Citrus Sinensis ID: 034299

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
Protein Sequence
MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH
Secondary Structure (PSIPRED)
cccccccHHHcccEEEEEEccccEEEEEEEEEEccccEEEEcEEEEEEEcccccEEEEEEEEEEEcccEEEEEEEccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHccEEEEEEccccEEEEEEEcHHHHHHHEHHHcEEEEEEccccccEEccEEEEEEccEEEEEEEEccHccccccHHHccccccccccc
Coil and Loop (DISEMBL)
msggpgleSLVEQQISVITNDGRNIVGVLKGfdqatniildeshervystKEGVQQLVLGLYIirgdnisivgevDEELdshldlsnlrahplkpvih
Flexible Loop (DISEMBL)
MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIIldeshervysTKEGVQQLVLGLYIIRGDNISIVGEVDEELDShldlsnlrahplkpvih
Low Complexity Region (SEG)
MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH
Disordered region (IsUnstruct)
************QQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEEL*******************
Disordered Region (DISOPRED)
****PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLK****
Disordered Region (DISEMBL)
MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH
Disordered Region (DISPRO)
****PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSHLDLSNLRAHPL*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH
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	98	2.2.26 [Sep-21-2011]
Q5RCP3	96	N-alpha-acetyltransferase	yes	no	0.959	0.979	0.617	3e-30
Q6ZWM4	96	N-alpha-acetyltransferase	yes	no	0.959	0.979	0.617	3e-30
O95777	96	N-alpha-acetyltransferase	yes	no	0.959	0.979	0.617	3e-30
Q3ZCE0	96	N-alpha-acetyltransferase	yes	no	0.959	0.979	0.617	3e-30
Q1ZXD5	94	N-alpha-acetyltransferase	yes	no	0.928	0.968	0.478	4e-22
O74483	94	U6 snRNA-associated Sm-li	yes	no	0.938	0.978	0.445	4e-19
Q54W83	129	Probable U6 snRNA-associa	no	no	0.744	0.565	0.421	4e-10
P47017	172	Sm-like protein LSm1 OS=S	yes	no	0.693	0.395	0.420	8e-09
P87173	140	U6 snRNA-associated Sm-li	no	no	0.908	0.635	0.326	2e-08
Q5E9Z8	133	U6 snRNA-associated Sm-li	no	no	0.887	0.654	0.318	3e-07

>sp|Q5RCP3|NAA38_PONAB N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Pongo abelii GN=NAA38 PE=3 SV=3

 Score =  130 bits (327), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 58/94 (61%), Positives = 77/94 (81%)

Query: 5  PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYII 64
            LE+ + + ++VIT+DGR IVG LKGFDQ  N+ILDESHERV+S+ +GV+Q+VLGLYI+
Sbjct: 3  SALENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLYIV 62

Query: 65 RGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          RGDN++++GE+DEE DS LDL N+RA PL  V H
Sbjct: 63 RGDNVAVIGEIDEETDSALDLGNIRAEPLNSVAH 96

Binds specifically to the 3'-terminal U-tract of U6 snRNA.
Pongo abelii (taxid: 9601)

>sp|Q6ZWM4|NAA38_MOUSE N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Mus musculus GN=Naa38 PE=3 SV=3

 Score =  130 bits (327), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 58/94 (61%), Positives = 77/94 (81%)

Query: 5  PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYII 64
            LE+ + + ++VIT+DGR IVG LKGFDQ  N+ILDESHERV+S+ +GV+Q+VLGLYI+
Sbjct: 3  SALENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLYIV 62

Query: 65 RGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          RGDN++++GE+DEE DS LDL N+RA PL  V H
Sbjct: 63 RGDNVAVIGEIDEETDSALDLGNIRAEPLNSVAH 96

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

Mus musculus (taxid: 10090)

>sp|O95777|NAA38_HUMAN N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Homo sapiens GN=NAA38 PE=1 SV=3

 Score =  130 bits (327), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 58/94 (61%), Positives = 77/94 (81%)

Query: 5  PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYII 64
            LE+ + + ++VIT+DGR IVG LKGFDQ  N+ILDESHERV+S+ +GV+Q+VLGLYI+
Sbjct: 3  SALENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLYIV 62

Query: 65 RGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          RGDN++++GE+DEE DS LDL N+RA PL  V H
Sbjct: 63 RGDNVAVIGEIDEETDSALDLGNIRAEPLNSVAH 96

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

Homo sapiens (taxid: 9606)

>sp|Q3ZCE0|NAA38_BOVIN N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Bos taurus GN=NAA38 PE=3 SV=3

 Score =  130 bits (327), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 58/94 (61%), Positives = 77/94 (81%)

Query: 5  PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYII 64
            LE+ + + ++VIT+DGR IVG LKGFDQ  N+ILDESHERV+S+ +GV+Q+VLGLYI+
Sbjct: 3  SALENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLYIV 62

Query: 65 RGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          RGDN++++GE+DEE DS LDL N+RA PL  V H
Sbjct: 63 RGDNVAVIGEIDEETDSALDLGNIRAEPLNSVAH 96

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

Bos taurus (taxid: 9913)

>sp|Q1ZXD5|NAA38_DICDI N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Dictyostelium discoideum GN=lsm8 PE=3 SV=1

 Score =  103 bits (256), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 44/92 (47%), Positives = 74/92 (80%), Gaps = 1/92 (1%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          LES +++Q+ V+T DGR+I+G L+G DQ  N++L++ HERVYS  EG++ + LG+++I+G
Sbjct: 4  LESYLKKQVLVLTADGRSIIGTLRGIDQTINVVLEKCHERVYSD-EGIEVIPLGVHLIKG 62

Query: 67 DNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          D+++++GEVD+ELD  L+L  + A P+KP++H
Sbjct: 63 DDVAVIGEVDDELDKKLNLKEIIAEPMKPIVH 94

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

Dictyostelium discoideum (taxid: 44689)

>sp|O74483|LSM8_SCHPO U6 snRNA-associated Sm-like protein LSm8 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm8 PE=3 SV=1

 Score = 93.2 bits (230), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 41/92 (44%), Positives = 67/92 (72%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L   +EQ++ VITNDGR ++G LKGFD  TN+IL +S ER+ S  + ++ + LG+Y++RG
Sbjct: 3  LADFMEQRVQVITNDGRVVLGSLKGFDHTTNLILSDSFERIISMDQDMETIPLGVYLLRG 62

Query: 67 DNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          +N+++VG V+EELDS ++ + +R   +  V+H
Sbjct: 63 ENVAMVGLVNEELDSEIEWTKIRGEAIPDVVH 94

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

>sp|Q54W83|LSM1_DICDI Probable U6 snRNA-associated Sm-like protein LSm1 OS=Dictyostelium discoideum GN=lsm1 PE=3 SV=1

 Score = 63.2 bits (152), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 50/76 (65%), Gaps = 3/76 (3%)

Query: 1  MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60
          MS G G E  V++++ V+  DGR  +G+++ FDQ  NI+L ++ ER+Y   +      LG
Sbjct: 1  MSSGLGDE--VDKKLIVVLRDGRKFIGIMRTFDQFANIVLQDTIERIY-VGDCYSDKNLG 57

Query: 61 LYIIRGDNISIVGEVD 76
          L+ IRGDN+ I+GE+D
Sbjct: 58 LFFIRGDNVVILGEID 73

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

Dictyostelium discoideum (taxid: 44689)

>sp|P47017|LSM1_YEAST Sm-like protein LSm1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM1 PE=1 SV=1

 Score = 58.9 bits (141), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 29/69 (42%), Positives = 48/69 (69%), Gaps = 1/69 (1%)

Query: 9   SLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEG-VQQLVLGLYIIRGD 67
           S V+++I V+  DGR + GVL+ FDQ  N+IL +  ER+Y ++E    +   G+++IRG+
Sbjct: 48  SSVDRKIFVLLRDGRMLFGVLRTFDQYANLILQDCVERIYFSEENKYAEEDRGIFMIRGE 107

Query: 68  NISIVGEVD 76
           N+ ++GEVD
Sbjct: 108 NVVMLGEVD 116

Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step.

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

>sp|P87173|LSM1_SCHPO U6 snRNA-associated Sm-like protein LSm1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm1 PE=3 SV=1

 Score = 57.8 bits (138), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 57/92 (61%), Gaps = 3/92 (3%)

Query: 7   LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
           L   V++++ V+  DG+ ++G+L+ FDQ  N++L  + ER+Y   +    +  G+YI+RG
Sbjct: 16  LVDYVDRKVIVVLRDGKKLIGILRSFDQFANLMLQYTIERIY-VDDMYGDIDRGVYIVRG 74

Query: 67  DNISIVGE--VDEELDSHLDLSNLRAHPLKPV 96
           +N+ ++GE  +D+E D+   L  + A  L P+
Sbjct: 75  ENVVLLGELDLDKEYDAVKQLRRMPAEELYPL 106

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

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

>sp|Q5E9Z8|LSM1_BOVIN U6 snRNA-associated Sm-like protein LSm1 OS=Bos taurus GN=LSM1 PE=2 SV=1

 Score = 53.5 bits (127), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 56/91 (61%), Gaps = 4/91 (4%)

Query: 1  MSGGPGLESLVE---QQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQL 57
          M+  PG  SL+E   ++  V+  DGR ++G L+  DQ  N++L ++ ER++  K+    +
Sbjct: 1  MNYMPGTASLIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKK-YGDI 59

Query: 58 VLGLYIIRGDNISIVGEVDEELDSHLDLSNL 88
            G++++RG+N+ ++GE+D E +S   L  +
Sbjct: 60 PRGIFVVRGENVVLLGEIDLEKESDTPLQQV 90

Plays a role in replication-dependent histone mRNA degradation. Binds specifically to the 3'-terminal U-tract of U6 snRNA.

Bos taurus (taxid: 9913)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	98
351723875	98	uncharacterized protein LOC100305829 [Gl	1.0	1.0	0.928	2e-44
313586493	98	U6 snRNA-associated Sm-like protein LSm8	1.0	1.0	0.928	3e-44
449439529	98	PREDICTED: N-alpha-acetyltransferase 38,	1.0	1.0	0.918	6e-44
225454559	98	PREDICTED: N-alpha-acetyltransferase 38,	1.0	1.0	0.928	6e-44
115465821	99	Os05g0594900 [Oryza sativa Japonica Grou	0.989	0.979	0.907	2e-43
224059783	98	predicted protein [Populus trichocarpa]	1.0	1.0	0.897	7e-43
226529351	99	LOC100284021 [Zea mays] gi|194699348|gb|	0.989	0.979	0.886	8e-42
255565755	98	lsm1, putative [Ricinus communis] gi|223	0.989	0.989	0.886	5e-41
357132320	99	PREDICTED: N-alpha-acetyltransferase 38,	0.989	0.979	0.865	8e-41
297841127	590	hypothetical protein ARALYDRAFT_315605 [	1.0	0.166	0.826	2e-39

>gi|351723875|ref|NP_001237294.1| uncharacterized protein LOC100305829 [Glycine max] gi|356525792|ref|XP_003531507.1| PREDICTED: N-alpha-acetyltransferase 38, NatC auxiliary subunit-like [Glycine max] gi|255626721|gb|ACU13705.1| unknown [Glycine max]

 Score =  182 bits (463), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 91/98 (92%), Positives = 94/98 (95%)

Query: 1  MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60
          MS GPGLESLV+Q ISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG
Sbjct: 1  MSAGPGLESLVDQTISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60

Query: 61 LYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          LYIIRGDNIS+VGE+DEELDS LDLS LRAHPLKPVIH
Sbjct: 61 LYIIRGDNISVVGELDEELDSSLDLSKLRAHPLKPVIH 98

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313586493|gb|ADR71257.1| U6 snRNA-associated Sm-like protein LSm8 [Hevea brasiliensis]

 Score =  182 bits (461), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 91/98 (92%), Positives = 95/98 (96%)

Query: 1  MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60
          MS G GLESLV+Q ISVITNDGRNIVG+LKGFDQATNIILDESHERVYSTKEGVQQLVLG
Sbjct: 1  MSTGLGLESLVDQTISVITNDGRNIVGILKGFDQATNIILDESHERVYSTKEGVQQLVLG 60

Query: 61 LYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          LYIIRGDNISIVGE+DEELDSH+DLSNLRAHPLKPVIH
Sbjct: 61 LYIIRGDNISIVGELDEELDSHIDLSNLRAHPLKPVIH 98

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439529|ref|XP_004137538.1| PREDICTED: N-alpha-acetyltransferase 38, NatC auxiliary subunit-like [Cucumis sativus] gi|449514856|ref|XP_004164499.1| PREDICTED: N-alpha-acetyltransferase 38, NatC auxiliary subunit-like [Cucumis sativus]

 Score =  181 bits (458), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 90/98 (91%), Positives = 95/98 (96%)

Query: 1  MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60
          M+ GPGL+SLV+Q ISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG
Sbjct: 1  MASGPGLDSLVDQTISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60

Query: 61 LYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          LYIIRGDNISIVGE+DEELDS+LDLS LRAHPLKPVIH
Sbjct: 61 LYIIRGDNISIVGELDEELDSNLDLSKLRAHPLKPVIH 98

