-c------eeeEcCe
Confidence            3456788999988776            346899999999999999999999998642      0 0      1367999


Q ss_pred             EEEeCCcEEEEEeC
Q 034273           84 MFLRGDSVIIVLRN   97 (99)
Q Consensus        84 i~IRGdnVv~V~~~   97 (99)
                      +|||||||++|++.
T Consensus        75 ilIRGnnV~~I~~~   88 (89)
T PTZ00138         75 ILLKGDNITLIMAA   88 (89)
T ss_pred             EEEcCCEEEEEEcC
Confidence            99999999999875

>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=99.74  E-value=6.2e-18  Score=107.82  Aligned_cols=64  Identities=23%  Similarity=0.330  Sum_probs=50.5

Q ss_pred             ccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           19 FNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        19 ~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      +.+.++.+   .+++||++.|+|+|||+||||+|+||.|+.....+           ..++.+|.++|||+||++|+.
T Consensus        10 ~l~k~v~V---~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~-----------~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728          10 DLDKKVVV---LLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDK-----------YGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             hcCCEEEE---EEcCCeEEEEEEEEECCcccEEecceEEEEecCCc-----------cceeEeeEEEEECCEEEEEEc
Confidence            34444444   56899999999999999999999999998753211           113679999999999999975

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.

>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=99.74  E-value=9.5e-18  Score=104.48  Aligned_cols=59  Identities=20%  Similarity=0.339  Sum_probs=48.1

Q ss_pred             Chhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 034273           23 PLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV   94 (99)
Q Consensus        23 Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V   94 (99)
                      |+.+|+.+        |++|+++.|+|.|||+||||+|+||+|....       .       ..+.+|.+||||+||++|
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~-------~-------~~~~~~~v~IRG~~I~~I   66 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNG-------Q-------LKNKYGDAFIRGNNVLYI   66 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCC-------c-------eeeEeCCEEEECCEEEEE
Confidence            55666555        4899999999999999999999999986421       1       135799999999999998


Q ss_pred             E
Q 034273           95 L   95 (99)
Q Consensus        95 ~   95 (99)
                      +
T Consensus        67 ~   67 (67)
T cd01726          67 S   67 (67)
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. 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.

>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=99.73  E-value=7.5e-18  Score=106.70  Aligned_cols=65  Identities=23%  Similarity=0.422  Sum_probs=52.7

Q ss_pred             cccccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273           16 EEEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL   95 (99)
Q Consensus        16 ~~~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~   95 (99)
                      -..+.+.++.+   .|++|+.+.|+|.|||+||||+|+||+|++..       .       ..+.+|.++|||+||++|+
T Consensus         5 L~~~i~k~V~V---~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~-------~-------~~~~lg~v~IRG~~I~~i~   67 (72)
T cd01719           5 LKKYMDKKLSL---KLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG-------G-------EKNNIGMVVIRGNSIVMLE   67 (72)
T ss_pred             hHHhCCCeEEE---EECCCeEEEEEEEEEcccccEEeccEEEEccC-------C-------ceeEeceEEECCCEEEEEE
Confidence            34455666655   57899999999999999999999999998631       1       1367999999999999998


Q ss_pred             eC
Q 034273           96 RN   97 (99)
Q Consensus        96 ~~   97 (99)
                      +.
T Consensus        68 ~~   69 (72)
T cd01719          68 AL   69 (72)
T ss_pred             cc
Confidence            75

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.

>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=99.72  E-value=1.4e-17  Score=105.65  Aligned_cols=59  Identities=19%  Similarity=0.383  Sum_probs=48.4

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeCC
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP   98 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~p   98 (99)
                      .+++||.+.|+|+|||+||||+|++|+|+....+.   +.       .++.+|.++|||+||++|++..
T Consensus        15 ~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~---~~-------~~~~lG~~~iRG~~I~~i~~~d   73 (74)
T cd01727          15 ITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDE---GV-------EQVVLGLYIIRGDNIAVVGEID   73 (74)
T ss_pred             EECCCcEEEEEEEEEccccCEEccceEEEEecCCC---Cc-------eeeEeceEEECCCEEEEEEccC
Confidence            56899999999999999999999999998642211   11       2467999999999999999864

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.

>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]

Probab=99.71  E-value=9.7e-19  Score=113.70  Aligned_cols=77  Identities=32%  Similarity=0.512  Sum_probs=60.6

Q ss_pred             cCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 034273           20 NTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV   91 (99)
Q Consensus        20 ~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV   91 (99)
                      +..||++|+.+|        +++|++.|+|+|||+|.||+|.|++|+++....+....++. ....+|.+..+|+|||+|
T Consensus         3 v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~-~k~~~r~~emlFvRGd~V   81 (91)
T KOG3460|consen    3 VEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEI-VKTTKRTVEMLFVRGDGV   81 (91)
T ss_pred             ccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHH-HhhhhcceeEEEEeCCeE
Confidence            567999999886        89999999999999999999999999987643322111111 123457899999999999


Q ss_pred             EEEEeC
Q 034273           92 IIVLRN   97 (99)
Q Consensus        92 v~V~~~   97 (99)
                      ++|+|-
T Consensus        82 ilvspp   87 (91)
T KOG3460|consen   82 ILVSPP   87 (91)
T ss_pred             EEEcCc
Confidence            999974

>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]

Probab=99.71  E-value=1.1e-18  Score=118.27  Aligned_cols=95  Identities=77%  Similarity=1.177  Sum_probs=81.2

Q ss_pred             CcccccccCCccccccccCCChhhhhhhh----------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCcccc
Q 034273            3 RAMDEDTTGGKTEEEEFNTGPLSVLMMSV----------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKA   72 (99)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~Pl~vL~~~l----------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~   72 (99)
                      .-..|+|.-+..|+.++..||++++..+.          ++++.+-|.+.|||.|+|++|+++.|.|++.++.+++.. +
T Consensus         5 ~pk~e~t~~~~~e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk-~   83 (114)
T KOG3459|consen    5 KPKEECTPLEVPEEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK-A   83 (114)
T ss_pred             chhhhcCccccccccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-C
Confidence            34456665455599999999999998876          778889999999999999999999999998887766654 5


Q ss_pred             ccCcceeeeceEEEeCCcEEEEEeCC
Q 034273           73 LPVNKDRFISKMFLRGDSVIIVLRNP   98 (99)
Q Consensus        73 ~~~~~~r~lg~i~IRGdnVv~V~~~p   98 (99)
                      +++.+.|++|.+|||||+|++|..+|
T Consensus        84 ~~~~~~r~isK~flRGdsvI~v~r~p  109 (114)
T KOG3459|consen   84 KPVNKDRFISKMFLRGDSVILVLRNP  109 (114)
T ss_pred             CccchhhhhheeeecCCeEEEEEecc
Confidence            66777899999999999999998776

>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=99.70  E-value=4.5e-17  Score=101.78  Aligned_cols=52  Identities=19%  Similarity=0.296  Sum_probs=43.8

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL   95 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~   95 (99)
                      .|++|+.+.|+|.|||+|||++|+||+|+...       ..       ...+|.+||||+||++|+
T Consensus        17 ~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~-------~~-------~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722          17 KLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG-------KS-------TGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             EECCCcEEEEEEEEECCCEEEEEeeEEEEeCC-------cc-------ccCcCcEEEECCEEEEEC
Confidence            45899999999999999999999999987421       11       246899999999999984

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.

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

Probab=99.70  E-value=4.3e-17  Score=104.17  Aligned_cols=66  Identities=15%  Similarity=0.325  Sum_probs=52.0

Q ss_pred             cCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           20 NTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        20 ~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      ...++.+   .+++||.+.|+|.|||+||||+|+||.|++...++..        ....|++|+++|||++|++|+.
T Consensus         9 l~~~v~V---~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~--------~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           9 LGRTMRI---HMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFS--------PTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             cCCeEEE---EEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccC--------CccEEEeeeEEEeCCeEEEEEE
Confidence            4444444   6789999999999999999999999999986433211        1135899999999999999874

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.

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

Probab=99.68  E-value=2.1e-16  Score=100.99  Aligned_cols=67  Identities=30%  Similarity=0.547  Sum_probs=51.9

Q ss_pred             cCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 034273           20 NTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV   91 (99)
Q Consensus        20 ~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV   91 (99)
                      ...|+++|+.++        ++|+++.|+|+|||+||||+|+||+|.+..  +   +...     ..+..+.++|||+||
T Consensus         5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--~---~~~~-----~~~~~~~~~IRG~~I   74 (79)
T COG1958           5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH--D---GEKN-----VRRLGGEVLIRGDNI   74 (79)
T ss_pred             cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc--C---Cccc-----cceeccEEEEECCcE
Confidence            346788887765        899999999999999999999999998741  1   1110     124455999999999


Q ss_pred             EEEEe
Q 034273           92 IIVLR   96 (99)
Q Consensus        92 v~V~~   96 (99)
                      ++|++
T Consensus        75 ~~I~~   79 (79)
T COG1958          75 VLISP   79 (79)
T ss_pred             EEEeC
Confidence            99974

>smart00651 Sm snRNP Sm proteins

Probab=99.66  E-value=1.7e-16  Score=97.56  Aligned_cols=56  Identities=29%  Similarity=0.603  Sum_probs=47.5

Q ss_pred             hhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           28 MMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        28 ~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      .+.+++|+.+.|+|.+||+||||+|+||+|++...             ...+++|.+||||++|++|++
T Consensus        12 ~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-------------~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651       12 LVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-------------EKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             EEEECCCcEEEEEEEEECccccEEEccEEEEecCC-------------cEEeEeCCEEEcCCEEEEEeC
Confidence            34678999999999999999999999999987521             124789999999999999974

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=99.65  E-value=2e-16  Score=97.31  Aligned_cols=54  Identities=28%  Similarity=0.489  Sum_probs=47.1

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      .+++|+.++|+|.+||+||||+|+||.|.+...+             ..+++|.+||||++|++|++
T Consensus        14 ~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-------------~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen   14 ELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-------------EKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             EETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-------------EEEEEEEEEEEGGGEEEEEE
T ss_pred             EEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-------------cEeECcEEEEECCEEEEEEC
Confidence            6689999999999999999999999999875210             24789999999999999985

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 ....

>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=99.60  E-value=3.6e-15  Score=94.98  Aligned_cols=61  Identities=25%  Similarity=0.359  Sum_probs=49.3

Q ss_pred             Chhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 034273           23 PLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV   94 (99)
Q Consensus        23 Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V   94 (99)
                      |+.+|+.+        |++|+.+.|+|.+||.|||++|+||+|....      +..       ...++.+||||++|.+|
T Consensus         2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~------g~~-------~~~~~~v~IRG~~I~~i   68 (76)
T cd01723           2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKD------GDK-------FWKMPECYIRGNTIKYL   68 (76)
T ss_pred             chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCC------CcE-------eeeCCcEEEeCCEEEEE
Confidence            77777766        4899999999999999999999999986321      111       13578999999999999


Q ss_pred             Ee
Q 034273           95 LR   96 (99)
Q Consensus        95 ~~   96 (99)
                      +.
T Consensus        69 ~~   70 (76)
T cd01723          69 RV   70 (76)
T ss_pred             Ec
Confidence            74

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

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

Probab=99.59  E-value=5.1e-15  Score=93.04  Aligned_cols=53  Identities=15%  Similarity=0.327  Sum_probs=43.7

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      .|++|..+.|+|.+||.|||++|+||+|....      +.        ...++.+||||+||.+|.-
T Consensus        16 eLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~------g~--------~~~~~~v~IRG~nI~~v~l   68 (70)
T cd01721          16 ELKTGEVYRGKLIEAEDNMNCQLKDVTVTARD------GR--------VSQLEQVYIRGSKIRFFIL   68 (70)
T ss_pred             EECCCcEEEEEEEEEcCCceeEEEEEEEECCC------Cc--------EeEcCcEEEeCCEEEEEEe
Confidence            35899999999999999999999999875321      11        1457999999999999863

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.

>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=99.57  E-value=5.3e-15  Score=89.57  Aligned_cols=52  Identities=38%  Similarity=0.631  Sum_probs=45.5

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL   95 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~   95 (99)
                      .+++|+.+.|+|.|||+|||++|.||.|++..      .        ..+.+|.+||||++|.+|.
T Consensus        12 ~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~------~--------~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600          12 ELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE------G--------KKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             EECCCcEEEEEEEEECCCCCEEECCEEEEecC------C--------cEEECCeEEEECCEEEEEC
Confidence            67899999999999999999999999998752      0        1367999999999999874

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.