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225454559|ref|XP_002263175.1| PREDICTED: N-alpha-acetyltransferase 38, NatC auxiliary subunit [Vitis vinifera] gi|297737198|emb|CBI26399.3| unnamed protein product [Vitis vinifera]

 Score =  181 bits (458), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 91/98 (92%), Positives = 93/98 (94%)

Query: 1  MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60
          MS GPGLESLV+Q ISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG
Sbjct: 1  MSTGPGLESLVDQTISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60

Query: 61 LYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          LYIIRGDNISIVGE+DEELDS LDLS LRAHPLKPV H
Sbjct: 61 LYIIRGDNISIVGELDEELDSSLDLSKLRAHPLKPVTH 98

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115465821|ref|NP_001056510.1| Os05g0594900 [Oryza sativa Japonica Group] gi|55733874|gb|AAV59381.1| unknown protein [Oryza sativa Japonica Group] gi|113580061|dbj|BAF18424.1| Os05g0594900 [Oryza sativa Japonica Group]

 Score =  179 bits (453), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 88/97 (90%), Positives = 93/97 (95%)

Query: 2  SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGL 61
          S GPGLESLV+Q ISVITNDGRNIVG L+GFDQATNIILDESHERVYST+EGVQQLVLGL
Sbjct: 3  SAGPGLESLVDQIISVITNDGRNIVGTLRGFDQATNIILDESHERVYSTREGVQQLVLGL 62

Query: 62 YIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          YIIRGDNIS+VGEVDEELD+ LDLSNLRAHPLKPVIH
Sbjct: 63 YIIRGDNISVVGEVDEELDARLDLSNLRAHPLKPVIH 99

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224059783|ref|XP_002299990.1| predicted protein [Populus trichocarpa] gi|118484411|gb|ABK94082.1| unknown [Populus trichocarpa] gi|222847248|gb|EEE84795.1| predicted protein [Populus trichocarpa]

 Score =  177 bits (449), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 88/98 (89%), Positives = 94/98 (95%)

Query: 1  MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60
          MS G GLESLV+Q IS+ITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG
Sbjct: 1  MSIGTGLESLVDQTISIITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60

Query: 61 LYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          LYIIRGDNI +VGE+DEELD+HLDLS+LRAHPLKPVIH
Sbjct: 61 LYIIRGDNIGVVGELDEELDAHLDLSSLRAHPLKPVIH 98

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226529351|ref|NP_001150391.1| LOC100284021 [Zea mays] gi|194699348|gb|ACF83758.1| unknown [Zea mays] gi|195638896|gb|ACG38916.1| LSM Sm-like protein family member [Zea mays] gi|195642734|gb|ACG40835.1| LSM Sm-like protein family member [Zea mays] gi|413946381|gb|AFW79030.1| LSM Sm-like protein family member [Zea mays]

 Score =  174 bits (440), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 86/97 (88%), Positives = 90/97 (92%)

Query: 2  SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGL 61
          SGGP LE LV+Q ISVITNDGRNIVG L+GFDQATNIILDESHERVYS KEGVQQLVLGL
Sbjct: 3  SGGPALEPLVDQVISVITNDGRNIVGTLRGFDQATNIILDESHERVYSRKEGVQQLVLGL 62

Query: 62 YIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          YIIRGDNIS+VGEVDEELDS LD+S LRAHPLKPVIH
Sbjct: 63 YIIRGDNISVVGEVDEELDSRLDMSKLRAHPLKPVIH 99

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255565755|ref|XP_002523867.1| lsm1, putative [Ricinus communis] gi|223536955|gb|EEF38593.1| lsm1, putative [Ricinus communis]

 Score =  171 bits (433), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 86/97 (88%), Positives = 93/97 (95%)

Query: 1  MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60
          MS GPGLESLV+Q ISVITNDGRNIVG+LKGFDQATNIILDESHERVYSTKEGVQ  VLG
Sbjct: 1  MSTGPGLESLVDQNISVITNDGRNIVGILKGFDQATNIILDESHERVYSTKEGVQLHVLG 60

Query: 61 LYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVI 97
          LYIIRGDNISIVGE+DEELDS+LDL++LRAHPLKP+I
Sbjct: 61 LYIIRGDNISIVGELDEELDSNLDLASLRAHPLKPLI 97

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357132320|ref|XP_003567778.1| PREDICTED: N-alpha-acetyltransferase 38, NatC auxiliary subunit-like [Brachypodium distachyon]

 Score =  170 bits (431), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 84/97 (86%), Positives = 89/97 (91%)

Query: 2  SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGL 61
          S GP LESLV+Q ISVITNDGRNIVG L+GFDQATNIILDESHERVYSTKEGVQQLVLGL
Sbjct: 3  SAGPTLESLVDQVISVITNDGRNIVGTLRGFDQATNIILDESHERVYSTKEGVQQLVLGL 62

Query: 62 YIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
          YIIRGDNI +VGEVDEELD+ LD+S LRA PLKPVIH
Sbjct: 63 YIIRGDNIGVVGEVDEELDAALDMSKLRAQPLKPVIH 99

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297841127|ref|XP_002888445.1| hypothetical protein ARALYDRAFT_315605 [Arabidopsis lyrata subsp. lyrata] gi|297334286|gb|EFH64704.1| hypothetical protein ARALYDRAFT_315605 [Arabidopsis lyrata subsp. lyrata]

 Score =  166 bits (419), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 81/98 (82%), Positives = 88/98 (89%)

Query: 1   MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60
           M+   GLE LV Q ISVITNDGRNIVGVLKGFDQATNIILDESHERV+STKEGVQQ VLG
Sbjct: 493 MATNTGLEDLVNQIISVITNDGRNIVGVLKGFDQATNIILDESHERVFSTKEGVQQHVLG 552

Query: 61  LYIIRGDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
           LYIIRGDNI ++GE+DEELD+ LDLS LRAHPLKPV+H
Sbjct: 553 LYIIRGDNIGVIGELDEELDAGLDLSKLRAHPLKPVVH 590

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	98
FB|FBgn0035271	95	CG2021 [Drosophila melanogaste	0.948	0.978	0.612	2.1e-29
UNIPROTKB|Q3ZCE0	96	NAA38 "N-alpha-acetyltransfera	0.938	0.958	0.630	2.7e-29
UNIPROTKB|O95777	96	NAA38 "N-alpha-acetyltransfera	0.938	0.958	0.630	2.7e-29
MGI|MGI:1923772	96	Naa38 "N(alpha)-acetyltransfer	0.938	0.958	0.630	2.7e-29
DICTYBASE|DDB_G0288479	94	lsm8 "putative U6 small nuclea	0.928	0.968	0.478	4.8e-23
GENEDB_PFALCIPARUM|MAL8P1.9	95	MAL8P1.9 "u6 snRNA-associated	0.918	0.947	0.489	3.9e-21
UNIPROTKB|C0H4Y9	95	MAL8P1.9 "U6 snRNA-associated	0.918	0.947	0.489	3.9e-21
POMBASE|SPCC1840.10	94	lsm8 "U6 snRNP-associated prot	0.938	0.978	0.445	9.2e-20
TAIR|locus:2011246	128	LSM1A "SM-like 1A" [Arabidopsi	0.775	0.593	0.4	5e-12
DICTYBASE|DDB_G0279837	129	lsm1 "LSM (like-Sm) domain-con	0.765	0.581	0.410	1.3e-11

FB|FBgn0035271 CG2021 [Drosophila melanogaster (taxid:7227)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 57/93 (61%), Positives = 75/93 (80%)

Query:     6 GLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIR 65
             GLES +   +S+IT DGRN +G LKGFDQ  NII+DE HERV+ST  G++Q+VLGL+IIR
Sbjct:     3 GLESYINHTVSIITADGRNFIGTLKGFDQTINIIIDECHERVFSTTSGIEQIVLGLHIIR 62

Query:    66 GDNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
             GDNI+++G +DE +DS LDL+N+R  PL PV+H
Sbjct:    63 GDNIAVIGLIDETIDSRLDLANIRGEPLGPVVH 95

GO:0005688 "U6 snRNP" evidence=ISS;NAS

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

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

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0071011 "precatalytic spliceosome" evidence=IDA

UNIPROTKB|Q3ZCE0 NAA38 "N-alpha-acetyltransferase 38, NatC auxiliary subunit" [Bos taurus (taxid:9913)]

 Score = 325 (119.5 bits), Expect = 2.7e-29, P = 2.7e-29
 Identities = 58/92 (63%), Positives = 77/92 (83%)

Query:     7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
             LE+ + + ++VIT+DGR IVG LKGFDQ  N+ILDESHERV+S+ +GV+Q+VLGLYI+RG
Sbjct:     5 LENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLYIVRG 64

Query:    67 DNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
             DN++++GE+DEE DS LDL N+RA PL  V H
Sbjct:    65 DNVAVIGEIDEETDSALDLGNIRAEPLNSVAH 96

GO:0005634 "nucleus" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|O95777 NAA38 "N-alpha-acetyltransferase 38, NatC auxiliary subunit" [Homo sapiens (taxid:9606)]

 Score = 325 (119.5 bits), Expect = 2.7e-29, P = 2.7e-29
 Identities = 58/92 (63%), Positives = 77/92 (83%)

Query:     7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
             LE+ + + ++VIT+DGR IVG LKGFDQ  N+ILDESHERV+S+ +GV+Q+VLGLYI+RG
Sbjct:     5 LENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLYIVRG 64

Query:    67 DNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
             DN++++GE+DEE DS LDL N+RA PL  V H
Sbjct:    65 DNVAVIGEIDEETDSALDLGNIRAEPLNSVAH 96

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

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

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:1923772 Naa38 "N(alpha)-acetyltransferase 38, NatC auxiliary subunit" [Mus musculus (taxid:10090)]

 Score = 325 (119.5 bits), Expect = 2.7e-29, P = 2.7e-29
 Identities = 58/92 (63%), Positives = 77/92 (83%)

Query:     7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
             LE+ + + ++VIT+DGR IVG LKGFDQ  N+ILDESHERV+S+ +GV+Q+VLGLYI+RG
Sbjct:     5 LENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLYIVRG 64

Query:    67 DNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
             DN++++GE+DEE DS LDL N+RA PL  V H
Sbjct:    65 DNVAVIGEIDEETDSALDLGNIRAEPLNSVAH 96

GO:0003674 "molecular_function" evidence=ND

GO:0003723 "RNA binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

DICTYBASE|DDB_G0288479 lsm8 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 266 (98.7 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 44/92 (47%), Positives = 74/92 (80%)

Query:     7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
             LES +++Q+ V+T DGR+I+G L+G DQ  N++L++ HERVYS  EG++ + LG+++I+G
Sbjct:     4 LESYLKKQVLVLTADGRSIIGTLRGIDQTINVVLEKCHERVYSD-EGIEVIPLGVHLIKG 62

Query:    67 DNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
             D+++++GEVD+ELD  L+L  + A P+KP++H
Sbjct:    63 DDVAVIGEVDDELDKKLNLKEIIAEPMKPIVH 94

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

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

GO:0006402 "mRNA catabolic process" evidence=ISS

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

GO:0005730 "nucleolus" evidence=ISS

GO:0005688 "U6 snRNP" evidence=ISS

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GENEDB_PFALCIPARUM|MAL8P1.9 MAL8P1.9 "u6 snRNA-associated sm-like protein, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 45/92 (48%), Positives = 67/92 (72%)

Query:     7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
             +ES +E +I VITND R   G LKGFDQ TNIIL   HER+Y  KE ++++ LG+YIIRG
Sbjct:     6 IESYLENEILVITNDSRIFTGKLKGFDQTTNIILGNCHERIY--KESMEKISLGVYIIRG 63

Query:    67 DNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
             D ++++GE+DE++D ++    ++   LKP++H
Sbjct:    64 DTVTLIGEIDEDVDKNILHQKIKPQMLKPIVH 95

GO:0017070 "U6 snRNA binding" evidence=ISS

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

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

UNIPROTKB|C0H4Y9 MAL8P1.9 "U6 snRNA-associated Sm-like protein, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 45/92 (48%), Positives = 67/92 (72%)

Query:     7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
             +ES +E +I VITND R   G LKGFDQ TNIIL   HER+Y  KE ++++ LG+YIIRG
Sbjct:     6 IESYLENEILVITNDSRIFTGKLKGFDQTTNIILGNCHERIY--KESMEKISLGVYIIRG 63

Query:    67 DNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
             D ++++GE+DE++D ++    ++   LKP++H
Sbjct:    64 DTVTLIGEIDEDVDKNILHQKIKPQMLKPIVH 95

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

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

GO:0017070 "U6 snRNA binding" evidence=ISS

POMBASE|SPCC1840.10 lsm8 "U6 snRNP-associated protein Lsm8 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 41/92 (44%), Positives = 67/92 (72%)

Query:     7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
             L   +EQ++ VITNDGR ++G LKGFD  TN+IL +S ER+ S  + ++ + LG+Y++RG
Sbjct:     3 LADFMEQRVQVITNDGRVVLGSLKGFDHTTNLILSDSFERIISMDQDMETIPLGVYLLRG 62

Query:    67 DNISIVGEVDEELDSHLDLSNLRAHPLKPVIH 98
             +N+++VG V+EELDS ++ + +R   +  V+H
Sbjct:    63 ENVAMVGLVNEELDSEIEWTKIRGEAIPDVVH 94