>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]

Probab=99.51  E-value=1e-14  Score=93.01  Aligned_cols=66  Identities=21%  Similarity=0.408  Sum_probs=51.5

Q ss_pred             ccccccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 034273           15 EEEEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV   94 (99)
Q Consensus        15 ~~~~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V   94 (99)
                      |=-.|+++.+.+   .|++||.+.|+|+|||.|||+||+|+.|....      +.        +..+|..+|||++|+++
T Consensus         8 eLkkymdKki~l---klnG~r~v~GiLrGyD~FmNiVlde~vE~~~~------~~--------~~~ig~~vIrgnsiv~~   70 (77)
T KOG1780|consen    8 ELKKYMDKKIVL---KLNGGRKVTGILRGYDPFMNIVLDETVEPNGD------GD--------KNNIGMVVIRGNSIVMV   70 (77)
T ss_pred             hHHHhhhheEEE---EeCCCcEEEEEEeccchHHhhhhhhceeecCc------CC--------cceeeeEEEeccEEEEE
Confidence            444455554444   67899999999999999999999999997431      11        24689999999999998


Q ss_pred             EeC
Q 034273           95 LRN   97 (99)
Q Consensus        95 ~~~   97 (99)
                      .+.
T Consensus        71 eaL   73 (77)
T KOG1780|consen   71 EAL   73 (77)
T ss_pred             eec
Confidence            765

>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=99.47  E-value=2e-13  Score=89.80  Aligned_cols=53  Identities=21%  Similarity=0.307  Sum_probs=44.8

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      .|++|..+.|+|.++|.|||++|+||+|+...      + .       ...++.++|||+||.+|..
T Consensus        17 eLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~------~-~-------~~~~~~v~IRG~nI~yi~l   69 (90)
T cd01724          17 ELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG------R-N-------PVPLDTLSIRGNNIRYFIL   69 (90)
T ss_pred             EECCCCEEEEEEEEEcCceeEEEEEEEEEcCC------C-c-------eeEcceEEEeCCEEEEEEc
Confidence            46999999999999999999999999987431      1 1       2468999999999999874

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.

>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=99.45  E-value=2.9e-13  Score=86.92  Aligned_cols=53  Identities=23%  Similarity=0.383  Sum_probs=43.8

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      .||+|..+.|+|.++|.|||++|+||++....      + .       ...+|.+||||+||.+|.-
T Consensus        25 eLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~------~-~-------~~~~~~v~IRG~nI~yI~l   77 (78)
T cd01733          25 ELRNETTVTGRIASVDAFMNIRLAKVTIIDRN------G-K-------QVQVEEIMVTGRNIRYVHI   77 (78)
T ss_pred             EECCCCEEEEEEEEEcCCceeEEEEEEEEcCC------C-c-------eeECCcEEEECCEEEEEEc
Confidence            46899999999999999999999999876321      1 1       2368999999999999863

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.

>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]

Probab=99.43  E-value=6.1e-15  Score=98.53  Aligned_cols=64  Identities=16%  Similarity=0.308  Sum_probs=51.7

Q ss_pred             hhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273           28 MMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN   97 (99)
Q Consensus        28 ~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~   97 (99)
                      ++.+.+||+++|+|+|||+.|||||+|++|+...++...   +   .....|.||++++||..+++|+|.
T Consensus        31 rvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~---~---~~~~tR~LGLvV~RGTalvlisp~   94 (108)
T KOG1781|consen   31 RVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPY---K---LTDETRKLGLVVCRGTALVLISPA   94 (108)
T ss_pred             EEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCcc---c---hhhhhheeeeEEEcccEEEEEcCC
Confidence            445689999999999999999999999999976543321   1   123348999999999999999985

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=99.40  E-value=1.3e-14  Score=104.72  Aligned_cols=63  Identities=25%  Similarity=0.516  Sum_probs=50.3

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      .+++||.+.|.+.+||+||||+|.||+|+....++..+.   +. .+++|-+|++++||+|||+.+.
T Consensus        20 ~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~---~~-~eEkr~lgLvllRgenIvs~tV   82 (177)
T KOG3168|consen   20 RLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKM---TD-GEEKRVLGLVLLRGENIVSMTV   82 (177)
T ss_pred             EeccCceeechhhhhHHHHHHHHHHHHHHhccccccccc---cc-cceeeEEEEEEecCCcEEEEec
Confidence            457899999999999999999999999987655443311   11 2346889999999999999764

>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=99.40  E-value=1.2e-12  Score=84.43  Aligned_cols=56  Identities=25%  Similarity=0.300  Sum_probs=44.1

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN   97 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~   97 (99)
                      .|++|..+.|+|.++|.|||++|+||++....  .    ..      ....++.++|||++|.+|+..
T Consensus        17 eLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~--~----~~------~~~~~~~v~IRG~~I~~I~lp   72 (81)
T cd01725          17 ELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE--K----YP------HMLSVKNCFIRGSVVRYVQLP   72 (81)
T ss_pred             EECCCcEEEEEEEEECCCcccEEEEEEEEcCC--C----cc------cccccCeEEEECCEEEEEEeC
Confidence            46899999999999999999999999876321  0    00      013579999999999999854

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.

>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]

Probab=99.39  E-value=2.4e-13  Score=86.60  Aligned_cols=56  Identities=18%  Similarity=0.294  Sum_probs=48.4

Q ss_pred             hhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeCC
Q 034273           29 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP   98 (99)
Q Consensus        29 ~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~p   98 (99)
                      .+|++|.++.|+|++.|.||||.|.+|+|++..       ..       ...+|.++||++||++|..-|
T Consensus        23 vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-------~~-------~g~lGEilIRCNNvlyi~gv~   78 (79)
T KOG3482|consen   23 VKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-------VS-------TGNLGEILIRCNNVLYIRGVP   78 (79)
T ss_pred             EEEecCcEEEEEEEEecchhheehhhhhhhhcc-------cc-------cccceeEEEEeccEEEEecCC
Confidence            367999999999999999999999999998752       21       247999999999999998765

>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]

Probab=99.35  E-value=9.6e-13  Score=85.39  Aligned_cols=67  Identities=21%  Similarity=0.515  Sum_probs=53.2

Q ss_pred             cccCCChhhhhhhhcC------------CeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEE
Q 034273           18 EFNTGPLSVLMMSVKN------------NTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMF   85 (99)
Q Consensus        18 ~~~~~Pl~vL~~~lk~------------gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~   85 (99)
                      ..+..|+.+|-..|++            +-.+.|.++|||+|||+||+||+|.....        +     ..+.+|.++
T Consensus         8 kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~--------~-----~rk~lGRil   74 (88)
T KOG1774|consen    8 KVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT--------K-----SRKELGRIL   74 (88)
T ss_pred             ceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc--------c-----CCCccccEE
Confidence            4567899998887743            45699999999999999999999975321        0     123799999


Q ss_pred             EeCCcEEEEEeC
Q 034273           86 LRGDSVIIVLRN   97 (99)
Q Consensus        86 IRGdnVv~V~~~   97 (99)
                      ++||||.+|...
T Consensus        75 LKGDnItli~~~   86 (88)
T KOG1774|consen   75 LKGDNITLIQSA   86 (88)
T ss_pred             EcCCcEEEEeec
Confidence            999999999764

>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]

Probab=99.33  E-value=5.5e-13  Score=85.66  Aligned_cols=66  Identities=24%  Similarity=0.488  Sum_probs=54.3

Q ss_pred             CCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273           21 TGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI   92 (99)
Q Consensus        21 ~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv   92 (99)
                      --|+.++.+++        ++.+++.|+|+|||.|.|++|+||+|+-..+.    ++       +-.+++++++.|+||.
T Consensus         6 llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e----gr-------~~tk~~~iLLnGNni~   74 (84)
T KOG1775|consen    6 LLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE----GR-------RMTKLDQILLNGNNIT   74 (84)
T ss_pred             cccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC----cc-------eeeeeeeeeecCCcEE
Confidence            36888888886        88999999999999999999999999865421    11       1246899999999999


Q ss_pred             EEEeC
Q 034273           93 IVLRN   97 (99)
Q Consensus        93 ~V~~~   97 (99)
                      ++.|.
T Consensus        75 mLvPG   79 (84)
T KOG1775|consen   75 MLVPG   79 (84)
T ss_pred             EEecC
Confidence            98774

>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]

Probab=99.18  E-value=1e-12  Score=90.76  Aligned_cols=58  Identities=26%  Similarity=0.369  Sum_probs=48.9

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeCC
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP   98 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~p   98 (99)
                      .|++||.+.|+|++||||-|++|++|.|.+....+           .+.+..|.++|||+||+++...+
T Consensus        25 lLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~-----------Y~di~~glfiIRGENVvllGeid   82 (129)
T KOG1782|consen   25 LLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNK-----------YCDIPRGLFIIRGENVVLLGEID   82 (129)
T ss_pred             EEecCcchhhhhhhHHHHHHHHHHhhhhheeecce-----------ecccCceEEEEecCcEEEEecCC
Confidence            46899999999999999999999999999875322           23456799999999999997654

>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]

Probab=99.12  E-value=3.2e-12  Score=81.40  Aligned_cols=54  Identities=20%  Similarity=0.389  Sum_probs=46.9

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN   97 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~   97 (99)
                      .|.+|..+.|+|.+.|.|||+.|+.++|+..       ++.       .+.+|..||||+||++|+..
T Consensus        22 Kl~sgvdyrG~l~~lDgymNiaLe~tee~~n-------gql-------~n~ygdaFirGnnVlyIs~~   75 (77)
T KOG1783|consen   22 KLNSGVDYRGTLVCLDGYMNIALESTEEYVN-------GQL-------KNKYGDAFIRGNNVLYISTQ   75 (77)
T ss_pred             EecCCccccceehhhhhHHHHHHHHHHHHhc-------Ccc-------cccccceeeccccEEEEEec
Confidence            5688999999999999999999999999864       333       36789999999999999875

>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]

Probab=99.05  E-value=5.1e-11  Score=78.72  Aligned_cols=67  Identities=16%  Similarity=0.397  Sum_probs=52.1

Q ss_pred             cccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273           18 EFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN   97 (99)
Q Consensus        18 ~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~   97 (99)
                      .|+++-+++++.   +||.+.|.|+|||+-.||+|+++.|++.....   +.+       ...+|..+|||+||.+|.+.
T Consensus         7 ~y~n~~V~vIt~---DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~---gv~-------q~~lGlyiirgeNva~ig~i   73 (96)
T KOG1784|consen    7 DYMNQRVSVITN---DGRVIVGSLKGFDQTTNLIIDESHERIFSETE---GVE-------QIVLGLYIIRGENVAVIGEI   73 (96)
T ss_pred             HHhhceEEEEec---CCeEEEEEeccccccceeeehhhHhhhhhhhc---chh-------heeeEEEEEecCccceeeec
Confidence            355555666555   69999999999999999999999998764221   222       35789999999999998763

>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=98.88  E-value=5.7e-10  Score=69.74  Aligned_cols=27  Identities=33%  Similarity=0.450  Sum_probs=25.1

Q ss_pred             eEEEEEEEEecCeeceEeeceEEEeec
Q 034273           35 TQLLGRVRAFDRHCNMVLENVREMWTE   61 (99)
Q Consensus        35 r~i~G~L~afD~hmNLvL~d~~E~~~~   61 (99)
                      ..++|.|.|||+||||+|.||+|.|..
T Consensus        23 G~~~G~lvAFDK~wNm~L~DV~E~y~~   49 (66)
T cd01739          23 GVCSGFLVAFDKFWNMALVDVDETYRK   49 (66)
T ss_pred             cEEEEEEEeeeeehhheehhhhhhhcc
Confidence            479999999999999999999999864

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.