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=NAS

GO:0006364 "rRNA processing" evidence=ISS

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

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=ISS

TAIR|locus:2011246 LSM1A "SM-like 1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 32/80 (40%), Positives = 56/80 (70%)

Query:     7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
             L + +++++ V+  DGR ++G+L+ FDQ  N +L+E++ERV    +    + LGLYIIRG
Sbjct:    15 LAAYLDKKLLVLLRDGRKLMGLLRSFDQFANAVLEEAYERVI-VGDLYCDIPLGLYIIRG 73

Query:    67 DNISIVGEVD---EELDSHL 83
             +N+ ++GE+D   EEL +H+
Sbjct:    74 ENVVLIGELDVEKEELPAHM 93

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0000932 "cytoplasmic mRNA processing body" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0016070 "RNA metabolic process" evidence=IGI

DICTYBASE|DDB_G0279837 lsm1 "LSM (like-Sm) domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 158 (60.7 bits), Expect = 1.3e-11, P = 1.3e-11
 Identities = 32/78 (41%), Positives = 51/78 (65%)

Query:     1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60
             MS G G E  V++++ V+  DGR  +G+++ FDQ  NI+L ++ ER+Y   +      LG
Sbjct:     1 MSSGLGDE--VDKKLIVVLRDGRKFIGIMRTFDQFANIVLQDTIERIY-VGDCYSDKNLG 57

Query:    61 LYIIRGDNISIVGEVDEE 78
             L+ IRGDN+ I+GE+D +
Sbjct:    58 LFFIRGDNVVILGEIDPD 75

GO:0006402 "mRNA catabolic process" evidence=ISS

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

GO:0000932 "cytoplasmic mRNA processing body" evidence=ISS

GO:0000339 "RNA cap binding" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

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)
Q3ZCE0	NAA38_BOVIN	No assigned EC number	0.6170	0.9591	0.9791	yes	no
O74483	LSM8_SCHPO	No assigned EC number	0.4456	0.9387	0.9787	yes	no
O95777	NAA38_HUMAN	No assigned EC number	0.6170	0.9591	0.9791	yes	no
Q5RCP3	NAA38_PONAB	No assigned EC number	0.6170	0.9591	0.9791	yes	no
Q1ZXD5	NAA38_DICDI	No assigned EC number	0.4782	0.9285	0.9680	yes	no
Q6ZWM4	NAA38_MOUSE	No assigned EC number	0.6170	0.9591	0.9791	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	98
cd01727	91	cd01727, LSm8, Like-Sm protein 8	1e-45
pfam01423	66	pfam01423, LSM, LSM domain	3e-15
smart00651	67	smart00651, Sm, snRNP Sm proteins	9e-15
cd01728	74	cd01728, LSm1, Like-Sm protein 1	1e-13
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	2e-11
cd00600	63	cd00600, Sm_like, Sm and related proteins	2e-09
cd01717	80	cd01717, Sm_B, Sm protein B	4e-09
cd01719	70	cd01719, Sm_G, Sm protein G	6e-08
cd01729	89	cd01729, LSm7, Like-Sm protein 7	2e-07
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	2e-06
cd06168	73	cd06168, LSMD1, LSM domain containing 1	6e-06
PTZ00138	89	PTZ00138, PTZ00138, small nuclear ribonucleoprotei	2e-05
cd01718	79	cd01718, Sm_E, Sm protein E	5e-05
cd01722	69	cd01722, Sm_F, Sm protein F	1e-04
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	4e-04
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	5e-04
pfam07957	217	pfam07957, DUF3294, Protein of unknown function (D	0.003
cd01732	76	cd01732, LSm5, Like-Sm protein 5	0.004

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

 Score =  141 bits (357), Expect = 1e-45
 Identities = 54/90 (60%), Positives = 71/90 (78%)

Query: 5  PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYII 64
            LE  + +++ VIT DGR IVG LKGFDQ TN+IL   HERVYS+ EGV+++ LGLY++
Sbjct: 2  SLLEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEVPLGLYLL 61

Query: 65 RGDNISIVGEVDEELDSHLDLSNLRAHPLK 94
          RGDN++++GEVDEELD  +DLS +RA PLK
Sbjct: 62 RGDNVAVIGEVDEELDGSIDLSKIRAEPLK 91

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

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

 Score = 63.7 bits (156), Expect = 3e-15
 Identities = 25/68 (36%), Positives = 41/68 (60%), Gaps = 4/68 (5%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L+ L+ ++++V   +GR + G LKGFDQ  N++LD+  E +   K       LGL +IRG
Sbjct: 3  LQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVN----KLGLVLIRG 58

Query: 67 DNISIVGE 74
          +NI ++  
Sbjct: 59 NNIVLISP 66

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

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

 Score = 62.5 bits (153), Expect = 9e-15
 Identities = 24/68 (35%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L+ L+ +++ V   +GR   G LKGFDQ  N++L++  E V   ++  +   LGL  IRG
Sbjct: 3  LKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRK---LGLVFIRG 59

Query: 67 DNISIVGE 74
          +NI  +  
Sbjct: 60 NNIVYIIL 67

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

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

 Score = 59.8 bits (146), Expect = 1e-13
 Identities = 26/75 (34%), Positives = 49/75 (65%), Gaps = 1/75 (1%)

Query: 1  MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLG 60
            G   LE  ++++I V+  DGR ++G+L+ FDQ  N++L+++ ER+    +    +  G
Sbjct: 1  PPGTASLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQ-YGDIPRG 59

Query: 61 LYIIRGDNISIVGEV 75
          L+IIRG+N+ ++GE+
Sbjct: 60 LFIIRGENVVLLGEI 74

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

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

 Score = 54.6 bits (132), Expect = 2e-11
 Identities = 23/63 (36%), Positives = 36/63 (57%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L+ L+ +++ V   +GR   G L GFDQ  N++LD+  E +    E   + + G  +IRG
Sbjct: 12 LKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRG 71

Query: 67 DNI 69
          DNI
Sbjct: 72 DNI 74

Length = 79

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

 Score = 48.8 bits (117), Expect = 2e-09
 Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 4/64 (6%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L+  + + +SV   DGR + G L  FD+  N++LD+  E     K      VLGL +IRG
Sbjct: 1  LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVR----VLGLVLIRG 56

Query: 67 DNIS 70
           NI 
Sbjct: 57 SNIV 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|212464 cd01717, Sm_B, Sm protein B

 Score = 48.3 bits (116), Expect = 4e-09
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 8/76 (10%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHE-RVYSTKEGV------QQLVL 59
          +   +  ++ V   DGR  VG    FD+  N++L +  E R    K+        ++ VL
Sbjct: 5  MLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEEREEKRVL 64

Query: 60 GLYIIRGDNI-SIVGE 74
          GL ++RG+N+ S+  E
Sbjct: 65 GLVLLRGENVVSMTVE 80

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. Length = 80

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

 Score = 45.2 bits (108), Expect = 6e-08
 Identities = 21/70 (30%), Positives = 43/70 (61%), Gaps = 4/70 (5%)

Query: 3  GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLY 62
            P L+  +++++S+  N  R + GVL+GFD   N++LD++ E V       ++  +G+ 
Sbjct: 1  HPPELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDG----EKTPIGMV 56

Query: 63 IIRGDNISIV 72
          +IRG++I ++
Sbjct: 57 VIRGNSIIMI 66

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

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

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVY----STKEGVQQLVLGLY 62
          L   V+++I V    GR + G+LKG+DQ  N++LD++ E +       K   +   LGL 
Sbjct: 7  LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDETRSLGLV 66

Query: 63 IIRGDNISIVGEVD 76
          + RG ++ ++  VD
Sbjct: 67 VCRGTSVVLISPVD 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. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 89

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

 Score = 41.4 bits (98), Expect = 2e-06
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 4/66 (6%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L   + + + V    G+ + GVLKGFDQ  N++L+ + E      EG     LG  ++RG
Sbjct: 6  LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEE----IIEGESVRKLGTVLVRG 61

Query: 67 DNISIV 72
          DN+  +
Sbjct: 62 DNVVFI 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|212486 cd06168, LSMD1, LSM domain containing 1

 Score = 40.2 bits (95), Expect = 6e-06
 Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 6  GLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHE-RVYSTKEGVQQLVLGLYII 64
           L  L+ + + V   DGR +VG     D+  NIIL  + E R  S     +   LGL ++
Sbjct: 3  KLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGAEEPRSLGLVMV 62

Query: 65 RGDNI 69
           G +I
Sbjct: 63 PGKHI 67

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

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

 Score = 39.3 bits (92), Expect = 2e-05
 Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 14 QISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVG 73
          QI +  +    I G + GFD+  N++LD++ E    TK+  ++  LG  +++GDNI+++ 
Sbjct: 30 QIWLYDHPNLRIEGKILGFDEYMNMVLDDAEE--VYTKKNTRK-DLGRILLKGDNITLIM 86

Query: 74 EV 75
            
Sbjct: 87 AA 88

Length = 89

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

 Score = 37.9 bits (89), Expect = 5e-05
 Identities = 16/50 (32%), Positives = 30/50 (60%), Gaps = 3/50 (6%)

Query: 25 IVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE 74
          I G + GFD+  N++LD++ E V+      +   LG  +++GDNI+++  
Sbjct: 33 IEGKIIGFDEYMNLVLDDAEE-VHLKTNTRKP--LGRILLKGDNITLIQN 79

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

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

 Score = 36.8 bits (86), Expect = 1e-04
 Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 4/70 (5%)

Query: 5  PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYII 64
          P L  L  + + V    G    G L   D   N+ L  + E +    +G     LG  +I
Sbjct: 4  PFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI----DGKFTGNLGEVLI 59

Query: 65 RGDNISIVGE 74
          R +N+  + E
Sbjct: 60 RCNNVLYIRE 69

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

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

 Score = 35.4 bits (82), Expect = 4e-04
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 4/63 (6%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L + +   + V    GR   G L+G+D   N++LD + E     ++G     LG  +IRG
Sbjct: 9  LNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEE----IQDGEVVRKLGKVVIRG 64

Query: 67 DNI 69
          DN+
Sbjct: 65 DNV 67

Length = 72

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

 Score = 35.2 bits (81), Expect = 5e-04
 Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 5/62 (8%)

Query: 9  SLVEQQISV-ITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGD 67
          SLV  +I V +  D   + G L   D   N+ L ++ E         +   LG  ++RG+
Sbjct: 7  SLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTME----CVGEEKVRSLGTVVLRGN 62

Query: 68 NI 69
          NI
Sbjct: 63 NI 64

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

>gnl|CDD|219663 pfam07957, DUF3294, Protein of unknown function (DUF3294)

 Score = 34.3 bits (79), Expect = 0.003
 Identities = 18/84 (21%), Positives = 37/84 (44%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L++LV++Q  +I   G++++ +     +     L +S             L +  Y    
Sbjct: 16 LQALVKKQSLLIAKTGQSVLDLQVRQVKRDMDGLGKSKWYSPKRISQAASLDMTDYATNE 75

Query: 67 DNISIVGEVDEELDSHLDLSNLRA 90
          D + +VGE+  +LD+  + S  R 
Sbjct: 76 DLVQLVGELQGQLDALEERSIRRT 99

This family was annotated as mitochondrial Ribosomal protein MRP8, based on the presumed similarity of the S.cerevisiae protein to an E.coli mitochondrial ribosomal protein; however, this similarity is spurious, and the function is not known [Wood, V]. Length = 217

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

 Score = 33.0 bits (76), Expect = 0.004
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 13 QQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISI 71
           +I +I    +  VG L GFD   N++L++  E    T EG +   L   ++ G+NI++
Sbjct: 14 SKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEI-TPEGRKITKLDQILLNGNNIAM 71

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	98
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.91
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	99.9
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.89
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.88
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.85
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.84
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.84
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.83
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.82
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.82
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.82
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.8
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.77
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.77
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.76
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.76
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.74
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.73
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	99.72
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.71
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	99.63
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.61
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.57
KOG3168	177	consensus U1 snRNP component [Transcription]	99.55
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	99.39
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	99.39
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	99.28
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	98.92
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	98.81
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	98.65
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.42
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	98.04
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.32
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	97.01
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.92
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.08
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	95.67
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	95.59
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	95.42
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	95.36
PRK14638	150	hypothetical protein; Provisional	95.17
COG1923	77	Hfq Uncharacterized host factor I protein [General	94.82
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	94.78
PRK14639	140	hypothetical protein; Provisional	94.48
PRK02001	152	hypothetical protein; Validated	94.47
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	94.07
PRK14644	136	hypothetical protein; Provisional	93.27
PRK14640	152	hypothetical protein; Provisional	92.97
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	92.39
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	92.04
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	91.87
PRK14633	150	hypothetical protein; Provisional	91.86
PRK14642	197	hypothetical protein; Provisional	91.48
PRK14645	154	hypothetical protein; Provisional	90.95
PRK14636	176	hypothetical protein; Provisional	90.95
PRK06955	300	biotin--protein ligase; Provisional	90.92
PRK00092	154	ribosome maturation protein RimP; Reviewed	90.37
PRK14632	172	hypothetical protein; Provisional	90.31
PRK14643	164	hypothetical protein; Provisional	89.78
PRK14634	155	hypothetical protein; Provisional	89.57
PRK14646	155	hypothetical protein; Provisional	88.97
PRK14091	165	RNA-binding protein Hfq; Provisional	88.86
PRK14647	159	hypothetical protein; Provisional	88.44
PRK14631	174	hypothetical protein; Provisional	87.88
PRK14091	165	RNA-binding protein Hfq; Provisional	87.67
PRK13325	592	bifunctional biotin--[acetyl-CoA-carboxylase] liga	87.32
PRK14641	173	hypothetical protein; Provisional	85.91
PRK14637	151	hypothetical protein; Provisional	85.89
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	84.53
PF14563	42	DUF4444: Domain of unknown function (DUF4444); PDB	84.12
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	84.07
TIGR00121	237	birA_ligase birA, biotin-[acetyl-CoA-carboxylase]	83.57
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	82.91
PRK08330	236	biotin--protein ligase; Provisional	82.27

>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=99.91  E-value=1.3e-23  Score=131.35  Aligned_cols=74  Identities=20%  Similarity=0.368  Sum_probs=67.0

Q ss_pred             CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEec
Q 034299            1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV   75 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~   75 (98)
                      |.|...|+++++++|+|++++||++.|+|.|||+|||++|+||.|++..++ +...+.+|.++|||++|++|.+.
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~-~~~~~~lg~v~iRG~nV~~i~p~   75 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPE-GRKITKLDQILLNGNNICMLVPG   75 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCC-CceeeEcCeEEEeCCeEEEEECC
Confidence            789999999999999999999999999999999999999999999985443 34567899999999999999863

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

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

Probab=99.91  E-value=1.5e-23  Score=130.14  Aligned_cols=73  Identities=71%  Similarity=1.122  Sum_probs=66.2

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      +.|++|++++|+|.++|||.+.|+|+|||+|||++|++|.|+...++++..++.+|.+++||++|++|++.|+
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~   74 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE   74 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence            4899999999999999999999999999999999999999987655445567889999999999999998864

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.