>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]

Probab=98.48  E-value=1.8e-07  Score=64.94  Aligned_cols=61  Identities=25%  Similarity=0.326  Sum_probs=49.7

Q ss_pred             CChhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 034273           22 GPLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII   93 (99)
Q Consensus        22 ~Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~   93 (99)
                      .||++|+.+        |++|-.|.|.|+..|.+|||.|.+|+++...      +.+       --.+..+.|||.+|-+
T Consensus         2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~D------gdk-------f~r~pEcYirGttIky   68 (134)
T KOG3293|consen    2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSED------GDK-------FFRMPECYIRGTTIKY   68 (134)
T ss_pred             cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccC------CCc-------eeecceeEEecceeEE
Confidence            588888877        4899999999999999999999999987542      111       1236889999999988


Q ss_pred             EE
Q 034273           94 VL   95 (99)
Q Consensus        94 V~   95 (99)
                      |.
T Consensus        69 lr   70 (134)
T KOG3293|consen   69 LR   70 (134)
T ss_pred             Ee
Confidence            75

>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]

Probab=98.09  E-value=1e-05  Score=53.52  Aligned_cols=56  Identities=23%  Similarity=0.342  Sum_probs=42.6

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN   97 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~   97 (99)
                      .|+++-.+.|+|.+.|+|.||-|.|+.-.-..  +        .|..  -.+..+||||..|-+|...
T Consensus        18 eLKnd~~i~GtL~svDqyLNlkL~di~v~d~~--k--------yPhm--~Sv~ncfIRGSvvrYv~l~   73 (96)
T KOG3448|consen   18 ELKNDLSICGTLHSVDQYLNLKLTDISVTDPD--K--------YPHM--LSVKNCFIRGSVVRYVQLP   73 (96)
T ss_pred             EEcCCcEEEEEecccchhheeEEeeeEeeCcc--c--------CCCe--eeeeeEEEeccEEEEEEeC
Confidence            46889999999999999999999997654211  1        1111  3567899999999988654

>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]

Probab=97.71  E-value=9.6e-05  Score=50.46  Aligned_cols=60  Identities=17%  Similarity=0.358  Sum_probs=45.7

Q ss_pred             CChhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 034273           22 GPLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII   93 (99)
Q Consensus        22 ~Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~   93 (99)
                      -|+.+|..+        +..|..|.|.|.-.+.+||++|+|++-+...      +.        .-++.++||||+.|-+
T Consensus         5 vpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d------g~--------vs~le~V~IRGS~IRF   70 (119)
T KOG3172|consen    5 VPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD------GR--------VSQLEQVFIRGSKIRF   70 (119)
T ss_pred             cceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccC------Cc--------ceeeeeEEEecCeEEE
Confidence            355555444        3778899999999999999999998865431      11        1368999999999977


Q ss_pred             EE
Q 034273           94 VL   95 (99)
Q Consensus        94 V~   95 (99)
                      +.
T Consensus        71 lv   72 (119)
T KOG3172|consen   71 LV   72 (119)
T ss_pred             EE
Confidence            64

>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]

Probab=96.80  E-value=0.0035  Score=42.75  Aligned_cols=51  Identities=22%  Similarity=0.368  Sum_probs=40.7

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL   95 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~   95 (99)
                      .|++|+.+.|++.+.|.+||..|.++.=+..       +.        ...+..++|||+||-++.
T Consensus        18 eLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-------~~--------pv~l~~lsirgnniRy~~   68 (109)
T KOG3428|consen   18 ELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-------GE--------PVRLDTLSIRGNNIRYYI   68 (109)
T ss_pred             EecCCcEEeeeEEEEEhhheeEEEEEEEecC-------CC--------ceeEEEEEeecceEEEEE
Confidence            4589999999999999999999999874432       11        125788999999998764

>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=90.41  E-value=0.3  Score=30.12  Aligned_cols=25  Identities=24%  Similarity=0.442  Sum_probs=21.2

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeec
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLEN   54 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d   54 (99)
                      .|.+|-.+.|.+.|||+|+=|+-.+
T Consensus        17 ~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716          17 YLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             EEeCCcEEEEEEEEEcceEEEEEEC
Confidence            5678999999999999999666554

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

>TIGR02383 Hfq RNA chaperone Hfq

Probab=89.32  E-value=0.4  Score=29.60  Aligned_cols=25  Identities=24%  Similarity=0.364  Sum_probs=21.1

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeec
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLEN   54 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d   54 (99)
                      .|.+|-.+.|.+.|||+|+=|+-.+
T Consensus        21 ~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383        21 FLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             EEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            5678999999999999999766544

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.

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=88.84  E-value=0.44  Score=30.85  Aligned_cols=26  Identities=19%  Similarity=0.368  Sum_probs=22.0

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeece
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENV   55 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~   55 (99)
                      .|.+|-.+.|.+.|||+|+=|+-.+-
T Consensus        25 fL~NG~~l~G~I~~fD~ftVll~~~g   50 (79)
T PRK00395         25 YLVNGIKLQGQIESFDNFVVLLRNTG   50 (79)
T ss_pred             EEeCCcEEEEEEEEEccEEEEEEECC
Confidence            56789999999999999997776554

>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=87.02  E-value=2.3  Score=27.16  Aligned_cols=68  Identities=21%  Similarity=0.296  Sum_probs=46.0

Q ss_pred             cccCCChhhhhhhhcCCeEEEEEEEEecCee-ceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273           18 EFNTGPLSVLMMSVKNNTQLLGRVRAFDRHC-NMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI   92 (99)
Q Consensus        18 ~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hm-NLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv   92 (99)
                      .+...+++++.+.   +-.++|.|..+|..- -+.|.||..+-++..+....  .. +. ...-+..++.||..|-
T Consensus         3 ~~IG~~isLISk~---~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~--~i-pp-~~~vyd~IvFrgsDIk   71 (74)
T cd01736           3 PYIGSKISLISKS---DIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGP--EI-PP-SDEVYDYIVFRGSDIK   71 (74)
T ss_pred             cccCceEEEEecC---CcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCC--cc-CC-CCcceeEEEEcCCccc
Confidence            4667777777765   788999999999887 56799998876653322111  00 01 1234688999998874

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.

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

Probab=85.24  E-value=3.6  Score=27.27  Aligned_cols=70  Identities=20%  Similarity=0.273  Sum_probs=47.0

Q ss_pred             cccCCChhhhhhhhcCCeEEEEEEEEecC-eeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273           18 EFNTGPLSVLMMSVKNNTQLLGRVRAFDR-HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL   95 (99)
Q Consensus        18 ~~~~~Pl~vL~~~lk~gr~i~G~L~afD~-hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~   95 (99)
                      .|....++++.+.   +-.|+|+|...|. -.++.|.+|.-+-++.++......     -....+..+.+||..|--+.
T Consensus         5 ~~IGs~ISlisk~---~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ip-----p~~~v~~~I~Fr~sDIkdL~   75 (96)
T PF12701_consen    5 PYIGSKISLISKS---DIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIP-----PSDEVYDYIVFRGSDIKDLK   75 (96)
T ss_dssp             CCTTCEEEEEETT---TEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS--------C-CSSSSEEEEETTTEEEEE
T ss_pred             cccCCEEEEEECC---CcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccC-----CCCceeeEEEEEccccceEE
Confidence            4556666776654   7899999999998 679999999987664322111000     11234689999999886554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	99
1b34_B	118	Crystal Structure Of The D1d2 Sub-Complex From The		2e-27
4emg_A	93	Crystal Structure Of Splsm3 Length = 93		5e-06

>pdb|1B34|B Chain B, Crystal Structure Of The D1d2 Sub-Complex From The Human Snrnp Core Domain Length = 118

Iteration: 1
 Score =  117 bits (292), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 70/90 (77%), Positives = 77/90 (85%), Gaps = 10/90 (11%)
Query: 19  FNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKG 68
           FNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKG
Sbjct: 24  FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 83
Query: 69  KKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
           KKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct: 84  KKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113

>pdb|4EMG|A Chain A, Crystal Structure Of Splsm3 Length = 93

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 25 SVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKM 84
           ++ + ++ + +L GR+ A+D H N VL +  E+ T        K KAL   +  +   +
Sbjct: 20 EIVYVKLRGDRELNGRLHAYDEHLNXVLGDAEEIVTIFDDEETDKDKALKTIRKHY-EXL 78
Query: 85 FLRGDSVIIV 94
          F+RGDSVI++
Sbjct: 79 FVRGDSVILI 88

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	99
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	6e-33
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	6e-21
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	4e-19
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	1e-15
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	6e-07
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	2e-06
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	4e-06
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	4e-06
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	5e-06
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	5e-06
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	9e-06
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	2e-05
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	2e-05
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	1e-04
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	2e-04
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	3e-04

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

 Score =  109 bits (274), Expect = 6e-33
 Identities = 75/96 (78%), Positives = 82/96 (85%), Gaps = 10/96 (10%)

Query: 13  KTEEEEFNTGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTEL 62
           K EEEEFNTGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+
Sbjct: 18  KREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEV 77

Query: 63  PKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 98
           PK+GKGKKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct: 78  PKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113

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

 Score = 78.7 bits (194), Expect = 6e-21
 Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 9/88 (10%)

Query: 15 EEEEFNTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTG 66
          E  +    PL ++ +S+        + + +L GR+ A+D H NMVL +  E+ T      
Sbjct: 2  ESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEE 61

Query: 67 KGKKKALPVNKDRFISKMFLRGDSVIIV 94
            K KAL   + +    +F+RGDSVI++
Sbjct: 62 TDKDKALKTIR-KHYEMLFVRGDSVILI 88

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

 Score = 74.6 bits (183), Expect = 4e-19
 Identities = 23/103 (22%), Positives = 45/103 (43%), Gaps = 9/103 (8%)

Query: 1   MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVL 52
           MS      + GG  ++      PL+++   +        K + +  G +R FD + NMVL
Sbjct: 7   MSETPANKSQGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVL 66

Query: 53  ENVREMWTEL-PKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 94
           ++V+E   +   +   G  K L       +  + L G++V ++
Sbjct: 67  DDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAML 109

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

 Score = 65.5 bits (160), Expect = 1e-15
 Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 15/88 (17%)

Query: 15 EEEEFNTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTG 66
                  PL +L +++        +    L+G ++AFD HCN+VL +  E   +L    
Sbjct: 3  HHHHHMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEE 62

Query: 67 KGKKKALPVNKDRFISKMFLRGDSVIIV 94
            + +       R    +F+RGD+V ++
Sbjct: 63 LSESE-------RRCEMVFIRGDTVTLI 83

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

 Score = 42.3 bits (100), Expect = 6e-07
 Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 14/63 (22%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          K   +  GR+  +D H N+VL +   +                    +   K+ +RGD+V
Sbjct: 22 KKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVV--------------KRYGKIVIRGDNV 67

Query: 92 IIV 94
          + +
Sbjct: 68 LAI 70

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

 Score = 41.8 bits (98), Expect = 2e-06
 Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 13/63 (20%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          K+  +  G +  FD + N+VL++V    TE        +K          S+M L G+ +
Sbjct: 38 KSEREFAGTLVGFDDYVNIVLKDV----TEYDTVTGVTEK---------HSEMLLNGNGM 84

Query: 92 IIV 94
           ++
Sbjct: 85 CML 87

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

 Score = 40.4 bits (95), Expect = 4e-06
 Identities = 13/63 (20%), Positives = 28/63 (44%), Gaps = 14/63 (22%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          K + +  G +++FD H N+VL +  E+                    R +  + +RGD++
Sbjct: 33 KGDREFRGVLKSFDLHMNLVLNDAEELEDGEVT--------------RRLGTVLIRGDNI 78

Query: 92 IIV 94
          + +
Sbjct: 79 VYI 81

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

 Score = 40.3 bits (95), Expect = 4e-06
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 14/63 (22%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          K   +  G +  +D H N+VL +  E+     + G+  +K         +  + +RGD+V
Sbjct: 22 KGGREFRGTLDGYDIHMNLVLLDAEEI-----QNGEVVRK---------VGSVVIRGDTV 67

Query: 92 IIV 94
          + V
Sbjct: 68 VFV 70

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

 Score = 40.0 bits (94), Expect = 5e-06
 Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 14/63 (22%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          K N ++ G +R++D+H N+VL +  E+ ++                 + +  + +RGD+V
Sbjct: 27 KGNKEVRGMLRSYDQHMNLVLSDSEEIQSD--------------GSGKKLGTIVIRGDNV 72

Query: 92 IIV 94
          I++
Sbjct: 73 ILI 75

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

 Score = 40.7 bits (95), Expect = 5e-06
 Identities = 12/63 (19%), Positives = 27/63 (42%), Gaps = 7/63 (11%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
              Q+ G ++ FD+  N+VL++V E                     R +  + +RG ++
Sbjct: 41 TGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAI-------RKLGLVVVRGTTL 93