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

Probab=99.90  E-value=2.5e-24  Score=137.40  Aligned_cols=93  Identities=67%  Similarity=1.133  Sum_probs=89.6

Q ss_pred             hHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCccccccCCC
Q 034299            6 GLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSHLDL   85 (98)
Q Consensus         6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e~~~~~   85 (98)
                      .|+.|++++|.|...|||.+.|.|+|||+..|++|+++.|++++..++.++..+|+.+|||+||..|+..|+++++.+|+
T Consensus         4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~~ld~   83 (96)
T KOG1784|consen    4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDSRLDL   83 (96)
T ss_pred             hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhhhhhh
Confidence            79999999999999999999999999999999999999999987766778889999999999999999999999999999


Q ss_pred             CccccccCCCccC
Q 034299           86 SNLRAHPLKPVIH   98 (98)
Q Consensus        86 ~~~~~~~~~~~~~   98 (98)
                      ..+|+||++|+.|
T Consensus        84 tkir~epl~~v~h   96 (96)
T KOG1784|consen   84 TKIRAEPLHPVVH   96 (96)
T ss_pred             hhcccCCCCCccC
Confidence            9999999999988

>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=99.90  E-value=2.9e-23  Score=131.07  Aligned_cols=73  Identities=32%  Similarity=0.560  Sum_probs=64.2

Q ss_pred             hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCC----eeEEEecEEEEcCCcEEEEEecC
Q 034299            4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEG----VQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~----~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      ...|.++++++|+|+|+|||++.|+|.|||+||||+|++|+|+...++++    ...+.+|.++|||++|++|++.+
T Consensus         4 ~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           4 ILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             hhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            35799999999999999999999999999999999999999998653321    35678999999999999998764

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

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

Probab=99.90  E-value=4.1e-23  Score=127.83  Aligned_cols=71  Identities=28%  Similarity=0.593  Sum_probs=64.0

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      |.+.|+++++|+|+|+|++|+++.|+|.|||+||||+|+||.|+..    +...+.+|.++|||++|++|++.|.
T Consensus         1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~----~~~~~~lg~v~IRG~~I~~i~~~~~   71 (72)
T cd01719           1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNS----GGEKNNIGMVVIRGNSIVMLEALER   71 (72)
T ss_pred             CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEcc----CCceeEeceEEECCCEEEEEEcccc
Confidence            4579999999999999999999999999999999999999999862    2346789999999999999998753

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

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

Probab=99.89  E-value=6.8e-23  Score=129.47  Aligned_cols=72  Identities=19%  Similarity=0.346  Sum_probs=63.6

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCC---------eeEEEecEEEEcCCcEEEEE
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEG---------VQQLVLGLYIIRGDNISIVG   73 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~---------~~~r~lg~v~irG~~I~~i~   73 (98)
                      |...|+.+++++|.|+++|||++.|+|.|||+||||+|+||+|++..++++         ...|.+|.++|||++|++|+
T Consensus         2 pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~   81 (82)
T cd01730           2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS   81 (82)
T ss_pred             chHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence            667889999999999999999999999999999999999999998653211         25789999999999999986


Q ss_pred             e
Q 034299           74 E   74 (98)
Q Consensus        74 ~   74 (98)
                      +
T Consensus        82 ~   82 (82)
T cd01730          82 P   82 (82)
T ss_pred             C
Confidence            3

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.

>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=99.89  E-value=1.4e-22  Score=127.06  Aligned_cols=70  Identities=30%  Similarity=0.500  Sum_probs=62.3

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecC------CCeeEEEecEEEEcCCcEEEEEe
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTK------EGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~------~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      ..|.+|++++|+|+++|||++.|+|.|||+||||+|+||.|++..+.      .+.+.+.+|+++|||++|++|..
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            57999999999999999999999999999999999999999886432      12467899999999999999974

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=99.89  E-value=1.4e-22  Score=123.70  Aligned_cols=68  Identities=25%  Similarity=0.385  Sum_probs=61.9

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      |...|+++++++|+|+|++|++|.|+|.|||+|||++|+||+|++..    ..++.+|.++|||++|++|.+
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----~~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG----EPVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC----CeEeEcCcEEEeCCEEEEEcC
Confidence            56789999999999999999999999999999999999999998642    256789999999999999864

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.

>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=99.89  E-value=2.7e-22  Score=124.88  Aligned_cols=72  Identities=33%  Similarity=0.742  Sum_probs=64.1

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      ++.+.|+++++++|.|.++|||++.|+|.|||+|||++|+||.|+....+ ...++.+|.++|||++|++|+.
T Consensus         2 ~~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~-~~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728           2 PGTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD-KYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             CchHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC-ccceeEeeEEEEECCEEEEEEc
Confidence            45678999999999999999999999999999999999999999876432 2356889999999999999975

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.

>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=99.88  E-value=4e-22  Score=124.38  Aligned_cols=70  Identities=31%  Similarity=0.453  Sum_probs=63.3

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecC--CCeeEEEecEEEEcCCcEEEEEe
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTK--EGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~--~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      ..|++|++++|+|+++|||.|.|+|.|||++|||+|+||.|++..+.  ...+.|.+|+++|||++|++|..
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence            57999999999999999999999999999999999999999986543  23568899999999999999863

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.88  E-value=2.7e-22  Score=123.95  Aligned_cols=68  Identities=31%  Similarity=0.432  Sum_probs=61.1

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      |...|.++++++|+|+|+||++|.|+|.+||+|||++|+||.|.+.    +...+.+|.++|||++|++|.+
T Consensus         5 P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~----~~~~~~lg~v~iRG~~V~~i~~   72 (72)
T PRK00737          5 PLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD----GEVVRKLGKVVIRGDNVVYVSP   72 (72)
T ss_pred             hHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC----CCeEeEcCcEEEeCCEEEEEcC
Confidence            5668999999999999999999999999999999999999999752    2356789999999999999863

>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=99.86  E-value=2.3e-21  Score=124.04  Aligned_cols=74  Identities=20%  Similarity=0.347  Sum_probs=64.1

Q ss_pred             CCChhhHHhhc--CCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecC-CC--------eeEEEecEEEEcCCcE
Q 034299            1 MSGGPGLESLV--EQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTK-EG--------VQQLVLGLYIIRGDNI   69 (98)
Q Consensus         1 m~~~~~L~~~i--~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~-~~--------~~~r~lg~v~irG~~I   69 (98)
                      +-|...|.+.+  +++|.|+|++|+++.|+|.|||+||||+|+||.|.+...+ ++        ..++.+|.+||||++|
T Consensus         1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~V   80 (87)
T cd01720           1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSV   80 (87)
T ss_pred             CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEE
Confidence            35778899997  8999999999999999999999999999999999886522 11        2467899999999999


Q ss_pred             EEEEe
Q 034299           70 SIVGE   74 (98)
Q Consensus        70 ~~i~~   74 (98)
                      ++|..
T Consensus        81 v~Is~   85 (87)
T cd01720          81 ILVLR   85 (87)
T ss_pred             EEEec
Confidence            99975

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.

>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=99.86  E-value=2.4e-21  Score=118.09  Aligned_cols=67  Identities=27%  Similarity=0.391  Sum_probs=60.1

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEE
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVG   73 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~   73 (98)
                      |...|++++|++|+|+|++|++|.|+|.+||+|||++|+||+|...    +...+.+|.++|||++|.+|.
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~----~~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVN----GQLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeC----CceeeEeCCEEEECCEEEEEC
Confidence            5678999999999999999999999999999999999999988642    235678999999999999984

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

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

Probab=99.85  E-value=3.6e-21  Score=117.69  Aligned_cols=68  Identities=25%  Similarity=0.289  Sum_probs=60.6

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEE
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVG   73 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~   73 (98)
                      .|.+.|++++|++|+|+|++|++|.|+|.+||++||++|+||+|+..    +.....+|.++|||++|.+|.
T Consensus         1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~----~~~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID----GKSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeC----CccccCcCcEEEECCEEEEEC
Confidence            36789999999999999999999999999999999999999998742    234567999999999999983

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.

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

Probab=99.84  E-value=1.3e-20  Score=113.86  Aligned_cols=66  Identities=32%  Similarity=0.511  Sum_probs=60.3

Q ss_pred             hHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            6 GLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      +|++++|++|+|++++|++++|+|.+||++||++|+||.|.+..+   .+.+++|.+||||++|.+|.+
T Consensus         2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~---~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNG---PEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTE---SEEEEEEEEEEEGGGEEEEEE
T ss_pred             hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCC---CcEeECcEEEEECCEEEEEEC
Confidence            689999999999999999999999999999999999999986432   167899999999999999974

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 ....

>smart00651 Sm snRNP Sm proteins

Probab=99.84  E-value=1.8e-20  Score=113.14  Aligned_cols=66  Identities=36%  Similarity=0.546  Sum_probs=60.1

Q ss_pred             hHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            6 GLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      .|++++|++|+|+++||+++.|+|.+||++||++|+||.|++..+   .+.+.+|.++|||++|++|.+
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~---~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG---EKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC---cEEeEeCCEEEcCCEEEEEeC
Confidence            689999999999999999999999999999999999999986531   467899999999999999863

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

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

Probab=99.83  E-value=4e-20  Score=115.79  Aligned_cols=72  Identities=31%  Similarity=0.445  Sum_probs=60.7

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCe-eEEEecEEEEcCCcEEEEEe
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGV-QQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~-~~r~lg~v~irG~~I~~i~~   74 (98)
                      .|...|.++++++|.|+|++|++|.|+|.|||+|||++|+||.|++.. +... ..+..|.++|||++|.+|.+
T Consensus         7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-~~~~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958           7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH-DGEKNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc-CCccccceeccEEEEECCcEEEEeC
Confidence            467899999999999999999999999999999999999999998741 1111 23444599999999999863

>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=99.82  E-value=8.6e-20  Score=114.91  Aligned_cols=70  Identities=23%  Similarity=0.403  Sum_probs=60.2

Q ss_pred             CChhhHHhhcCC--eEEEEEC--CCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            2 SGGPGLESLVEQ--QISVITN--DGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         2 ~~~~~L~~~i~k--~V~V~l~--~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      .|...+.+|+++  +|.|.++  +|+++.|+|.|||+|||++|+||+|+...   +...+.+|.++|||+||++|++
T Consensus         6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~---~~~~~~lG~iliRGnnV~~I~p   79 (79)
T cd01718           6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK---TKTRKPLGRILLKGDNITLIQN   79 (79)
T ss_pred             CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC---CceEeEcCcEEEeCCEEEEEcC
Confidence            478899999999  6666665  89999999999999999999999998642   2356789999999999999864

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.