Query: 92 IIV 94
          +++
Sbjct: 94 VLI 96

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

 Score = 39.3 bits (92), Expect = 9e-06
 Identities = 13/63 (20%), Positives = 30/63 (47%), Gaps = 15/63 (23%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          +++ ++ G +R+FD+H N++LE+  E+                         M +RG++V
Sbjct: 29 RDSHEIRGILRSFDQHVNLLLEDAEEIIDG---------------NVYKRGTMVVRGENV 73

Query: 92 IIV 94
          + +
Sbjct: 74 LFI 76

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

 Score = 39.1 bits (91), Expect = 2e-05
 Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          ++    +G  +AFD+H N++L +  E     PK  K  ++     + R +  + LRG+++
Sbjct: 22 QDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAER----EEKRVLGLVLLRGENL 77

Query: 92 IIV 94
          + +
Sbjct: 78 VSM 80

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

 Score = 38.6 bits (90), Expect = 2e-05
 Identities = 13/63 (20%), Positives = 32/63 (50%), Gaps = 13/63 (20%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          + N ++ G +  FD + N+VL++      E+    K +K+         + ++ L+GD++
Sbjct: 38 QVNMRIEGCIIGFDEYMNLVLDDA----EEIHSKTKSRKQ---------LGRIMLKGDNI 84

Query: 92 IIV 94
           ++
Sbjct: 85 TLL 87

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

 Score = 36.1 bits (84), Expect = 1e-04
 Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 14/62 (22%)

Query: 33 NNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 92
             QL+G++   D + N+ L N  E   E               K R + ++ LRG++V+
Sbjct: 25 EENQLVGKLEGVDDYMNLYLTNAMECKGE--------------EKVRSLGEIVLRGNNVV 70

Query: 93 IV 94
          ++
Sbjct: 71 LI 72

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

 Score = 35.8 bits (83), Expect = 2e-04
 Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 14/63 (22%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
               + G +R FD   N+V++   EM                  +   I  + +RG+S+
Sbjct: 22 NGGRHVQGILRGFDPFMNLVIDECVEM--------------ATSGQQNNIGMVVIRGNSI 67

Query: 92 IIV 94
          I++
Sbjct: 68 IML 70

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

 Score = 35.4 bits (82), Expect = 3e-04
 Identities = 13/63 (20%), Positives = 21/63 (33%), Gaps = 14/63 (22%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
           +     G +   D + N+ LE   E        GK                 F+RG++V
Sbjct: 22 SSGVDYKGILSCLDGYMNLALERTEEY-----VNGKKTNV---------YGDAFIRGNNV 67

Query: 92 IIV 94
          + V
Sbjct: 68 LYV 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	99
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.91
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.84
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.83
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.83
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.83
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.81
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.79
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.79
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.79
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.78
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.78
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.77
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.77
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.77
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.76
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.76
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.75
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.75
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.74
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.7
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.69
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.68
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.6
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.58
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	94.72
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	91.53
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	90.44
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	89.84
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	89.81
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	89.7
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	87.86
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	86.37
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	83.48

>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=99.91  E-value=9.8e-25  Score=148.27  Aligned_cols=88  Identities=82%  Similarity=1.281  Sum_probs=56.4

Q ss_pred             CccccccccCCChhhhhhhh----------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeee
Q 034273           12 GKTEEEEFNTGPLSVLMMSV----------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFI   81 (99)
Q Consensus        12 ~~~~~~~~~~~Pl~vL~~~l----------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~l   81 (99)
                      ++||+++++.+|+++|..++          ++|+.+.|+|+|||+||||+|+||+|++...++.+++....+...++|++
T Consensus        17 ~~~e~~~~~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~l   96 (118)
T 1b34_B           17 QKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYI   96 (118)
T ss_dssp             ---------CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEE
T ss_pred             hhhhhhhcccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCc
Confidence            57899999999999998875          78999999999999999999999999986543332221111223446889


Q ss_pred             ceEEEeCCcEEEEEeCCC
Q 034273           82 SKMFLRGDSVIIVLRNPK   99 (99)
Q Consensus        82 g~i~IRGdnVv~V~~~p~   99 (99)
                      |.+||||+||++|++.|+
T Consensus        97 g~v~IRG~nVv~I~~~~~  114 (118)
T 1b34_B           97 SKMFLRGDSVIVVLRNPL  114 (118)
T ss_dssp             EEEEECGGGEEEEEECCC
T ss_pred             CeEEEcCCEEEEEEeCch
Confidence            999999999999999874

>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=6.6e-21  Score=124.82  Aligned_cols=79  Identities=29%  Similarity=0.476  Sum_probs=56.2

Q ss_pred             ccCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 034273           19 FNTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS   90 (99)
Q Consensus        19 ~~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn   90 (99)
                      ....|+.+|+.++        ++|+.+.|+|+|||+||||+|+||+|++...+++++..+ ......+|++|++||||+|
T Consensus         6 ~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~-~~~~~~~r~lG~v~iRG~n   84 (93)
T 4emg_A            6 AVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKD-KALKTIRKHYEMLFVRGDS   84 (93)
T ss_dssp             ---CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC---------------CEEEEEEEEEECGGG
T ss_pred             ccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCcccc-ccccccEeEeceEEECCCe
Confidence            3468999998864        899999999999999999999999999875443321100 0011235899999999999


Q ss_pred             EEEEEeCC
Q 034273           91 VIIVLRNP   98 (99)
Q Consensus        91 Vv~V~~~p   98 (99)
                      |++|+|.-
T Consensus        85 Vv~I~p~~   92 (93)
T 4emg_A           85 VILIAPPR   92 (93)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEecC
Confidence            99999853

>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=99.83  E-value=1.1e-20  Score=124.16  Aligned_cols=73  Identities=29%  Similarity=0.552  Sum_probs=59.3

Q ss_pred             ccCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 034273           19 FNTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS   90 (99)
Q Consensus        19 ~~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn   90 (99)
                      .++.|+..|...+        ++||.+.|+|+|||+||||+|+||+|++...++...       ....|.+|.+||||+|
T Consensus         7 ~~~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~-------~~~~r~lG~v~IRG~n   79 (96)
T 3bw1_A            7 HMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEEL-------SESERRCEMVFIRGDT   79 (96)
T ss_dssp             CCCCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCC-------CEEEEEEEEEEECGGG
T ss_pred             hhhhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEecccccccc-------CcceeEcCEEEECCCE
Confidence            4667888887665        899999999999999999999999999875432110       1235789999999999


Q ss_pred             EEEEEeCC
Q 034273           91 VIIVLRNP   98 (99)
Q Consensus        91 Vv~V~~~p   98 (99)
                      |++|++.+
T Consensus        80 Vv~I~~~d   87 (96)
T 3bw1_A           80 VTLISTPS   87 (96)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEecC
Confidence            99999875

>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=99.83  E-value=7.4e-21  Score=124.66  Aligned_cols=71  Identities=18%  Similarity=0.446  Sum_probs=57.2

Q ss_pred             cccccCCChhhhhhhh------------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeece
Q 034273           16 EEEFNTGPLSVLMMSV------------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISK   83 (99)
Q Consensus        16 ~~~~~~~Pl~vL~~~l------------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~   83 (99)
                      ....+..|+++|..++            ++|++++|+|+|||+||||+|+||+|++..      +.       ..+.+|.
T Consensus        10 ~~~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~------~~-------~~~~lg~   76 (92)
T 3s6n_E           10 VQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSK------TK-------SRKQLGR   76 (92)
T ss_dssp             ----CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSS------SC-------CEEEEEE
T ss_pred             cceeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecC------CC-------ceeEcCe
Confidence            3457889999998775            789999999999999999999999998742      11       2478999


Q ss_pred             EEEeCCcEEEEEeCCC
Q 034273           84 MFLRGDSVIIVLRNPK   99 (99)
Q Consensus        84 i~IRGdnVv~V~~~p~   99 (99)
                      +||||+||++|++.+|
T Consensus        77 v~iRG~nV~~i~~~~~   92 (92)
T 3s6n_E           77 IMLKGDNITLLQSVSN   92 (92)
T ss_dssp             EEECGGGEEEEEEC--
T ss_pred             EEEeCCEEEEEEeCCC
Confidence            9999999999999876

>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=99.83  E-value=4e-21  Score=130.98  Aligned_cols=96  Identities=23%  Similarity=0.346  Sum_probs=58.4

Q ss_pred             CCCcccccccCCccccccccCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCC---CCc
Q 034273            1 MSRAMDEDTTGGKTEEEEFNTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTG---KGK   69 (99)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~---~~~   69 (99)
                      ||.+|.-.+.+..-.-......|+.+|...+        ++||++.|+|+|||+||||+|+||+|++...++..   .+.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~   86 (121)
T 2fwk_A            7 MSETPANKSQGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNK   86 (121)
T ss_dssp             -----------------CCCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC------------
T ss_pred             hhhhhhccCccccccccccccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCc
Confidence            4555554332211012335679999998775        89999999999999999999999999986421110   011


Q ss_pred             cccccCcceeeeceEEEeCCcEEEEEeCC
Q 034273           70 KKALPVNKDRFISKMFLRGDSVIIVLRNP   98 (99)
Q Consensus        70 ~~~~~~~~~r~lg~i~IRGdnVv~V~~~p   98 (99)
                      ..  ...+.+.+|++||||+||++|++.+
T Consensus        87 ~~--~~~~~r~lG~v~IRG~nVv~I~~~~  113 (121)
T 2fwk_A           87 KL--KRVMVNRLETILLSGNNVAMLVPGG  113 (121)
T ss_dssp             -----CEECCCCSEEEECGGGEEEEESSS
T ss_pred             cc--ccccceEcceEEECCCEEEEEEecC
Confidence            10  0112578999999999999999865

>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=99.81  E-value=4.9e-20  Score=121.27  Aligned_cols=68  Identities=24%  Similarity=0.367  Sum_probs=55.7

Q ss_pred             cccCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCC
Q 034273           18 EFNTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD   89 (99)
Q Consensus        18 ~~~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd   89 (99)
                      ..+..|+.+|..++        ++|+++.|+|+|||+||||+|+||+|++..      +.       ..+.+|.+||||+
T Consensus        16 ~~~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~------~~-------~~~~lg~v~IRG~   82 (94)
T 4emk_A           16 SMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTV------TG-------VTEKHSEMLLNGN   82 (94)
T ss_dssp             ----CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETT------TC-------CEEEEEEEEECST
T ss_pred             cccccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecC------CC-------cEeEcCEEEEcCC
Confidence            45678999998885        899999999999999999999999999731      11       1478999999999


Q ss_pred             cEEEEEeCC
Q 034273           90 SVIIVLRNP   98 (99)
Q Consensus        90 nVv~V~~~p   98 (99)
                      ||++|++..
T Consensus        83 nI~~i~p~~   91 (94)
T 4emk_A           83 GMCMLIPGG   91 (94)
T ss_dssp             TEEEEEECC
T ss_pred             EEEEEEeCC
Confidence            999999864

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

Probab=99.79  E-value=2e-19  Score=112.82  Aligned_cols=64  Identities=27%  Similarity=0.440  Sum_probs=53.8

Q ss_pred             CCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273           21 TGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI   92 (99)
Q Consensus        21 ~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv   92 (99)
                      ..|+.+|...+        ++|+.+.|+|+|||+||||+|+||+|++..       .       ..+.+|.+||||+||+
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------~-------~~~~lg~v~iRG~~I~   68 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG-------E-------VVKRYGKIVIRGDNVL   68 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETT-------E-------EEEEEEEEEECGGGEE
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeC-------C-------ceeECCEEEECCCEEE
Confidence            46777777664        899999999999999999999999998741       1       2478999999999999


Q ss_pred             EEEeCC
Q 034273           93 IVLRNP   98 (99)
Q Consensus        93 ~V~~~p   98 (99)
                      +|++..
T Consensus        69 ~i~~~~   74 (75)
T 1h64_1           69 AISPTE   74 (75)
T ss_dssp             EEEEC-
T ss_pred             EEEeCC
Confidence            999854

>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=99.79  E-value=2.2e-19  Score=113.01  Aligned_cols=64  Identities=31%  Similarity=0.525  Sum_probs=54.7

Q ss_pred             CCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273           21 TGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI   92 (99)
Q Consensus        21 ~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv   92 (99)
                      ..|+++|...+        ++|+.+.|+|+|||+||||+|+||+|++..       .       ..+++|.+||||+||+
T Consensus         3 ~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------~-------~~~~lg~v~iRG~~I~   68 (77)
T 1i4k_A            3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG-------E-------VVRKVGSVVIRGDTVV   68 (77)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETT-------E-------EEEEEEEEEECGGGEE
T ss_pred             ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecC-------C-------cEeECCEEEECCCEEE
Confidence            46888887664        899999999999999999999999998741       1       2478999999999999


Q ss_pred             EEEeCC
Q 034273           93 IVLRNP   98 (99)
Q Consensus        93 ~V~~~p   98 (99)
                      +|++.+
T Consensus        69 ~i~~~d   74 (77)
T 1i4k_A           69 FVSPAP   74 (77)
T ss_dssp             EEEECC
T ss_pred             EEEeCC
Confidence            998754

>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=99.79  E-value=3.2e-19  Score=114.19  Aligned_cols=63  Identities=27%  Similarity=0.505  Sum_probs=54.8

Q ss_pred             cCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 034273           20 NTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV   91 (99)
Q Consensus        20 ~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV   91 (99)
                      ...|+.+|...+        ++|+.+.|+|+|||+||||+|+||+|++..       .       ..+.+|.+||||+||
T Consensus        13 ~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------~-------~~~~lg~v~IRG~~I   78 (83)
T 1mgq_A           13 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG-------E-------VTRRLGTVLIRGDNI   78 (83)
T ss_dssp             TTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETT-------E-------EEEEEEEEEECGGGE
T ss_pred             CcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecC-------C-------cccCCCEEEECCCEE
Confidence            468999888765        899999999999999999999999998741       1       247899999999999


Q ss_pred             EEEEe
Q 034273           92 IIVLR   96 (99)
Q Consensus        92 v~V~~   96 (99)
                      ++|+|
T Consensus        79 ~~i~p   83 (83)
T 1mgq_A           79 VYISP   83 (83)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            99986

>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=99.78  E-value=2.2e-19  Score=114.33  Aligned_cols=66  Identities=27%  Similarity=0.506  Sum_probs=55.3

Q ss_pred             ccCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 034273           19 FNTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS   90 (99)
Q Consensus        19 ~~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn   90 (99)
                      ....|+.+|...+        ++|+.+.|+|+|||+||||+|+||+|++..       .       ..+.+|.+||||+|
T Consensus         6 ~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------~-------~~~~lg~v~iRG~~   71 (81)
T 1th7_A            6 LAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD-------G-------SGKKLGTIVIRGDN   71 (81)
T ss_dssp             TCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSS-------S-------CEEEEEEEEECGGG
T ss_pred             cccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecC-------C-------ceeECCEEEECCCE
Confidence            4457888887664        899999999999999999999999998742       1       14789999999999


Q ss_pred             EEEEEeCC
Q 034273           91 VIIVLRNP   98 (99)
Q Consensus        91 Vv~V~~~p   98 (99)
                      |++|++.+
T Consensus        72 I~~i~~~~   79 (81)
T 1th7_A           72 VILISPLQ   79 (81)
T ss_dssp             EEEEEEC-
T ss_pred             EEEEEecC
Confidence            99998764

>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=99.78  E-value=3.6e-19  Score=115.26  Aligned_cols=74  Identities=20%  Similarity=0.395  Sum_probs=54.9

Q ss_pred             ccccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           17 EEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        17 ~~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      ..+...++.+   .+++||++.|+|+|||+||||+|+||+|++...+++.+..    .....+.+|.+||||+||++|++
T Consensus        10 ~~~~~k~V~V---~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~----~~~~~~~lg~v~iRG~~I~~i~~   82 (91)
T 1d3b_B           10 LQHIDYRMRC---ILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQA----EREEKRVLGLVLLRGENLVSMTV   82 (91)
T ss_dssp             GGGTTSEEEE---EETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSC----CEEEEEEEEEEEECGGGEEEEEE
T ss_pred             HHHcCCcEEE---EECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccc----cCccEeECCEEEECCCeEEEEEc
Confidence            3455555444   6789999999999999999999999999875432211100    01235889999999999999986


Q ss_pred             C
Q 034273           97 N   97 (99)
Q Consensus        97 ~   97 (99)
                      .
T Consensus        83 ~   83 (91)
T 1d3b_B           83 E   83 (91)
T ss_dssp             E
T ss_pred             C
Confidence            4

>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=99.77  E-value=5.7e-19  Score=111.30  Aligned_cols=64  Identities=28%  Similarity=0.420  Sum_probs=54.4

Q ss_pred             cCCChhhhhhhh--------cCC-eEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 034273           20 NTGPLSVLMMSV--------KNN-TQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS   90 (99)
Q Consensus        20 ~~~Pl~vL~~~l--------k~g-r~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn   90 (99)
                      +..|+.+|...+        ++| +++.|+|+|||+||||+|+||+|++..       .       ..+.+|.+||||+|
T Consensus         3 m~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~-------~-------~~~~lg~v~iRG~n   68 (77)
T 1ljo_A            3 MVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE-------E-------KVRSLGEIVLRGNN   68 (77)
T ss_dssp             CCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETT-------E-------EEEEEEEEEECGGG
T ss_pred             ccchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecC-------C-------cEeECCeEEEeCCe
Confidence            347888887664        899 999999999999999999999998731       1       24789999999999


Q ss_pred             EEEEEeC
Q 034273           91 VIIVLRN   97 (99)
Q Consensus        91 Vv~V~~~   97 (99)
                      |++|++.
T Consensus        69 I~~i~~~   75 (77)
T 1ljo_A           69 VVLIQPQ   75 (77)
T ss_dssp             EEEEEEC
T ss_pred             EEEEEeC
Confidence            9999875

>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=99.77  E-value=2.5e-19  Score=112.68  Aligned_cols=64  Identities=25%  Similarity=0.388  Sum_probs=53.3

Q ss_pred             CCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273           21 TGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI   92 (99)
Q Consensus        21 ~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv   92 (99)
                      ..|+++|+..+        ++|+.+.|+|.|||+||||+|+||+|++.       +.       ..+.+|.++|||+||+
T Consensus         3 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-------~~-------~~~~lg~v~iRG~~I~   68 (75)
T 4emk_B            3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVN-------GK-------KTNVYGDAFIRGNNVL   68 (75)
T ss_dssp             SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEET-------TE-------EEEEEEEEEEEGGGSS
T ss_pred             CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEec-------CC-------cccEecEEEEcCCeEE
Confidence            45777777664        89999999999999999999999999863       11       1368999999999999


Q ss_pred             EEEeCC
Q 034273           93 IVLRNP   98 (99)
Q Consensus        93 ~V~~~p   98 (99)
                      +|++..
T Consensus        69 ~i~~~~   74 (75)
T 4emk_B           69 YVSALD   74 (75)
T ss_dssp             EEEEC-
T ss_pred             EEEecC
Confidence            999864

>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=99.77  E-value=1.1e-18  Score=111.15  Aligned_cols=64  Identities=25%  Similarity=0.446  Sum_probs=54.3

Q ss_pred             cCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 034273           20 NTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV   91 (99)
Q Consensus        20 ~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV   91 (99)
                      ...|+.+|..++        ++|+.+.|+|+|||+||||+|+||+|+ ..       .       ..+.+|.+||||+||
T Consensus         9 ~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~-------~-------~~~~lg~v~iRG~~I   73 (81)
T 1i8f_A            9 FATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-ID-------G-------NVYKRGTMVVRGENV   73 (81)
T ss_dssp             -CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ET-------T-------EEEEEEEEEECGGGE
T ss_pred             ccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cC-------C-------cccCCCEEEECCCEE
Confidence            568888887765        899999999999999999999999998 21       1       147899999999999


Q ss_pred             EEEEeCC
Q 034273           92 IIVLRNP   98 (99)
Q Consensus        92 v~V~~~p   98 (99)
                      ++|++..
T Consensus        74 ~~i~~~d   80 (81)
T 1i8f_A           74 LFISPVP   80 (81)
T ss_dssp             EEEEECC
T ss_pred             EEEEeCC
Confidence            9999864

>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=99.76  E-value=9.7e-19  Score=114.62  Aligned_cols=66  Identities=24%  Similarity=0.357  Sum_probs=50.9

Q ss_pred             cCCChhhhhhhh--------cCC-eEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 034273           20 NTGPLSVLMMSV--------KNN-TQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS   90 (99)
Q Consensus        20 ~~~Pl~vL~~~l--------k~g-r~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn   90 (99)
                      ...|+.+|...+        ++| +.+.|+|+|||+||||+|+||+|++.       +.       ..+.+|.+||||+|
T Consensus        19 ~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~-------~~-------~~~~lg~v~IRG~n   84 (93)
T 1n9r_A           19 PVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVA-------GV-------SHGTLGEIFIRCNN   84 (93)
T ss_dssp             -------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEET-------TE-------EEEECCSEEECGGG
T ss_pred             cCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcC-------CC-------eEeEcCEEEEcCCe
Confidence            357888887654        899 99999999999999999999999863       11       13689999999999


Q ss_pred             EEEEEeCCC
Q 034273           91 VIIVLRNPK   99 (99)
Q Consensus        91 Vv~V~~~p~   99 (99)
                      |++|.+.+|
T Consensus        85 I~~I~~~~~   93 (93)
T 1n9r_A           85 VLYIRELPN   93 (93)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEeCCC
Confidence            999998875

>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=99.76  E-value=8.1e-19  Score=131.13  Aligned_cols=79  Identities=20%  Similarity=0.393  Sum_probs=59.3

Q ss_pred             CCccccccccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 034273           11 GGKTEEEEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS   90 (99)
Q Consensus        11 ~~~~~~~~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn   90 (99)
                      +.+-+-.++.+..+.|   .|++||+|+|+|+|||+||||||+||+|++...+++.+..    ....+|++|++||||||
T Consensus         4 ~k~~kL~klIdKrV~V---~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~----~~~~~R~LGlV~IRGdn   76 (231)
T 3pgw_B            4 GKSSKMLQHIDYRMRC---ILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQA----EREEKRVLGLVLLRGEN   76 (231)
T ss_pred             CchHHHHHhcCCeEEE---EECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccc----cccceeEeceEEECCCc
Confidence            3344555666666655   6789999999999999999999999999985433321110    12346899999999999


Q ss_pred             EEEEEe
Q 034273           91 VIIVLR   96 (99)
Q Consensus        91 Vv~V~~   96 (99)
                      |++|+.
T Consensus        77 IV~Isv   82 (231)
T 3pgw_B           77 LVSMTV   82 (231)
T ss_pred             EEEEEe
Confidence            999984

>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=99.75  E-value=1.3e-18  Score=117.66  Aligned_cols=61  Identities=20%  Similarity=0.355  Sum_probs=47.4

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN   97 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~   97 (99)
                      .|++||.|.|+|+|||+||||||+||+|++....    +.   ......|.+|.+||||+||++|++.
T Consensus        39 ~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~----~~---~~~~~~r~lG~v~IRG~nIv~I~~~   99 (113)
T 4emk_C           39 TFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPE----DG---KLTGAIRKLGLVVVRGTTLVLIAPM   99 (113)
T ss_dssp             EETTSCEEEEEEEEECTTCCEEEEEEEEEC----------------CCEEEEEEEEECTTTEEEEEEC
T ss_pred             EEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCC----Cc---ccccceeEccEEEECCCeEEEEEec
Confidence            3489999999999999999999999999986311    10   0112358999999999999999975

>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=99.75  E-value=2.5e-18  Score=111.00  Aligned_cols=64  Identities=20%  Similarity=0.241  Sum_probs=54.1

Q ss_pred             CCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273           21 TGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI   92 (99)
Q Consensus        21 ~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv   92 (99)
                      ..|+.+|+..+        ++|+.+.|+|+|||+||||+|+||+|+..       +.       ..+.+|.+||||+||+
T Consensus         5 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-------g~-------~~~~lg~v~IRG~nI~   70 (86)
T 3s6n_F            5 LNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYID-------GA-------LSGHLGEVLIRCNNVL   70 (86)
T ss_dssp             CCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEET-------TE-------EEEEESSEEECGGGEE
T ss_pred             cCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcC-------Cc-------eeeEccEEEEeCCeEE
Confidence            46888887764        89999999999999999999999999752       11       1368999999999999