>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=99.82  E-value=1.5e-19  Score=112.73  Aligned_cols=73  Identities=23%  Similarity=0.178  Sum_probs=63.2

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcc
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEE   78 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~   78 (98)
                      |...|+++.|++|.|+|++|+++.|+|.+||+|||++|+||++...   ++.....++.+||||++|.+|..++..
T Consensus         2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~---~g~~~~~~~~v~IRG~~I~~i~~p~~~   74 (76)
T cd01723           2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSK---DGDKFWKMPECYIRGNTIKYLRVPDEI   74 (76)
T ss_pred             chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECC---CCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence            6778999999999999999999999999999999999999988632   233345679999999999999887643

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=99.82  E-value=1.6e-19  Score=111.08  Aligned_cols=70  Identities=20%  Similarity=0.134  Sum_probs=61.3

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      |...|.++.|++|.|+|++|.+|+|+|.++|++||++|+||.+...   ++ +...+|.+||||++|.++..+|
T Consensus         1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~---~g-~~~~~~~v~IRG~nI~~v~lPd   70 (70)
T cd01721           1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTAR---DG-RVSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECC---CC-cEeEcCcEEEeCCEEEEEEeCC
Confidence            5678999999999999999999999999999999999999987532   12 3456899999999999998875

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=99.80  E-value=4.4e-19  Score=105.66  Aligned_cols=63  Identities=41%  Similarity=0.682  Sum_probs=57.4

Q ss_pred             HHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEE
Q 034299            7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVG   73 (98)
Q Consensus         7 L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~   73 (98)
                      |++++|++|+|+++||+.+.|+|.+||++||++|+||.|.+..    ...+.+|.++|||++|.+|.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~----~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE----GKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC----CcEEECCeEEEECCEEEEEC
Confidence            5789999999999999999999999999999999999998653    35688999999999999873

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.

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

Probab=99.77  E-value=3.7e-20  Score=119.77  Aligned_cols=79  Identities=27%  Similarity=0.503  Sum_probs=69.6

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCC----eeEEEecEEEEcCCcEEEEEecCcc--
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEG----VQQLVLGLYIIRGDNISIVGEVDEE--   78 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~----~~~r~lg~v~irG~~I~~i~~~d~~--   78 (98)
                      .+|.+|++++|+|++.+||+.+|+|+|||+.||+||++++|+..+|+++    .+.|++|+++|||..+++|++.|-.  
T Consensus        20 lDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e~   99 (108)
T KOG1781|consen   20 LDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSEE   99 (108)
T ss_pred             hhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchhh
Confidence            4799999999999999999999999999999999999999998777654    3569999999999999999998843  


Q ss_pred             ccccC
Q 034299           79 LDSHL   83 (98)
Q Consensus        79 ~e~~~   83 (98)
                      +.+++
T Consensus       100 I~npf  104 (108)
T KOG1781|consen  100 IANPF  104 (108)
T ss_pred             hccch
Confidence            34444

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

Probab=99.77  E-value=1.1e-18  Score=107.66  Aligned_cols=68  Identities=32%  Similarity=0.630  Sum_probs=61.3

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      +.|++|++|++.+++..||.+.|.|+|||.|||++|++++|....    ..+..+|.++|||++|+.+.+.+
T Consensus         7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~----~~~~~ig~~vIrgnsiv~~eaL~   74 (77)
T KOG1780|consen    7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD----GDKNNIGMVVIRGNSIVMVEALE   74 (77)
T ss_pred             chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc----CCcceeeeEEEeccEEEEEeecc
Confidence            699999999999999999999999999999999999999997422    24567999999999999998875

>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=99.76  E-value=5.3e-18  Score=109.04  Aligned_cols=70  Identities=23%  Similarity=0.294  Sum_probs=62.3

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcc
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEE   78 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~   78 (98)
                      ..|+++.|++|+|+|++|.+|.|+|.++|.+||++|+||++...    +.....+|.++|||++|.+|..+|+-
T Consensus         4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~----~~~~~~~~~v~IRG~nI~yi~lPd~l   73 (90)
T cd01724           4 RFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLK----GRNPVPLDTLSIRGNNIRYFILPDSL   73 (90)
T ss_pred             HHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcC----CCceeEcceEEEeCCEEEEEEcCCcC
Confidence            47899999999999999999999999999999999999988742    22456799999999999999998763

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.

>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=99.76  E-value=4.9e-18  Score=107.16  Aligned_cols=75  Identities=24%  Similarity=0.249  Sum_probs=62.6

Q ss_pred             hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcccc
Q 034299            4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELD   80 (98)
Q Consensus         4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e   80 (98)
                      ...|+++.|++|.|+|++|.++.|+|.++|++||++|+||++..  ++.......++.++|||++|.+|..+|..++
T Consensus         3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~--~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~   77 (81)
T cd01725           3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTD--PEKYPHMLSVKNCFIRGSVVRYVQLPADEVD   77 (81)
T ss_pred             hHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEc--CCCcccccccCeEEEECCEEEEEEeChhHcC
Confidence            35789999999999999999999999999999999999997653  2111223457899999999999999976554

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.

>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=99.74  E-value=2.3e-17  Score=103.55  Aligned_cols=68  Identities=19%  Similarity=0.144  Sum_probs=58.7

Q ss_pred             hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEec
Q 034299            4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV   75 (98)
Q Consensus         4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~   75 (98)
                      ...|+++.|++|.|+|++|.+|.|+|.++|++||++|+||.+...    +.....+|.++|||++|.+|..+
T Consensus        11 ~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~----~~~~~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733          11 IILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDR----NGKQVQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             HHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcC----CCceeECCcEEEECCEEEEEEcC
Confidence            347899999999999999999999999999999999999986531    12344789999999999999764

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.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.73  E-value=3.7e-17  Score=104.99  Aligned_cols=71  Identities=23%  Similarity=0.374  Sum_probs=58.0

Q ss_pred             CChhhHHhhcCCe--EEEEECC--CcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEec
Q 034299            2 SGGPGLESLVEQQ--ISVITND--GRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV   75 (98)
Q Consensus         2 ~~~~~L~~~i~k~--V~V~l~~--Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~   75 (98)
                      +|...+.+++.++  |.|.+++  ++++.|+|.|||+|||++|+||+|++..   +...+.+|.++|||+||++|.+.
T Consensus        14 ~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~---~~~~~~lG~ilIRGnnV~~I~~~   88 (89)
T PTZ00138         14 QPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK---KNTRKDLGRILLKGDNITLIMAA   88 (89)
T ss_pred             CCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC---CceeeEcCeEEEcCCEEEEEEcC
Confidence            4667788888765  4555556  5999999999999999999999998642   23567899999999999999764

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

Probab=99.72  E-value=4.9e-19  Score=118.43  Aligned_cols=87  Identities=30%  Similarity=0.612  Sum_probs=75.2

Q ss_pred             hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCccccccC
Q 034299            4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSHL   83 (98)
Q Consensus         4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e~~~   83 (98)
                      ...|.+++++++.|.|+|||.+.|.|++||||.|++|++|+|+++-.+. +..+..|..+|||+||++++..|.++| ..
T Consensus        11 t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~-Y~di~~glfiIRGENVvllGeid~dkE-~~   88 (129)
T KOG1782|consen   11 TTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNK-YCDIPRGLFIIRGENVVLLGEIDLDKE-EE   88 (129)
T ss_pred             hhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecce-ecccCceEEEEecCcEEEEecCCcchh-hc
Confidence            4568999999999999999999999999999999999999999986543 456678999999999999999999888 45


Q ss_pred             CCCcccccc
Q 034299           84 DLSNLRAHP   92 (98)
Q Consensus        84 ~~~~~~~~~   92 (98)
                      .+.+++.+.
T Consensus        89 ~l~~i~~~e   97 (129)
T KOG1782|consen   89 PLEQISFEE   97 (129)
T ss_pred             cceeCCHHH
Confidence            555555444

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

Probab=99.71  E-value=2e-17  Score=101.92  Aligned_cols=70  Identities=27%  Similarity=0.326  Sum_probs=63.7

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      |.++|+.+.||+|.|+|++|.+|.|+|.+.|+||||.|.+|+|++.    +...-.+|.++||-+||.+|...+
T Consensus         9 PKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~id----G~~~g~lGEilIRCNNvlyi~gv~   78 (79)
T KOG3482|consen    9 PKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYID----GVSTGNLGEILIRCNNVLYIRGVP   78 (79)
T ss_pred             chHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhc----ccccccceeEEEEeccEEEEecCC
Confidence            6789999999999999999999999999999999999999999874    344567999999999999998664

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

Probab=99.63  E-value=1.3e-16  Score=100.59  Aligned_cols=74  Identities=19%  Similarity=0.328  Sum_probs=64.0

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCC---C------eeEEEecEEEEcCCcEEEEE
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKE---G------VQQLVLGLYIIRGDNISIVG   73 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~---~------~~~r~lg~v~irG~~I~~i~   73 (98)
                      |...|.-+++.+|.|+++++|++.|+|+|||+|.||+|.|+.|.++.-+.   .      ..+|.+..+|+||++|.+|+
T Consensus         6 PldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvs   85 (91)
T KOG3460|consen    6 PLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVS   85 (91)
T ss_pred             cHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEc
Confidence            66788889999999999999999999999999999999999998864211   1      24678899999999999998


Q ss_pred             ecC
Q 034299           74 EVD   76 (98)
Q Consensus        74 ~~d   76 (98)
                      ++-
T Consensus        86 pp~   88 (91)
T KOG3460|consen   86 PPL   88 (91)
T ss_pred             Ccc
Confidence            864

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

Probab=99.61  E-value=8.8e-16  Score=95.44  Aligned_cols=75  Identities=23%  Similarity=0.383  Sum_probs=66.5

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      .|...+.+++|.+++|.+++.|++.|+|.|||.|.|++|+|++|+...+. +.....++++++.|++|+.+.+..+
T Consensus         7 lPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e-gr~~tk~~~iLLnGNni~mLvPGGe   81 (84)
T KOG1775|consen    7 LPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE-GRRMTKLDQILLNGNNITMLVPGGE   81 (84)
T ss_pred             ccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC-cceeeeeeeeeecCCcEEEEecCCC
Confidence            36678899999999999999999999999999999999999999987653 3556689999999999999987653

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

Probab=99.57  E-value=5e-16  Score=95.71  Aligned_cols=70  Identities=27%  Similarity=0.374  Sum_probs=63.6

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEec
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV   75 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~   75 (98)
                      +|...|++.+||+|.|+|.+|-.|+|+|.|.|.|||+-|+.+.|+.    ++..++..|-+||||++|.+|...
T Consensus         6 ~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~----ngql~n~ygdaFirGnnVlyIs~~   75 (77)
T KOG1783|consen    6 MPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV----NGQLKNKYGDAFIRGNNVLYISTQ   75 (77)
T ss_pred             CcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh----cCcccccccceeeccccEEEEEec
Confidence            3778999999999999999999999999999999999999999985    245678899999999999999764

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=99.55  E-value=7.6e-16  Score=107.99  Aligned_cols=75  Identities=27%  Similarity=0.469  Sum_probs=65.4

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeec------CCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYST------KEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~------~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      ....|.++++.+++|.++|||+|.|+|.+||+|||++|.+|+|++...      .+++++|.+|+|++||++|++.+.-+
T Consensus         5 ~sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg   84 (177)
T KOG3168|consen    5 KSSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG   84 (177)
T ss_pred             chhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence            345788999999999999999999999999999999999999987432      12368999999999999999998765


Q ss_pred             c
Q 034299           77 E   77 (98)
Q Consensus        77 ~   77 (98)
                      .
T Consensus        85 p   85 (177)
T KOG3168|consen   85 P   85 (177)
T ss_pred             C
Confidence            3

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

Probab=99.39  E-value=8.4e-13  Score=88.66  Aligned_cols=77  Identities=23%  Similarity=0.201  Sum_probs=69.3

Q ss_pred             CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcccc
Q 034299            1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELD   80 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e   80 (98)
                      |-|..+|.-..+.++.|+|++|.+|.|.|..+|..|||.|.+++++..   ++.+...+..+.|||++|.++..+|+-++
T Consensus         1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~---Dgdkf~r~pEcYirGttIkylri~d~iid   77 (134)
T KOG3293|consen    1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSE---DGDKFFRMPECYIRGTTIKYLRIPDEIID   77 (134)
T ss_pred             CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEecc---CCCceeecceeEEecceeEEEeccHHHHH
Confidence            889999999999999999999999999999999999999999998753   34456778999999999999999987543

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

Probab=99.39  E-value=2.2e-12  Score=82.27  Aligned_cols=74  Identities=23%  Similarity=0.279  Sum_probs=62.8

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcccc
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELD   80 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e   80 (98)
                      ..++.++|++|.|+|+++-.+.|+|.++|+|.|+.|.|..-.  ++++..+--.+..+||||+.|.++..+.+..+
T Consensus         5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~--d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vd   78 (96)
T KOG3448|consen    5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVT--DPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVD   78 (96)
T ss_pred             HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEee--CcccCCCeeeeeeEEEeccEEEEEEeChhHHH
Confidence            467899999999999999999999999999999999997543  44344466678899999999999998866544

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

Probab=99.28  E-value=3.2e-12  Score=80.42  Aligned_cols=72  Identities=25%  Similarity=0.385  Sum_probs=56.7

Q ss_pred             CChhhHHhhcCCeEEEE--E--CCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            2 SGGPGLESLVEQQISVI--T--NDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~--l--~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      +|-..+.+|+..+.+|.  +  +-|-.++|.+.|||.|||+||++|+|...+.   ...+.+|.++++|+||.+|...+
T Consensus        12 ~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~---~~rk~lGRilLKGDnItli~~~~   87 (88)
T KOG1774|consen   12 QPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT---KSRKELGRILLKGDNITLIQSAG   87 (88)
T ss_pred             CcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc---cCCCccccEEEcCCcEEEEeecC
Confidence            35556777887665555  4  3489999999999999999999999975432   23448999999999999997653

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

Probab=98.92  E-value=5.1e-09  Score=69.05  Aligned_cols=77  Identities=18%  Similarity=0.093  Sum_probs=65.2