Q ss_pred             EEEeCC
Q 034273           93 IVLRNP   98 (99)
Q Consensus        93 ~V~~~p   98 (99)
                      +|++.+
T Consensus        71 ~i~~~d   76 (86)
T 3s6n_F           71 YIRGVE   76 (86)
T ss_dssp             EEEECC
T ss_pred             EEEeCC
Confidence            999864

>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=99.74  E-value=2.1e-18  Score=108.77  Aligned_cols=64  Identities=28%  Similarity=0.487  Sum_probs=48.3

Q ss_pred             cccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273           18 EFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN   97 (99)
Q Consensus        18 ~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~   97 (99)
                      ++...++.+   .|++|+.+.|+|.|||+||||+|+||+|++..      +        ..+.+|.++|||+||++|++.
T Consensus        11 ~~~~k~V~V---~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~------~--------~~~~lg~v~iRG~~I~~i~~~   73 (76)
T 3s6n_G           11 KFMDKKLSL---KLNGGRHVQGILRGFDPFMNLVIDECVEMATS------G--------QQNNIGMVVIRGNSIIMLEAL   73 (76)
T ss_dssp             ---CCEEEE---EETTTEEEEEEEEEECTTCCEEEEEEEECCCC------------------CBSSEEECSSSEEEEEC-
T ss_pred             HhCCCeEEE---EECCCcEEEEEEEEECCcceEEEeceEEEccC------C--------cEeEcCEEEECCCeEEEEEec
Confidence            344444444   67899999999999999999999999998642      1        136799999999999999975


Q ss_pred             C
Q 034273           98 P   98 (99)
Q Consensus        98 p   98 (99)
                      .
T Consensus        74 d   74 (76)
T 3s6n_G           74 E   74 (76)
T ss_dssp             -
T ss_pred             c
Confidence            3

>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=99.70  E-value=3.1e-17  Score=103.32  Aligned_cols=62  Identities=15%  Similarity=0.340  Sum_probs=52.4

Q ss_pred             CCChhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273           21 TGPLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI   92 (99)
Q Consensus        21 ~~Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv   92 (99)
                      ..|+.+|+.+        |++|+++.|+|.|||+|||++|+||+|+...      +        ..+.+|.+||||+||.
T Consensus         4 ~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~------~--------~~~~lg~v~IRG~nI~   69 (75)
T 1d3b_A            4 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD------G--------RVAQLEQVYIRGCKIR   69 (75)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTT------S--------CEEEEEEEEECGGGEE
T ss_pred             cCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCC------C--------cEEEcCeEEEeCCEEE
Confidence            4688888765        4999999999999999999999999998521      1        1368999999999999


Q ss_pred             EEEe
Q 034273           93 IVLR   96 (99)
Q Consensus        93 ~V~~   96 (99)
                      +|+.
T Consensus        70 ~i~l   73 (75)
T 1d3b_A           70 FLIL   73 (75)
T ss_dssp             EEEE
T ss_pred             EEEc
Confidence            9975

>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=99.69  E-value=3.1e-17  Score=109.76  Aligned_cols=64  Identities=22%  Similarity=0.359  Sum_probs=45.7

Q ss_pred             CCChhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273           21 TGPLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI   92 (99)
Q Consensus        21 ~~Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv   92 (99)
                      ..|+.+|..+        |++|+.|.|+|.|||+||||+|+||+|++..      +.       ..+.+|.+||||+||+
T Consensus        15 ~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~d------g~-------~~~~lg~v~IRG~nI~   81 (105)
T 4emh_A           15 MLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPD------GD-------KFFRLPECYIRGNNIK   81 (105)
T ss_dssp             -----------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTT------SC-------EEEEEEEEEECGGGEE
T ss_pred             CcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccC------Cc-------eeeEcCeEEEeCCeEE
Confidence            4677777665        4899999999999999999999999998531      11       1367999999999999


Q ss_pred             EEEeC
Q 034273           93 IVLRN   97 (99)
Q Consensus        93 ~V~~~   97 (99)
                      +|+..
T Consensus        82 ~I~~p   86 (105)
T 4emh_A           82 YLRIQ   86 (105)
T ss_dssp             EEEC-
T ss_pred             EEecC
Confidence            99864

>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=99.68  E-value=7.2e-17  Score=109.66  Aligned_cols=55  Identities=20%  Similarity=0.306  Sum_probs=46.6

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeCC
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP   98 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~p   98 (99)
                      .|++|++|.|+|.+||+||||+|+||+|+...      + .       .+++|.+||||+||++|++..
T Consensus        18 ~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~------~-~-------~~~lg~v~IRG~nI~~I~~pd   72 (119)
T 1b34_A           18 ELKNGTQVHGTITGVDVSMNTHLKAVKMTLKN------R-E-------PVQLETLSIRGNNIRYFILPD   72 (119)
T ss_dssp             EETTCCEEEEEEEEECTTCCEEEEEEEEECTT------S-C-------CEEEEEEEECGGGEEEEECCT
T ss_pred             EEcCCCEEEEEEEEEcccceEEeccEEEecCC------C-c-------eeEcceEEEcCCeEEEEEecc
Confidence            35899999999999999999999999998521      1 1       267999999999999998753

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

Probab=99.60  E-value=1.5e-15  Score=104.36  Aligned_cols=63  Identities=14%  Similarity=0.349  Sum_probs=52.5

Q ss_pred             CCChhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273           21 TGPLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI   92 (99)
Q Consensus        21 ~~Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv   92 (99)
                      ..|+.+|...        |++|++|.|+|.+||.||||+|+||+|+...      +.        ..+++.+||||+||+
T Consensus         4 ~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~------g~--------~~~l~~v~IRGnnI~   69 (126)
T 2y9a_D            4 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD------GR--------VAQLEQVYIRGSKIR   69 (126)
T ss_dssp             CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTT------SC--------CEEEEEEEECGGGEE
T ss_pred             ccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCC------Cc--------EeecccEEEeCCEEE
Confidence            4688888755        4999999999999999999999999998521      11        257999999999999


Q ss_pred             EEEeC
Q 034273           93 IVLRN   97 (99)
Q Consensus        93 ~V~~~   97 (99)
                      +|+..
T Consensus        70 ~I~lp   74 (126)
T 2y9a_D           70 FLILP   74 (126)
T ss_dssp             EEECC
T ss_pred             EEEcc
Confidence            99853

>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=99.58  E-value=8.2e-16  Score=106.22  Aligned_cols=51  Identities=20%  Similarity=0.287  Sum_probs=45.3

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeCC
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP   98 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~p   98 (99)
                      .|++|+.+.|+|.|||+||||+|+||+|+.        +          +.+|.+||||+||++|++..
T Consensus        16 ~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~--------~----------~~lg~v~IRG~nI~~I~~~d   66 (130)
T 1m5q_A           16 VLSNGEVYKGVLHAVDNQLNIVLANASNKA--------G----------EKFNRVFIMYRYIVHIDSTE   66 (130)
T ss_dssp             EETTSCEEEEEEEEECTTCCEEEEEEECTT--------C----------CEEEEEEECGGGEEEEEECC
T ss_pred             EECCCcEEEEEEEEEcccceeEEeeEEEEc--------C----------CEeceEEEeCCeEEEEEcCC
Confidence            678999999999999999999999999962        1          35899999999999998754

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

Probab=94.72  E-value=0.02  Score=36.64  Aligned_cols=46  Identities=26%  Similarity=0.237  Sum_probs=35.4

Q ss_pred             hhcCCeEEEEEEEEec-CeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273           30 SVKNNTQLLGRVRAFD-RHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL   95 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD-~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~   95 (99)
                      .+.+|+.++|.|.+|| ...|++|.|+-|          +          .....++|-|..|.-|-
T Consensus        23 ~l~dg~~y~G~l~tvDp~s~sIvL~n~~~----------~----------~~~~~~iI~G~aI~eI~   69 (86)
T 1y96_A           23 TASEKNEYKGWVLTTDPVSANIVLVNFLE----------D----------GSMSVTGIMGHAVQTVE   69 (86)
T ss_dssp             EETTTEEEEEEEEEECTTTCCEEEEEECT----------T----------SCEEEEEECGGGEEEEE
T ss_pred             EEcCCCEEEEEEEEECCCceEEEEeeccc----------C----------CeEEEEEEecceEEEEE
Confidence            4578999999999999 999999998811          0          12467788888776653

>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=91.53  E-value=0.082  Score=33.51  Aligned_cols=24  Identities=21%  Similarity=0.447  Sum_probs=20.1

Q ss_pred             hhcCCeEEEEEEEEecCeeceEee
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLE   53 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~   53 (99)
                      .|.+|-.+.|.+.+||+|+=|+-.
T Consensus        25 ~L~NG~~l~G~I~~fD~ftVlL~~   48 (82)
T 1u1s_A           25 YLVNGIKLQGQIESFDQFVILLKN   48 (82)
T ss_dssp             EETTSCEEEEEEEEECSSEEEEES
T ss_pred             EEeCCcEEEEEEEEEcceEEEEec
Confidence            567899999999999999865543

>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=90.44  E-value=0.12  Score=31.99  Aligned_cols=23  Identities=22%  Similarity=0.453  Sum_probs=19.4

Q ss_pred             hhcCCeEEEEEEEEecCeeceEe
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVL   52 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL   52 (99)
                      .|.+|-.+.|.+.+||+|+=++-
T Consensus        27 ~L~nG~~l~G~I~~fD~f~vlL~   49 (74)
T 2ylb_A           27 YLVNGIKLQGQIESFDQFVILLK   49 (74)
T ss_dssp             EETTSCEEEEEEEEECSSEEEEE
T ss_pred             EEeCCCEEEEEEEEECCcEEEEE
Confidence            45789999999999999985554

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

Probab=89.84  E-value=0.14  Score=32.11  Aligned_cols=22  Identities=27%  Similarity=0.474  Sum_probs=19.1

Q ss_pred             hhcCCeEEEEEEEEecCeeceE
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMV   51 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLv   51 (99)
                      .|.+|-.++|.+.+||+|+=++
T Consensus        26 ~LvnG~~L~G~I~~fD~f~VlL   47 (79)
T 3sb2_A           26 YLVNGIKLQGHVESFDQYVVLL   47 (79)
T ss_dssp             EETTSCEEEEEEEEECSSEEEE
T ss_pred             EEeCCCEEEEEEEEECCcEEEE
Confidence            5678999999999999999554

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

Probab=89.81  E-value=0.2  Score=31.37  Aligned_cols=25  Identities=28%  Similarity=0.404  Sum_probs=20.6

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeec
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLEN   54 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d   54 (99)
                      .|.+|-.+.|.+.+||+|+=|+-.+
T Consensus        29 ~L~nG~~l~G~I~~fD~f~VlL~~~   53 (78)
T 3ahu_A           29 FLLNGFQLRGQVKGFDNFTVLLESE   53 (78)
T ss_dssp             EETTSCEEEEEEEEECSSEEEEESS
T ss_pred             EEeCCeEEEEEEEEEcceEEEEEEC
Confidence            4678999999999999999665433

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

Probab=89.70  E-value=0.23  Score=30.62  Aligned_cols=25  Identities=20%  Similarity=0.081  Sum_probs=20.7

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeec
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLEN   54 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d   54 (99)
                      .|.+|-.+.|.+.|||+|+=|+-.+
T Consensus        31 ~L~NG~~l~G~I~~fD~ftVll~~~   55 (71)
T 2qtx_A           31 FLRNGEVLDAEVTGVSNYEIMVKVG   55 (71)
T ss_dssp             EETTSCEEEEEEEEECSSEEEEEET
T ss_pred             EEeCCeEEEEEEEEEcceEEEEEeC
Confidence            4678999999999999999666544

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

Probab=87.86  E-value=0.23  Score=32.70  Aligned_cols=25  Identities=20%  Similarity=0.436  Sum_probs=20.4

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeec
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLEN   54 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d   54 (99)
                      .|.+|-.++|.+.+||+|+=|+-++
T Consensus        27 ~LvNG~~L~G~I~~fD~f~VlL~~~   51 (104)
T 2y90_A           27 YLVNGIKLQGQIESFDQFVILLKNT   51 (104)
T ss_dssp             EETTSCEEEEEEEEECSSEEEEESS
T ss_pred             EEeCCCEEEEEEEEECCcEEEEECC
Confidence            4578999999999999998655543