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcccccc
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSH   82 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e~~   82 (98)
                      |...|.+.-|.-|.++++.|..|.|.|.-.|.+||+.|+|.+-...+    ..-..+..|||||+.|.++..+|.-+.++
T Consensus         6 piKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d----g~vs~le~V~IRGS~IRFlvlPdmLKnAP   81 (119)
T KOG3172|consen    6 PIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD----GRVSQLEQVFIRGSKIRFLVLPDMLKNAP   81 (119)
T ss_pred             ceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccC----CcceeeeeEEEecCeEEEEECchHhhcCc
Confidence            45678889999999999999999999999999999999998765432    23456889999999999999998766655


Q ss_pred             C
Q 034299           83 L   83 (98)
Q Consensus        83 ~   83 (98)
                      +
T Consensus        82 m   82 (119)
T KOG3172|consen   82 M   82 (119)
T ss_pred             c
Confidence            4

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

Probab=98.81  E-value=4.7e-08  Score=64.50  Aligned_cols=69  Identities=23%  Similarity=0.304  Sum_probs=60.2

Q ss_pred             hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      ...|.++.+.++.|+|++|....|++.++|.+||..|.++.-...    + +...+-.+++||++|-|+-.+|.
T Consensus         4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~----~-~pv~l~~lsirgnniRy~~lpD~   72 (109)
T KOG3428|consen    4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK----G-EPVRLDTLSIRGNNIRYYILPDS   72 (109)
T ss_pred             HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC----C-CceeEEEEEeecceEEEEEccCC
Confidence            457899999999999999999999999999999999999866532    2 34578899999999999988874

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

Probab=98.65  E-value=3.5e-09  Score=69.98  Aligned_cols=62  Identities=23%  Similarity=0.427  Sum_probs=53.3

Q ss_pred             CCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEee-cCC--C------eeEEEecEEEEcCCcEEEEE
Q 034299           12 EQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYS-TKE--G------VQQLVLGLYIIRGDNISIVG   73 (98)
Q Consensus        12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~-~~~--~------~~~r~lg~v~irG~~I~~i~   73 (98)
                      ...|.|.++|++.+.|+..|||.|+|++|+++.|-|.. ++.  +      ...|++|.+||||++|+.+.
T Consensus        36 ~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~  106 (114)
T KOG3459|consen   36 NTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVL  106 (114)
T ss_pred             CceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEE
Confidence            46889999999999999999999999999999998864 221  1      23789999999999999886

>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=98.42  E-value=2e-07  Score=56.61  Aligned_cols=37  Identities=24%  Similarity=0.280  Sum_probs=31.2

Q ss_pred             CeEEEEECC--C--cEEEEEEEEEcCCCceEecceEEEEee
Q 034299           13 QQISVITND--G--RNIVGVLKGFDQATNIILDESHERVYS   49 (98)
Q Consensus        13 k~V~V~l~~--G--r~i~G~L~~~D~~~NlvL~~~~e~~~~   49 (98)
                      ++|+|.++.  |  -.++|.|.+||+|+||+|.|+.|.+..
T Consensus         9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~   49 (66)
T cd01739           9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK   49 (66)
T ss_pred             cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence            677777754  3  489999999999999999999998754

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.

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

Probab=98.04  E-value=1.4e-05  Score=49.36  Aligned_cols=65  Identities=18%  Similarity=0.290  Sum_probs=39.8

Q ss_pred             hHHhhcCCeEEEEECCCcEEEEEEEEEcC---CCceEecceEEEEeecC--C-CeeEEEecEEEEcCCcEE
Q 034299            6 GLESLVEQQISVITNDGRNIVGVLKGFDQ---ATNIILDESHERVYSTK--E-GVQQLVLGLYIIRGDNIS   70 (98)
Q Consensus         6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~---~~NlvL~~~~e~~~~~~--~-~~~~r~lg~v~irG~~I~   70 (98)
                      .+..++|++|.|+++||..|+|.|.+++.   .+.++|+.|........  . .........++++++.|+
T Consensus         6 l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    6 LLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred             HHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence            46788999999999999999999999998   89999988866432111  1 112334556677777665

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

Probab=97.32  E-value=0.001  Score=43.24  Aligned_cols=72  Identities=17%  Similarity=0.277  Sum_probs=54.3

Q ss_pred             HhhcCCeEEEEECCCcEEEEEEEEEcC-CCceEecceEEEEeecC--CC---eeEEEecEEEEcCCcEEEEEecCccc
Q 034299            8 ESLVEQQISVITNDGRNIVGVLKGFDQ-ATNIILDESHERVYSTK--EG---VQQLVLGLYIIRGDNISIVGEVDEEL   79 (98)
Q Consensus         8 ~~~i~k~V~V~l~~Gr~i~G~L~~~D~-~~NlvL~~~~e~~~~~~--~~---~~~r~lg~v~irG~~I~~i~~~d~~~   79 (98)
                      .+|+|++|.+..+++-.|+|+|..+|. ...+.|.|+..+-....  ..   ........+..||+.|.-+...+...
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~   81 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP   81 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence            479999999999999999999999994 88899999866532110  00   11224678899999999998876544

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

Probab=97.01  E-value=0.003  Score=44.82  Aligned_cols=63  Identities=21%  Similarity=0.341  Sum_probs=45.5

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcc
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEE   78 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~   78 (98)
                      ..+.+|++|+|+|.+.| +++.|.+.++| -..|++|-+-.|      ++  +  ...-+|.|..|..+...+++
T Consensus        10 ~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e------~~--~--~sv~~I~ghaVk~vevl~~~   73 (166)
T PF06372_consen   10 LEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE------DG--K--RSVKVIMGHAVKSVEVLSEG   73 (166)
T ss_dssp             HHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T------TS-----EEEEEE-GGGEEEEEEEE--
T ss_pred             HHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc------CC--c--eeEEEEEccceEEEEEccCC
Confidence            46789999999999999 99999999999 788999976433      11  2  24578999999999998864

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

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

Probab=96.92  E-value=0.0065  Score=34.29  Aligned_cols=35  Identities=20%  Similarity=0.386  Sum_probs=30.3

Q ss_pred             hcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEE
Q 034299           10 LVEQQISVITNDGRNIVGVLKGFDQATNIILDESHE   45 (98)
Q Consensus        10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e   45 (98)
                      .+|++|++.. ++..++|+..++|.+..|+++....
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g   35 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG   35 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence            4799999999 6777799999999999999977544

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

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

Probab=96.08  E-value=0.048  Score=33.93  Aligned_cols=64  Identities=19%  Similarity=0.299  Sum_probs=45.0

Q ss_pred             HhhcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeecCC--C----eeEEEecEEEEcCCcEEE
Q 034299            8 ESLVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYSTKE--G----VQQLVLGLYIIRGDNISI   71 (98)
Q Consensus         8 ~~~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~~~--~----~~~r~lg~v~irG~~I~~   71 (98)
                      .+|+|+++.+..+.+-.|+|.|.++| +..-+.|.|+..+=+..-.  +    ........++.||+.|.-
T Consensus         2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD   72 (74)
T cd01736           2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD   72 (74)
T ss_pred             ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence            36999999999999999999999999 5555779998655322110  0    122345567777777643

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.

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

Probab=95.67  E-value=0.038  Score=33.13  Aligned_cols=33  Identities=21%  Similarity=0.284  Sum_probs=28.4

Q ss_pred             hcCCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299           10 LVEQQISVITNDGRNIVGVLKGFDQATNIILDE   42 (98)
Q Consensus        10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~   42 (98)
                      .+|..|++++..|.+|+|.+.+||...+++.=.
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk   36 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILK   36 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence            479999999999999999999999777776433

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

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

Probab=95.59  E-value=0.067  Score=33.75  Aligned_cols=60  Identities=12%  Similarity=0.211  Sum_probs=44.4

Q ss_pred             hHHhhcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            6 GLESLVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      .|....|+++.+.|.++.++.|++.++| ...|+..++-    ..|- |    .....++|.+.|+++..
T Consensus        18 ~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L----~TPl-G----v~~eAlLR~~DVi~~~f   78 (80)
T PF11095_consen   18 SLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNL----QTPL-G----VQPEALLRCSDVISISF   78 (80)
T ss_dssp             HHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEE----ETTT-T----EEEEEEEEGGGEEEEEE
T ss_pred             HHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhc----CCCc-c----cChhheeecCCEEEEEe
Confidence            5677789999999999999999999999 6677776653    1221 1    24677999999999875

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

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

Probab=95.42  E-value=0.034  Score=33.36  Aligned_cols=31  Identities=16%  Similarity=0.400  Sum_probs=25.9

Q ss_pred             CCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299           12 EQQISVITNDGRNIVGVLKGFDQATNIILDE   42 (98)
Q Consensus        12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~   42 (98)
                      ..+|.|-|.+|-.+.|.+.+||+|+=++-.+
T Consensus        11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716          11 KIPVTIYLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence            5678888999999999999999999544333

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

>TIGR02383 Hfq RNA chaperone Hfq

Probab=95.36  E-value=0.036  Score=33.25  Aligned_cols=31  Identities=23%  Similarity=0.455  Sum_probs=26.1

Q ss_pred             CCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299           12 EQQISVITNDGRNIVGVLKGFDQATNIILDE   42 (98)
Q Consensus        12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~   42 (98)
                      ..+|.|-|.+|-.+.|.+.+||+|+=++-.+
T Consensus        15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383        15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            5678888999999999999999999555433

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.

>PRK14638 hypothetical protein; Provisional

Probab=95.17  E-value=0.049  Score=37.81  Aligned_cols=36  Identities=17%  Similarity=0.442  Sum_probs=31.3

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      ..+.+++|++|.|++++++.++|+|.++|.. ++.|.
T Consensus        93 ~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         93 KDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            5788999999999999999999999999964 45554

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

Probab=94.82  E-value=0.057  Score=33.77  Aligned_cols=31  Identities=16%  Similarity=0.468  Sum_probs=26.6

Q ss_pred             CCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299           12 EQQISVITNDGRNIVGVLKGFDQATNIILDES   43 (98)
Q Consensus        12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~   43 (98)
                      ..+|.|-|.+|-.+.|.+.+||+|. +.|++.
T Consensus        19 ~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~~   49 (77)
T COG1923          19 KIPVTIFLVNGFKLQGQVESFDNFV-VLLKNT   49 (77)
T ss_pred             CCeEEEEEEcCEEEEEEEEeeeeEE-EEEEcC
Confidence            5789999999999999999999998 555553

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=94.78  E-value=0.061  Score=33.86  Aligned_cols=31  Identities=13%  Similarity=0.363  Sum_probs=26.5

Q ss_pred             CCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299           12 EQQISVITNDGRNIVGVLKGFDQATNIILDE   42 (98)
Q Consensus        12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~   42 (98)
                      ..+|.|-|.+|-.+.|.+.+||+|.=++-.+
T Consensus        19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~   49 (79)
T PRK00395         19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNT   49 (79)
T ss_pred             CCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence            5788999999999999999999999555444

>PRK14639 hypothetical protein; Provisional

Probab=94.48  E-value=0.097  Score=35.93  Aligned_cols=36  Identities=19%  Similarity=0.375  Sum_probs=31.4

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      ..+.+++|++|.|.+.+++.+.|+|.++|.. ++.|.
T Consensus        81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~  116 (140)
T PRK14639         81 EHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE  116 (140)
T ss_pred             HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            5788999999999999999999999999984 45553

>PRK02001 hypothetical protein; Validated

Probab=94.47  E-value=0.096  Score=36.55  Aligned_cols=36  Identities=28%  Similarity=0.530  Sum_probs=31.4

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      ..+.+++|+.|+|.+.+++.+.|+|.++|.. ++.|.
T Consensus        83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~  118 (152)
T PRK02001         83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE  118 (152)
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence            4788999999999999999999999999975 45554

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

Probab=94.07  E-value=0.44  Score=28.97  Aligned_cols=52  Identities=31%  Similarity=0.385  Sum_probs=39.3

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEE
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVG   73 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~   73 (98)
                      ..|++++|+++.|.+..|.. .|+|.+.-..- ++|+..               -...+||=..|++|.
T Consensus        14 q~lq~liG~~vvV~T~~g~v-~G~L~~V~pDh-Ivl~~~---------------~~~~~IR~~~IV~v~   65 (66)
T PF10842_consen   14 QTLQSLIGQRVVVQTTRGSV-RGILVDVKPDH-IVLEEN---------------GTPFFIRIAQIVWVM   65 (66)
T ss_pred             HHHHHhcCCEEEEEEcCCcE-EEEEEeecCCE-EEEEeC---------------CcEEEEEeeeEEEEc
Confidence            46899999999999988776 99999987543 455432               245678888888775

>PRK14644 hypothetical protein; Provisional

Probab=93.27  E-value=0.3  Score=33.45  Aligned_cols=36  Identities=28%  Similarity=0.272  Sum_probs=30.7

Q ss_pred             hhHHhhcCCeEEEEECCC----cEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVITNDG----RNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~G----r~i~G~L~~~D~~~NlvL~   41 (98)
                      .++.+++|+.|.|++++.    +.+.|.|.++|.. ++.|.
T Consensus        78 ~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         78 DELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             HHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            368899999999999886    8999999999974 56664

>PRK14640 hypothetical protein; Provisional

Probab=92.97  E-value=0.35  Score=33.55  Aligned_cols=36  Identities=31%  Similarity=0.418  Sum_probs=30.2

Q ss_pred             hhHHhhcCCeEEEEE----CCCcEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVIT----NDGRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l----~~Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      ..+.+++|++|.|++    .+++.++|+|.++|.. ++.|.
T Consensus        90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~  129 (152)
T PRK14640         90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT  129 (152)
T ss_pred             HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence            578899999999999    4669999999999874 46664

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

Probab=92.39  E-value=0.37  Score=29.90  Aligned_cols=36  Identities=28%  Similarity=0.489  Sum_probs=29.5

Q ss_pred             hhHHhhcCCeEEEEEC---CC-cEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVITN---DG-RNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~---~G-r~i~G~L~~~D~~~NlvL~   41 (98)
                      ..+.+++|+.|.|+++   +| +.+.|.|.++|.. ++.|.
T Consensus        18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l~   57 (83)
T cd01734          18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTLE   57 (83)
T ss_pred             HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEEE
Confidence            4788999999999997   56 6999999999985 35553

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

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

Probab=92.04  E-value=0.4  Score=32.45  Aligned_cols=35  Identities=20%  Similarity=0.368  Sum_probs=26.9

Q ss_pred             hhHHhhcCCeEEEEEC----CCcEEEEEEEEEcCCCceEe
Q 034299            5 PGLESLVEQQISVITN----DGRNIVGVLKGFDQATNIIL   40 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~----~Gr~i~G~L~~~D~~~NlvL   40 (98)
                      .++.+++|++|.|.++    +.+.+.|+|.++|. ..++|
T Consensus        80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            5789999999999994    45799999999998 44555

; PDB: 1IB8_A.