>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=86.37  E-value=0.48  Score=29.46  Aligned_cols=25  Identities=16%  Similarity=0.203  Sum_probs=20.6

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeec
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLEN   54 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d   54 (99)
                      .|.+|-.+.|.+.+||+|+=++-.+
T Consensus        25 ~L~nG~~l~G~I~~fD~f~VlL~~~   49 (77)
T 1kq1_A           25 FFLNGFQMKGVIEEYDKYVVSLNSQ   49 (77)
T ss_dssp             EETTSCEEEEEEEEECSSEEEEEET
T ss_pred             EEeCCCEEEEEEEEECCcEEEEEEC
Confidence            4578999999999999999665544

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

Probab=83.48  E-value=6.6  Score=24.95  Aligned_cols=73  Identities=16%  Similarity=0.162  Sum_probs=50.6

Q ss_pred             ccccCCChhhhhhhhcCCeEEEEEEEEecCee-ceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273           17 EEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHC-NMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL   95 (99)
Q Consensus        17 ~~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hm-NLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~   95 (99)
                      ..+...+++++.++   +-.++|+|...|..- -+.|.+|.-+-++.++.....    +. ...-+..++.||..|--+.
T Consensus         9 ~~yIGs~iSLISk~---dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~i----pp-~~~vy~yIvFrgsDIKdL~   80 (88)
T 2vxe_A            9 LPELGSKISLISKA---DIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQI----AP-QSQIYDYILFRGSDIKDIR   80 (88)
T ss_dssp             SCCTTCEEEEEETT---TEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCC----CC-CCSCEEEEEEETTTEEEEE
T ss_pred             CcccCCeEEEEECC---CceEEEEEeeecCcccEEEEEeeeEecCcCCCCCccc----CC-CCceeeEEEEccCCccEEE
Confidence            45677778877765   889999999999764 788999998876533221111    11 1234689999999987765


Q ss_pred             eC
Q 034273           96 RN   97 (99)
Q Consensus        96 ~~   97 (99)
                      -+
T Consensus        81 V~   82 (88)
T 2vxe_A           81 VV   82 (88)
T ss_dssp             EC
T ss_pred             Ee
Confidence            43

---

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	99
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	3e-28
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	3e-14
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	1e-11
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	2e-09
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	3e-08
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	6e-08
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-07
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	1e-07
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-05
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	2e-04
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	7e-04
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	0.003

>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 96.1 bits (239), Expect = 3e-28
 Identities = 68/89 (76%), Positives = 75/89 (84%), Gaps = 10/89 (11%)

Query: 21 TGPLSVLMMSVKNNTQ----------LLGRVRAFDRHCNMVLENVREMWTELPKTGKGKK 70
          TGPLSVL  SVKNNTQ          LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKGKK
Sbjct: 1  TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKK 60

Query: 71 KALPVNKDRFISKMFLRGDSVIIVLRNPK 99
          K+ PVNKDR+ISKMFLRGDSVI+VLRNP 
Sbjct: 61 KSKPVNKDRYISKMFLRGDSVIVVLRNPL 89

>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 = 60.3 bits (146), Expect = 3e-14
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 9/81 (11%)

Query: 23 PLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGK-GKKKAL 73
          PL+++   +        K + +  G +R FD + NMVL++V+E   +  +    G  K L
Sbjct: 6  PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKL 65

Query: 74 PVNKDRFISKMFLRGDSVIIV 94
                 +  + L G++V ++
Sbjct: 66 KRVMVNRLETILLSGNNVAML 86

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.3 bits (128), Expect = 1e-11
 Identities = 15/68 (22%), Positives = 35/68 (51%), Gaps = 4/68 (5%)

Query: 27 LMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFL 86
          +   +++    +G  +AFD+H N++L +  E     PK  K  ++     + R +  + L
Sbjct: 11 MRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAER----EEKRVLGLVLL 66

Query: 87 RGDSVIIV 94
          RG++++ +
Sbjct: 67 RGENLVSM 74

>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 = 47.4 bits (113), Expect = 2e-09
 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 22/80 (27%)

Query: 23 PLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALP 74
          PL V+  S+        K   +  GR+  +D H N+VL +   +                
Sbjct: 3  PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG------------- 49

Query: 75 VNKDRFISKMFLRGDSVIIV 94
              +   K+ +RGD+V+ +
Sbjct: 50 -EVVKRYGKIVIRGDNVLAI 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 = 44.3 bits (105), Expect = 3e-08
 Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 22/80 (27%)

Query: 23 PLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALP 74
          PL VL  S+        K   +  G +  +D H N+VL +  E+                
Sbjct: 4  PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG------------- 50

Query: 75 VNKDRFISKMFLRGDSVIIV 94
              R +  + +RGD+V+ V
Sbjct: 51 -EVVRKVGSVVIRGDTVVFV 69

>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 = 43.9 bits (104), Expect = 6e-08
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 22/80 (27%)

Query: 23 PLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALP 74
          PL  L  S+        K + +  G +++FD H N+VL +  E+                
Sbjct: 7  PLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG------------- 53

Query: 75 VNKDRFISKMFLRGDSVIIV 94
              R +  + +RGD+++ +
Sbjct: 54 -EVTRRLGTVLIRGDNIVYI 72

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

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

 Score = 43.2 bits (102), Expect = 1e-07
 Identities = 14/67 (20%), Positives = 31/67 (46%), Gaps = 15/67 (22%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          +++ ++ G +R+FD+H N++LE+  E+                         M +RG++V
Sbjct: 20 RDSHEIRGILRSFDQHVNLLLEDAEEIIDG---------------NVYKRGTMVVRGENV 64

Query: 92 IIVLRNP 98
          + +   P
Sbjct: 65 LFISPVP 71

>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 = 42.8 bits (101), Expect = 1e-07
 Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 14/63 (22%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
          K N ++ G +R++D+H N+VL +  E+ ++                 + +  + +RGD+V
Sbjct: 25 KGNKEVRGMLRSYDQHMNLVLSDSEEIQSD--------------GSGKKLGTIVIRGDNV 70

Query: 92 IIV 94
          I++
Sbjct: 71 ILI 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 = 37.4 bits (87), Expect = 1e-05
 Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 14/69 (20%)

Query: 26 VLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMF 85
          + +       QL+G++   D + N+ L N  E   E               K R + ++ 
Sbjct: 18 IRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE--------------EKVRSLGEIV 63

Query: 86 LRGDSVIIV 94
          LRG++V+++
Sbjct: 64 LRGNNVVLI 72

>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 = 34.3 bits (79), Expect = 2e-04
 Identities = 11/66 (16%), Positives = 25/66 (37%), Gaps = 14/66 (21%)

Query: 33 NNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 92
          N+T+  G + + D + N+ L    E                       + ++F+R ++V+
Sbjct: 16 NSTEYRGTLVSTDNYFNLQLNEAEEFVAG--------------VSHGTLGEIFIRCNNVL 61

Query: 93 IVLRNP 98
           +   P
Sbjct: 62 YIRELP 67

>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 = 33.2 bits (76), Expect = 7e-04
 Identities = 7/63 (11%), Positives = 20/63 (31%), Gaps = 14/63 (22%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
                 G++   + + N  + N+            G+   L         ++++RG  +
Sbjct: 20 NTGEVYRGKLIEAEDNMNCQMSNITVT------YRDGRVAQLE--------QVYIRGCKI 65

Query: 92 IIV 94
            +
Sbjct: 66 RFL 68

>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 = 32.4 bits (74), Expect = 0.003
 Identities = 10/63 (15%), Positives = 21/63 (33%), Gaps = 18/63 (28%)

Query: 32 KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91
           N     G + A D   N+VL N                       ++F +++F+    +
Sbjct: 18 SNGEVYKGVLHAVDNQLNIVLANASN-----------------KAGEKF-NRVFIMYRYI 59

Query: 92 IIV 94
          + +
Sbjct: 60 VHI 62

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	99
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.92
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.86
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.82
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.81
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.8
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.79
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.78
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.76
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.74
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.74
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.63
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.42
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.29
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	88.17
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	88.07
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	84.94

>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=99.92  E-value=3.2e-26  Score=148.83  Aligned_cols=79  Identities=82%  Similarity=1.312  Sum_probs=56.1

Q ss_pred             CCChhhhhhhh----------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 034273           21 TGPLSVLMMSV----------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS   90 (99)
Q Consensus        21 ~~Pl~vL~~~l----------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn   90 (99)
                      .|||++|..++          +++|.+.|+|+|||+||||+|+||+|++...++..+.....+...++|++|++||||||
T Consensus         1 tGPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdn   80 (93)
T d1b34b_           1 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDS   80 (93)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGG
T ss_pred             CCcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCE
Confidence            38999998886          68899999999999999999999999998765543222222334567899999999999


Q ss_pred             EEEEEeCCC
Q 034273           91 VIIVLRNPK   99 (99)
Q Consensus        91 Vv~V~~~p~   99 (99)
                      |++|.++|.
T Consensus        81 Vv~I~~~p~   89 (93)
T d1b34b_          81 VIVVLRNPL   89 (93)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEcChh
Confidence            999999984

>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=99.86  E-value=9.7e-23  Score=131.30  Aligned_cols=80  Identities=23%  Similarity=0.340  Sum_probs=58.1

Q ss_pred             cCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCC-ccccccCcceeeeceEEEeCCc
Q 034273           20 NTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKG-KKKALPVNKDRFISKMFLRGDS   90 (99)
Q Consensus        20 ~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~-~~~~~~~~~~r~lg~i~IRGdn   90 (99)
                      +..|+++|..++        ++|+.+.|+|+|||+||||+|+||+|++....++... ..+.......|++|++||||+|
T Consensus         3 ~~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~   82 (92)
T d2fwka1           3 IILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNN   82 (92)
T ss_dssp             CCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGG
T ss_pred             ccChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCE
Confidence            457888887775        8999999999999999999999999998754432111 0111123446889999999999


Q ss_pred             EEEEEeCCC
Q 034273           91 VIIVLRNPK   99 (99)
Q Consensus        91 Vv~V~~~p~   99 (99)
                      |++|+|..+
T Consensus        83 Vv~I~p~~~   91 (92)
T d2fwka1          83 VAMLVPGGD   91 (92)
T ss_dssp             EEEEESSSC
T ss_pred             EEEEEeCCC
Confidence            999998753

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=99.82  E-value=1e-20  Score=116.49  Aligned_cols=63  Identities=27%  Similarity=0.450  Sum_probs=54.5

Q ss_pred             CCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273           21 TGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI   92 (99)
Q Consensus        21 ~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv   92 (99)
                      ++|+.+|+.++        ++|+.+.|+|.+||+||||+|+||+|+...       .       ..+++|.+||||+||+
T Consensus         1 ~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------~-------~~~~l~~~~IRG~~I~   66 (71)
T d1h641_           1 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG-------E-------VVKRYGKIVIRGDNVL   66 (71)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETT-------E-------EEEEEEEEEECGGGEE
T ss_pred             CCchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecC-------C-------cEeEcCcEEEECCeEE
Confidence            47888887775        899999999999999999999999998531       1       2368999999999999


Q ss_pred             EEEeC
Q 034273           93 IVLRN   97 (99)
Q Consensus        93 ~V~~~   97 (99)
                      +|+|+
T Consensus        67 ~Isp~   71 (71)
T d1h641_          67 AISPT   71 (71)
T ss_dssp             EEEEC
T ss_pred             EEeCC
Confidence            99985

>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=99.81  E-value=1.4e-20  Score=118.74  Aligned_cols=65  Identities=23%  Similarity=0.486  Sum_probs=51.8

Q ss_pred             hhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273           29 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN   97 (99)
Q Consensus        29 ~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~   97 (99)
                      +.+++||.+.|+|+|||+||||+|+||+|++...+++.+...    ....|++|++||||+||++|+..
T Consensus        13 V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~----~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_          13 CILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE----REEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             EEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCC----EEEEEEEEEEEECGGGEEEEEEE
T ss_pred             EEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccc----cceEEEeeeEEEeCCEEEEEEcc
Confidence            356899999999999999999999999999865443322111    23468999999999999999863