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.87  E-value=0.66  Score=32.48  Aligned_cols=37  Identities=14%  Similarity=0.323  Sum_probs=32.0

Q ss_pred             hhhHHhhcCCeEEEEE----CCCcEEEEEEEEEcCCCceEec
Q 034299            4 GPGLESLVEQQISVIT----NDGRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         4 ~~~L~~~i~k~V~V~l----~~Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      ...+..++|+.|.|.+    .+++.+.|+|.++|... +++.
T Consensus        91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~~  131 (153)
T COG0779          91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTLE  131 (153)
T ss_pred             HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEEE
Confidence            4578899999999999    78899999999999887 4443

>PRK14633 hypothetical protein; Provisional

Probab=91.86  E-value=0.44  Score=32.98  Aligned_cols=36  Identities=25%  Similarity=0.410  Sum_probs=30.0

Q ss_pred             hhHHhhcCCeEEEEE----CCCcEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVIT----NDGRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l----~~Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      .++.+++|++|.|++    .+++.++|+|.+++.. ++.|.
T Consensus        87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~  126 (150)
T PRK14633         87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN  126 (150)
T ss_pred             HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence            578899999999998    3568999999999875 56664

>PRK14642 hypothetical protein; Provisional

Probab=91.48  E-value=0.43  Score=34.74  Aligned_cols=35  Identities=11%  Similarity=0.272  Sum_probs=29.8

Q ss_pred             hhHHhhcCCeEEEEEC-------------CCcEEEEEEEEEcCCCceEe
Q 034299            5 PGLESLVEQQISVITN-------------DGRNIVGVLKGFDQATNIIL   40 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~-------------~Gr~i~G~L~~~D~~~NlvL   40 (98)
                      .++.+++|+.|.|+++             +.+.|.|+|.++|.. ++.|
T Consensus        93 ~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         93 QDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             HHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            5788999999999998             679999999999974 4444

>PRK14645 hypothetical protein; Provisional

Probab=90.95  E-value=0.51  Score=32.90  Aligned_cols=35  Identities=20%  Similarity=0.334  Sum_probs=29.2

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      .++.+++|++|.|.+ +++.+.|+|.++|.. .+.|.
T Consensus        95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l~  129 (154)
T PRK14645         95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTFD  129 (154)
T ss_pred             HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEEE
Confidence            478899999999986 789999999999875 35553

>PRK14636 hypothetical protein; Provisional

Probab=90.95  E-value=0.53  Score=33.52  Aligned_cols=36  Identities=19%  Similarity=0.432  Sum_probs=29.7

Q ss_pred             hhHHhhcCCeEEEEEC---CC-cEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVITN---DG-RNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~---~G-r~i~G~L~~~D~~~NlvL~   41 (98)
                      ..+.+++|++|.|+++   +| +.++|+|.++|.. ++.|.
T Consensus        91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~  130 (176)
T PRK14636         91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTIA  130 (176)
T ss_pred             HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence            5788999999999997   55 6999999999874 45553

>PRK06955 biotin--protein ligase; Provisional

Probab=90.92  E-value=1.5  Score=33.22  Aligned_cols=34  Identities=18%  Similarity=0.446  Sum_probs=29.5

Q ss_pred             hhcCCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299            9 SLVEQQISVITNDGRNIVGVLKGFDQATNIILDE   42 (98)
Q Consensus         9 ~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~   42 (98)
                      -++|++|++...+++.+.|++.++|..+.|+++.
T Consensus       246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~  279 (300)
T PRK06955        246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLDT  279 (300)
T ss_pred             hcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence            3678999997667788999999999999999864

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=90.37  E-value=0.71  Score=31.84  Aligned_cols=35  Identities=17%  Similarity=0.395  Sum_probs=29.1

Q ss_pred             hhHHhhcCCeEEEEE----CCCcEEEEEEEEEcCCCceEe
Q 034299            5 PGLESLVEQQISVIT----NDGRNIVGVLKGFDQATNIIL   40 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l----~~Gr~i~G~L~~~D~~~NlvL   40 (98)
                      ..+.+++|+.|.|++    .+++.++|+|.++|... +.|
T Consensus        91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~-i~l  129 (154)
T PRK00092         91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGET-VTL  129 (154)
T ss_pred             HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCCE-EEE
Confidence            578899999999997    56789999999999843 444

>PRK14632 hypothetical protein; Provisional

Probab=90.31  E-value=0.66  Score=32.87  Aligned_cols=36  Identities=22%  Similarity=0.346  Sum_probs=29.9

Q ss_pred             hhHHhhcCCeEEEEECC-------CcEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVITND-------GRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~-------Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      ..+.+++|+.|.|++++       .+.+.|+|.++|.. ++.|.
T Consensus        91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            47889999999999975       57999999999864 46554

>PRK14643 hypothetical protein; Provisional

Probab=89.78  E-value=0.96  Score=31.85  Aligned_cols=32  Identities=19%  Similarity=0.247  Sum_probs=27.7

Q ss_pred             hhHHhhcCCeEEEEECC----CcEEEEEEEEEcCCC
Q 034299            5 PGLESLVEQQISVITND----GRNIVGVLKGFDQAT   36 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~----Gr~i~G~L~~~D~~~   36 (98)
                      ..+..++|++|.|+++.    .+.+.|+|.++|...
T Consensus        97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~  132 (164)
T PRK14643         97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNT  132 (164)
T ss_pred             HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCc
Confidence            57889999999999865    589999999999654

>PRK14634 hypothetical protein; Provisional

Probab=89.57  E-value=0.82  Score=31.83  Aligned_cols=36  Identities=11%  Similarity=0.284  Sum_probs=29.4

Q ss_pred             hhHHhhcCCeEEEEECC---C-cEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVITND---G-RNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~---G-r~i~G~L~~~D~~~NlvL~   41 (98)
                      ..+.+++|++|.|+++.   | +.|.|+|.++|.. ++.|.
T Consensus        93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l~  132 (155)
T PRK14634         93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQIN  132 (155)
T ss_pred             HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEEE
Confidence            57889999999999864   2 7999999999974 46554

>PRK14646 hypothetical protein; Provisional

Probab=88.97  E-value=0.97  Score=31.47  Aligned_cols=36  Identities=11%  Similarity=0.199  Sum_probs=29.5

Q ss_pred             hhHHhhcCCeEEEEECC---C-cEEEEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVITND---G-RNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~---G-r~i~G~L~~~D~~~NlvL~   41 (98)
                      ..+.+++|++|.|++++   | +.+.|.|.++|.. ++.|.
T Consensus        93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~  132 (155)
T PRK14646         93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN  132 (155)
T ss_pred             HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            57889999999999865   3 6889999999985 46664

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=88.86  E-value=0.77  Score=32.61  Aligned_cols=32  Identities=13%  Similarity=0.300  Sum_probs=26.5

Q ss_pred             CCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299           12 EQQISVITNDGRNIVGVLKGFDQATNIILDES   43 (98)
Q Consensus        12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~   43 (98)
                      ..+|.|-|.+|-.+.|.+.+||+|.=+.-.+.
T Consensus       104 k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g  135 (165)
T PRK14091        104 GEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG  135 (165)
T ss_pred             CCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            46788889999999999999999995554443

>PRK14647 hypothetical protein; Provisional

Probab=88.44  E-value=1.1  Score=31.24  Aligned_cols=35  Identities=17%  Similarity=0.333  Sum_probs=28.6

Q ss_pred             hhHHhhcCCeEEEEEC---------CCcEEEEEEEEEcCCCceEe
Q 034299            5 PGLESLVEQQISVITN---------DGRNIVGVLKGFDQATNIIL   40 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~---------~Gr~i~G~L~~~D~~~NlvL   40 (98)
                      ..+.+++|+.|.|+++         +.+.+.|+|.++|.. .+.|
T Consensus        92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~-~v~l  135 (159)
T PRK14647         92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG-VVTI  135 (159)
T ss_pred             HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC-EEEE
Confidence            5788999999999995         348999999999963 3444

>PRK14631 hypothetical protein; Provisional

Probab=87.88  E-value=1.1  Score=31.81  Aligned_cols=36  Identities=19%  Similarity=0.233  Sum_probs=29.4

Q ss_pred             hhhHHhhcCCeEEEEEC----CCcEEEEEEEEEc--CCCceEe
Q 034299            4 GPGLESLVEQQISVITN----DGRNIVGVLKGFD--QATNIIL   40 (98)
Q Consensus         4 ~~~L~~~i~k~V~V~l~----~Gr~i~G~L~~~D--~~~NlvL   40 (98)
                      ...+.+++|+.|.|+++    +.+.|+|+|.++|  . .++.|
T Consensus       109 ~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~-~~v~l  150 (174)
T PRK14631        109 LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLEN-EEIQV  150 (174)
T ss_pred             HHHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCC-CEEEE
Confidence            35788999999999995    4599999999998  4 34555

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=87.67  E-value=1  Score=32.02  Aligned_cols=32  Identities=13%  Similarity=0.371  Sum_probs=26.1

Q ss_pred             CCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299           12 EQQISVITNDGRNIVGVLKGFDQATNIILDES   43 (98)
Q Consensus        12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~   43 (98)
                      ..+|.|-|.+|-.+.|.+.+||+|.=+.-.+.
T Consensus        24 k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g   55 (165)
T PRK14091         24 KTPVTMFLVKGVKLQGIITWFDNFSILLRRDG   55 (165)
T ss_pred             CCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            46778889999999999999999985554443

>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed

Probab=87.32  E-value=3.2  Score=34.61  Aligned_cols=34  Identities=15%  Similarity=0.233  Sum_probs=29.5

Q ss_pred             hhcCCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299            9 SLVEQQISVITNDGRNIVGVLKGFDQATNIILDE   42 (98)
Q Consensus         9 ~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~   42 (98)
                      -++|++|++...+++++.|+..++|....|+|+.
T Consensus       275 ~~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~  308 (592)
T PRK13325        275 RDHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET  308 (592)
T ss_pred             ccCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence            3679999987677788999999999999999964

>PRK14641 hypothetical protein; Provisional

Probab=85.91  E-value=1.6  Score=31.08  Aligned_cols=29  Identities=17%  Similarity=0.231  Sum_probs=25.3

Q ss_pred             hhHHhhcCCeEEEEECC----CcEEEEEEEEEc
Q 034299            5 PGLESLVEQQISVITND----GRNIVGVLKGFD   33 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~----Gr~i~G~L~~~D   33 (98)
                      ..+.+++|+.|.|++++    .+.+.|+|.++|
T Consensus        97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            46889999999999976    469999999996

>PRK14637 hypothetical protein; Provisional

Probab=85.89  E-value=1.9  Score=29.93  Aligned_cols=36  Identities=17%  Similarity=0.258  Sum_probs=28.2

Q ss_pred             hhHHhhcCCeEEEEECCCcEE-EEEEEEEcCCCceEec
Q 034299            5 PGLESLVEQQISVITNDGRNI-VGVLKGFDQATNIILD   41 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i-~G~L~~~D~~~NlvL~   41 (98)
                      ..+.+++|++|.|++.+.+.+ +|+|.++|.. ++.|.
T Consensus        91 ~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~  127 (151)
T PRK14637         91 AEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT  127 (151)
T ss_pred             HHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence            578899999999999444455 7999999875 45554

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=84.53  E-value=5.8  Score=30.04  Aligned_cols=31  Identities=19%  Similarity=0.617  Sum_probs=27.3

Q ss_pred             hcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299           10 LVEQQISVITNDGRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus        10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      ++|++|++.. ++..++|++.++|..+.|++.
T Consensus       270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~  300 (319)
T PRK11886        270 FLGREVKLII-GDKEISGIARGIDEQGALLLE  300 (319)
T ss_pred             ccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence            6789999987 456799999999999999996