>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=99.80  E-value=3.1e-20  Score=114.72  Aligned_cols=62  Identities=31%  Similarity=0.501  Sum_probs=53.0

Q ss_pred             CChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 034273           22 GPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII   93 (99)
Q Consensus        22 ~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~   93 (99)
                      .|+.+|+.++        ++|+.+.|+|.|||+||||+|+||+|+...       .       ..+++|.+||||+||++
T Consensus         3 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------~-------~~~~~g~~~IRG~~I~~   68 (72)
T d1i4k1_           3 RPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG-------E-------VVRKVGSVVIRGDTVVF   68 (72)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSS-------S-------EEEEEEEEEECGGGEEE
T ss_pred             ChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecC-------C-------eEeEcceEEEeCCeEEE
Confidence            5788887775        899999999999999999999999998531       1       13689999999999999


Q ss_pred             EEeC
Q 034273           94 VLRN   97 (99)
Q Consensus        94 V~~~   97 (99)
                      |+|+
T Consensus        69 Ispa   72 (72)
T d1i4k1_          69 VSPA   72 (72)
T ss_dssp             EECC
T ss_pred             EEcC
Confidence            9874

>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=99.79  E-value=1.1e-19  Score=112.68  Aligned_cols=63  Identities=27%  Similarity=0.505  Sum_probs=54.7

Q ss_pred             cCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 034273           20 NTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV   91 (99)
Q Consensus        20 ~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV   91 (99)
                      ...|+++|+.++        ++|+.+.|+|.|||+||||+|+||+|+...       .       ..+++|.+||||+||
T Consensus         4 ~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~-------~-------~~~~~~~~~IRG~~I   69 (74)
T d1mgqa_           4 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG-------E-------VTRRLGTVLIRGDNI   69 (74)
T ss_dssp             TTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETT-------E-------EEEEEEEEEECGGGE
T ss_pred             ccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCC-------C-------eEeEcceEEEeCCEE
Confidence            357999998886        899999999999999999999999998531       1       136899999999999


Q ss_pred             EEEEe
Q 034273           92 IIVLR   96 (99)
Q Consensus        92 v~V~~   96 (99)
                      ++|+|
T Consensus        70 ~~I~p   74 (74)
T d1mgqa_          70 VYISP   74 (74)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99986

>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=99.78  E-value=7.4e-20  Score=113.08  Aligned_cols=54  Identities=26%  Similarity=0.541  Sum_probs=48.3

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeCC
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP   98 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~p   98 (99)
                      .|++|+.+.|+|.+||+||||+|+||+|++..               ..+.+|.+||||+||++|++.|
T Consensus        18 ~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~---------------~~~~~g~v~iRG~~I~~I~~~P   71 (71)
T d1i8fa_          18 KLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG---------------NVYKRGTMVVRGENVLFISPVP   71 (71)
T ss_dssp             EEGGGEEEEEEEEEECTTCCEEEEEEEEEETT---------------EEEEEEEEEECGGGEEEEEECC
T ss_pred             EECCCCEEEEEEEEECCCcceEEccEEEEECC---------------CEEEcceEEEeCCeEEEEeCCC
Confidence            56899999999999999999999999998631               1367999999999999999988

>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=99.76  E-value=5.6e-19  Score=110.14  Aligned_cols=64  Identities=28%  Similarity=0.404  Sum_probs=53.3

Q ss_pred             ccCCChhhhhhhh--------cCC-eEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCC
Q 034273           19 FNTGPLSVLMMSV--------KNN-TQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD   89 (99)
Q Consensus        19 ~~~~Pl~vL~~~l--------k~g-r~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd   89 (99)
                      .+..|+.+|+.++        ++| +.+.|+|.|||+||||+|+||+|+...       .       ..+++|.+||||+
T Consensus         2 ~~~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~-------~-------~~~~~g~~~IRG~   67 (75)
T d1ljoa_           2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE-------E-------KVRSLGEIVLRGN   67 (75)
T ss_dssp             CCCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETT-------E-------EEEEEEEEEECGG
T ss_pred             CccccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCC-------C-------cEeEcceEEEeCC
Confidence            3567888888775        654 899999999999999999999998531       1       1368999999999


Q ss_pred             cEEEEEe
Q 034273           90 SVIIVLR   96 (99)
Q Consensus        90 nVv~V~~   96 (99)
                      ||++|+|
T Consensus        68 ~I~~I~p   74 (75)
T d1ljoa_          68 NVVLIQP   74 (75)
T ss_dssp             GEEEEEE
T ss_pred             EEEEEEC
Confidence            9999996

>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=99.74  E-value=1.3e-18  Score=106.68  Aligned_cols=56  Identities=21%  Similarity=0.376  Sum_probs=47.8

Q ss_pred             hhc-CCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeCCC
Q 034273           30 SVK-NNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK   99 (99)
Q Consensus        30 ~lk-~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~p~   99 (99)
                      .|+ ++++|+|+|.+||+|||++|+||+|....       .       ..+.+|.+||||+||++|.+.|.
T Consensus        12 ~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~-------~-------~~~~lg~~~IRG~nI~~I~~~pd   68 (68)
T d1n9ra_          12 KLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG-------V-------SHGTLGEIFIRCNNVLYIRELPN   68 (68)
T ss_dssp             EESSTTEEEEEEEEECCTTTCEEEEEEEEEETT-------E-------EEEECCSEEECGGGEEEEEECCC
T ss_pred             EEEcCCEEEEEEEEEECCcCceEEeeEEEEecC-------C-------cccCcCeEEEECCEEEEEEeCCC
Confidence            567 66889999999999999999999997531       1       13679999999999999999884

>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=99.74  E-value=2.3e-18  Score=107.24  Aligned_cols=62  Identities=31%  Similarity=0.572  Sum_probs=51.2

Q ss_pred             CChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 034273           22 GPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII   93 (99)
Q Consensus        22 ~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~   93 (99)
                      .|..+|..++        ++|+.++|+|.|||+||||+|+||+|+...      +        ..+++|.+||||+||++
T Consensus         7 ~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~------~--------~~~~~~~v~iRG~~I~~   72 (76)
T d1th7a1           7 TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD------G--------SGKKLGTIVIRGDNVIL   72 (76)
T ss_dssp             HHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSS------S--------CEEEEEEEEECGGGEEE
T ss_pred             cHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecC------C--------cccCcceEEEECCEEEE
Confidence            3556665554        899999999999999999999999997532      1        13689999999999999


Q ss_pred             EEeC
Q 034273           94 VLRN   97 (99)
Q Consensus        94 V~~~   97 (99)
                      |+|.
T Consensus        73 I~~~   76 (76)
T d1th7a1          73 ISPL   76 (76)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9984

>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=99.63  E-value=2.9e-16  Score=96.73  Aligned_cols=61  Identities=15%  Similarity=0.352  Sum_probs=50.5

Q ss_pred             CChhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 034273           22 GPLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII   93 (99)
Q Consensus        22 ~Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~   93 (99)
                      -|+.+|+.+        |++|+.++|+|.+||.|||++|+||+|+...      +        ...+++.+||||+||.+
T Consensus         2 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~------~--------~~~~~~~v~IRG~~I~~   67 (72)
T d1d3ba_           2 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD------G--------RVAQLEQVYIRGCKIRF   67 (72)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTT------S--------CEEEEEEEEECGGGEEE
T ss_pred             CchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCC------C--------cEeEcCeEEEECCEEEE
Confidence            477777766        4999999999999999999999999987421      1        12578999999999999


Q ss_pred             EEe
Q 034273           94 VLR   96 (99)
Q Consensus        94 V~~   96 (99)
                      |..
T Consensus        68 i~l   70 (72)
T d1d3ba_          68 LIL   70 (72)
T ss_dssp             EEE
T ss_pred             EEc
Confidence            874

>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=99.42  E-value=1.2e-13  Score=86.49  Aligned_cols=55  Identities=20%  Similarity=0.325  Sum_probs=46.0

Q ss_pred             hhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273           29 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN   97 (99)
Q Consensus        29 ~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~   97 (99)
                      +.|++|..+.|+|.++|.|||+.|+||+++...      + .       ..+++.+||||+||.+|+..
T Consensus        16 VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~------~-~-------~~~~~~v~IRG~~Ir~i~lP   70 (80)
T d1b34a_          16 IELKNGTQVHGTITGVDVSMNTHLKAVKMTLKN------R-E-------PVQLETLSIRGNNIRYFILP   70 (80)
T ss_dssp             EEETTCCEEEEEEEEECTTCCEEEEEEEEECTT------S-C-------CEEEEEEEECGGGEEEEECC
T ss_pred             EEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCC------C-C-------EEEcccEEEcCCEEEEEECC
Confidence            356999999999999999999999999986421      1 1       25789999999999999863

>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=99.29  E-value=7.9e-13  Score=89.43  Aligned_cols=49  Identities=18%  Similarity=0.246  Sum_probs=42.3

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      .|++|+.+.|+|.+||+|||++|+||++...                  ..++.++|||++|.+|..
T Consensus        16 eLkng~~~~G~L~~~D~~mNivL~da~~~~~------------------~k~~~v~IRG~~I~~I~~   64 (127)
T d1m5q1_          16 VLSNGEVYKGVLHAVDNQLNIVLANASNKAG------------------EKFNRVFIMYRYIVHIDS   64 (127)
T ss_dssp             EETTSCEEEEEEEEECTTCCEEEEEEEETTC------------------CEEEEEEECGGGEEEEEE
T ss_pred             EECCCCEEEEEEEEECCCceEEEeEEEECCC------------------CcccEEEEeCCeEEEEEc
Confidence            5789999999999999999999999987421                  136889999999999974

>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=88.17  E-value=0.11  Score=30.25  Aligned_cols=22  Identities=23%  Similarity=0.505  Sum_probs=18.7

Q ss_pred             hhcCCeEEEEEEEEecCeeceE
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMV   51 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLv   51 (99)
                      .|.+|-.++|.+.|||+|.=|+
T Consensus        20 fL~nGvkl~G~I~~fD~ftvLL   41 (66)
T d1u1sa1          20 YLVNGIKLQGQIESFDQFVILL   41 (66)
T ss_dssp             EETTSCEEEEEEEEECSSEEEE
T ss_pred             EEEcCcEEEEEEEEEcceEEEE
Confidence            4678999999999999997644

>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=88.07  E-value=0.17  Score=28.85  Aligned_cols=28  Identities=14%  Similarity=0.195  Sum_probs=23.1

Q ss_pred             hhcCCeEEEEEEEEecCeeceEeeceEE
Q 034273           30 SVKNNTQLLGRVRAFDRHCNMVLENVRE   57 (99)
Q Consensus        30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E   57 (99)
                      .|.+|-.++|.+.|||+|.=|+-.+...
T Consensus        20 fL~nGvkl~G~I~~fD~ftvlL~~~~~q   47 (60)
T d1kq1a_          20 FFLNGFQMKGVIEEYDKYVVSLNSQGKQ   47 (60)
T ss_dssp             EETTSCEEEEEEEEECSSEEEEEETTEE
T ss_pred             EEECCcEEEEEEEEEcceEEEEEeCCcE
Confidence            5678999999999999999777666543

>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=84.94  E-value=1.9  Score=25.49  Aligned_cols=70  Identities=19%  Similarity=0.274  Sum_probs=47.4

Q ss_pred             ccCCChhhhhhhhcCCeEEEEEEEEecCee-ceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273           19 FNTGPLSVLMMSVKNNTQLLGRVRAFDRHC-NMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR   96 (99)
Q Consensus        19 ~~~~Pl~vL~~~lk~gr~i~G~L~afD~hm-NLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~   96 (99)
                      |....++++.++   +-.++|+|...|..- -+.|.||.-+-++.++......   +  ...-++.++.||+.|--+.-
T Consensus         2 yIGs~IsLISk~---dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ip---p--~~~vy~~IvFrgsDIKdL~v   72 (80)
T d2vxfa1           2 YIGSKISLISKA---EIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIA---P--RDETFEYIIFRGSDIKDLTV   72 (80)
T ss_dssp             STTSEEEEEETT---SCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCC---C--CCCCEEEEEEETTTEEEEEE
T ss_pred             ccCCEEEEEEcC---CcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccC---C--CCcceeEEEEcCcCcceEEe
Confidence            445566666664   788999999999876 5889999887665432211111   1  12347899999999866553