>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A

Probab=84.12  E-value=2.1  Score=23.79  Aligned_cols=22  Identities=18%  Similarity=0.495  Sum_probs=14.9

Q ss_pred             EEEEEEEEcCCCceEecceEEE
Q 034299           25 IVGVLKGFDQATNIILDESHER   46 (98)
Q Consensus        25 i~G~L~~~D~~~NlvL~~~~e~   46 (98)
                      .+|++.|+|..+.|.|.+....
T Consensus        10 ~tGtFlGvDE~FGmLLr~~~~T   31 (42)
T PF14563_consen   10 LTGTFLGVDEDFGMLLRDDDTT   31 (42)
T ss_dssp             EEEEEEEE-TT--EEEE-SS-E
T ss_pred             cceeEEeeccccceEEEeCCcc
Confidence            6899999999999999987554

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

Probab=84.07  E-value=2.5  Score=29.78  Aligned_cols=35  Identities=20%  Similarity=0.364  Sum_probs=31.6

Q ss_pred             hhcCCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299            9 SLVEQQISVITNDGRNIVGVLKGFDQATNIILDES   43 (98)
Q Consensus         9 ~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~   43 (98)
                      +.-+-+|+|.+.||.+|.|-+.+|+.--|.+|..+
T Consensus        26 r~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~   60 (165)
T PF03614_consen   26 RFNDIPVRVVSENGQVFCMYVSGFMSKENKILAPD   60 (165)
T ss_pred             HhcCCceEEEecCCcEEEEEEeccCcccCEEeccC
Confidence            44578999999999999999999999999999775

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

>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region

Probab=83.57  E-value=7.3  Score=28.29  Aligned_cols=32  Identities=22%  Similarity=0.543  Sum_probs=27.4

Q ss_pred             hhcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299            9 SLVEQQISVITNDGRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         9 ~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      .++|++|.+... +..+.|++.++|....|+++
T Consensus       190 ~~~g~~V~v~~~-~~~~~G~~~gI~~~G~L~v~  221 (237)
T TIGR00121       190 AHIGREVSLTTG-NGEIEGIARGIDKDGALLLE  221 (237)
T ss_pred             hccCCeEEEEeC-CcEEEEEEEeECCCceEEEE
Confidence            356999999865 46799999999999999996

The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.

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

Probab=82.91  E-value=1.4  Score=31.03  Aligned_cols=24  Identities=33%  Similarity=0.495  Sum_probs=21.6

Q ss_pred             cCCeEEEEECCCcEEEEEEEEEcC
Q 034299           11 VEQQISVITNDGRNIVGVLKGFDQ   34 (98)
Q Consensus        11 i~k~V~V~l~~Gr~i~G~L~~~D~   34 (98)
                      .|+-++|.+.|||+++|.=.|.|.
T Consensus       119 qg~sIrVyM~DgR~ieG~stGvna  142 (165)
T PF03614_consen  119 QGKSIRVYMADGREIEGKSTGVNA  142 (165)
T ss_pred             CCCeEEEEEcCCcEEEeeecccce
Confidence            378999999999999999999883

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

>PRK08330 biotin--protein ligase; Provisional

Probab=82.27  E-value=6.9  Score=28.43  Aligned_cols=34  Identities=21%  Similarity=0.453  Sum_probs=27.9

Q ss_pred             hhcCCeEEEEECCCcEE-EEEEEEEcCCCceEecce
Q 034299            9 SLVEQQISVITNDGRNI-VGVLKGFDQATNIILDES   43 (98)
Q Consensus         9 ~~i~k~V~V~l~~Gr~i-~G~L~~~D~~~NlvL~~~   43 (98)
                      .++|++|.+.. ++..+ .|++.++|....|++...
T Consensus       185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~  219 (236)
T PRK08330        185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD  219 (236)
T ss_pred             HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence            46799999875 56665 799999999999999753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	98
3cw1_G	76	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		2e-06
3swn_C	117	Structure Of The Lsm657 Complex: An Assembly Interm		3e-06
4emk_C	113	Crystal Structure Of Splsm567 Length = 113		5e-06
1d3b_B	91	Crystal Structure Of The D3b Subcomplex Of The Huma		5e-04
2y9a_A	95	Structure Of The Spliceosomal U4 Snrnp Core Domain		5e-04
3pgw_B	231	Crystal Structure Of Human U1 Snrnp Length = 231		6e-04
3cw1_A	174	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		7e-04

>pdb|3CW1|G Chain G, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 76

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 42/65 (64%), Gaps = 4/65 (6%)
Query: 5  PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYII 64
          P L+  +++++S+  N GR++ G+L+GFD   N+++DE  E   S     QQ  +G+ +I
Sbjct: 7  PELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSG----QQNNIGMVVI 62
Query: 65 RGDNI 69
          RG++I
Sbjct: 63 RGNSI 67

>pdb|3SWN|C Chain C, Structure Of The Lsm657 Complex: An Assembly Intermediate Of The Lsm1 7 And Lsm2 8 Rings Length = 117

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 7/75 (9%)
Query: 7   LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLV-----LGL 61
           L    +Q+I      GR I G+LKGFDQ  N++LD+  E++ + ++G  +L      LGL
Sbjct: 32  LSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDG--KLTGAIRKLGL 89
Query: 62  YIIRGDNISIVGEVD 76
            ++RG  + ++  +D
Sbjct: 90  VVVRGTTLVLIAPMD 104

>pdb|4EMK|C Chain C, Crystal Structure Of Splsm567 Length = 113

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 7/75 (9%)
Query: 7   LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLV-----LGL 61
           L    +Q+I      GR I G+LKGFDQ  N++LD+  E++ + ++G  +L      LGL
Sbjct: 28  LSRYQDQRIQATFTGGRQITGILKGFDQLXNLVLDDVEEQLRNPEDG--KLTGAIRKLGL 85
Query: 62  YIIRGDNISIVGEVD 76
            ++RG  + ++   D
Sbjct: 86  VVVRGTTLVLIAPXD 100

>pdb|1D3B|B Chain B, Crystal Structure Of The D3b Subcomplex Of The Human Core Snrnp Domain At 2.0a Resolution Length = 91

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 11 VEQQISVITNDGRNIVGVLKGFDQATNIILDESHE-RVYSTKEGVQ-----QLVLGLYII 64
          ++ ++  I  DGR  +G  K FD+  N+IL +  E R    K   Q     + VLGL ++
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL 72
Query: 65 RGDNI 69
          RG+N+
Sbjct: 73 RGENL 77

>pdb|2Y9A|A Chain A, Structure Of The Spliceosomal U4 Snrnp Core Domain Length = 95

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 11 VEQQISVITNDGRNIVGVLKGFDQATNIILDESHE-RVYSTKEGVQ-----QLVLGLYII 64
          ++ ++  I  DGR  +G  K FD+  N+IL +  E R    K   Q     + VLGL ++
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL 72
Query: 65 RGDNI 69
          RG+N+
Sbjct: 73 RGENL 77

>pdb|3PGW|B Chain B, Crystal Structure Of Human U1 Snrnp Length = 231

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 11 VEQQISVITNDGRNIVGVLKGFDQATNIILDESHE-RVYSTKEGVQ-----QLVLGLYII 64
          ++ ++  I  DGR  +G  K FD+  N+IL +  E R    K   Q     + VLGL ++
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL 72
Query: 65 RGDNI 69
          RG+N+
Sbjct: 73 RGENL 77

>pdb|3CW1|A Chain A, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 174

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 11 VEQQISVITNDGRNIVGVLKGFDQATNIILDESHE-RVYSTKEGVQ-----QLVLGLYII 64
          ++ ++  I  DGR  +G  K FD+  N+IL +  E R    K   Q     + VLGL ++
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL 72
Query: 65 RGDNI 69
          RG+N+
Sbjct: 73 RGENL 77

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	98
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	9e-23
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	1e-20
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	2e-20
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	4e-18
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	6e-18
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	2e-14
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	1e-13
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	1e-12
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	9e-12
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	4e-11
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	9e-11
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-10
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	6e-10
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	9e-10
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	1e-09
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	2e-08
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	3e-08
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	2e-06
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	3e-06
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	4e-06
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	5e-05
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	7e-05

>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 = 83.2 bits (206), Expect = 9e-23
 Identities = 18/82 (21%), Positives = 42/82 (51%), Gaps = 3/82 (3%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYST---KEGVQQLVLGLYI 63
          L+  +++++ +     R +VG L+ FD   NI+L ++ E +Y     +    +    +  
Sbjct: 15 LKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVF 74

Query: 64 IRGDNISIVGEVDEELDSHLDL 85
          IRGD ++++    E+ D  +++
Sbjct: 75 IRGDTVTLISTPSEDDDGAVEI 96

>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 = 77.4 bits (191), Expect = 1e-20
 Identities = 25/78 (32%), Positives = 48/78 (61%), Gaps = 6/78 (7%)

Query: 1  MS--GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLV 58
          MS    P L+  +++++S+  N GR++ G+L+GFD   N+++DE  E   S     QQ  
Sbjct: 1  MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSG----QQNN 56

Query: 59 LGLYIIRGDNISIVGEVD 76
          +G+ +IRG++I ++  ++
Sbjct: 57 IGMVVIRGNSIIMLEALE 74

>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 = 78.1 bits (192), Expect = 2e-20
 Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 5/81 (6%)

Query: 5   PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGV---QQLVLGL 61
             L    +Q+I      GR I G+LKGFDQ  N++LD+  E++ + ++G        LGL
Sbjct: 26  LDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGL 85

Query: 62  YIIRGDNISIVGEVD--EELD 80
            ++RG  + ++  +D  EE+ 
Sbjct: 86  VVVRGTTLVLIAPMDGSEEIP 106

>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 = 70.9 bits (174), Expect = 4e-18
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 5/70 (7%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L+  + +Q+ V   D   I G+L+ FDQ  N++L+++ E +            G  ++RG
Sbjct: 16 LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYK-----RGTMVVRG 70

Query: 67 DNISIVGEVD 76
          +N+  +  V 
Sbjct: 71 ENVLFISPVP 80

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

 Score = 70.7 bits (173), Expect = 6e-18
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 1  MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERV------YSTKEGV 54
          +     +   ++ ++  I  DGR  +G  K FD+  N+IL +  E            E  
Sbjct: 3  VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAERE 62

Query: 55 QQLVLGLYIIRGDNISIVGEVDE 77
          ++ VLGL ++RG+N+  +  V+ 
Sbjct: 63 EKRVLGLVLLRGENLVSM-TVEG 84

>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 = 61.5 bits (150), Expect = 2e-14
 Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 4/72 (5%)

Query: 5  PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYII 64
            L   +   + V     + + G+L+ +DQ  N++L +S E             LG  +I
Sbjct: 12 KVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQ----SDGSGKKLGTIVI 67

Query: 65 RGDNISIVGEVD 76
          RGDN+ ++  + 
Sbjct: 68 RGDNVILISPLQ 79

>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 = 59.2 bits (144), Expect = 1e-13
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 6/79 (7%)

Query: 1  MSGGPG--LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLV 58
          M+  P   +   +++ + VI   G    G L G+D   N++L ++       ++G     
Sbjct: 1  MAERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEM----IQDGEVVKR 56

Query: 59 LGLYIIRGDNISIVGEVDE 77
           G  +IRGDN+  +   +E
Sbjct: 57 YGKIVIRGDNVLAISPTEE 75

>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 = 56.9 bits (138), Expect = 1e-12
 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 1  MSGGPG--LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLV 58
          M   P   L   ++  + V    GR   G L G+D   N++L ++ E     + G     
Sbjct: 1  MPPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEE----IQNGEVVRK 56

Query: 59 LGLYIIRGDNISIVGEVDE 77
          +G  +IRGD +  V     
Sbjct: 57 VGSVVIRGDTVVFVSPAPG 75

>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 = 54.6 bits (132), Expect = 9e-12
 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 1  MSGGPG--LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLV 58
          M   P   L  ++ +++ +  + G +  G+L   D   N+ L+ + E V     G +  V
Sbjct: 1  MDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYV----NGKKTNV 56

Query: 59 LGLYIIRGDNISIVGEVDE 77
           G   IRG+N+  V  +D+
Sbjct: 57 YGDAFIRGNNVLYVSALDD 75

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

 Score = 53.2 bits (128), Expect = 4e-11
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 4/74 (5%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L  L  + + V    G    G L   D   N+ L  + E +    +G     LG  +IR 
Sbjct: 11 LNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYI----DGALSGHLGEVLIRC 66

Query: 67 DNISIVGEVDEELD 80
          +N+  +  V+EE +
Sbjct: 67 NNVLYIRGVEEEEE 80

>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 = 52.3 bits (126), Expect = 9e-11
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 4/66 (6%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L + +   + +     R   GVLK FD   N++L+++ E     ++G     LG  +IRG
Sbjct: 20 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE----LEDGEVTRRLGTVLIRG 75

Query: 67 DNISIV 72
          DNI  +
Sbjct: 76 DNIVYI 81

>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 Length = 231

 Score = 54.3 bits (130), Expect = 2e-10
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 1  MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHE-RVYSTK-----EGV 54
          +     +   ++ ++  I  DGR  +G  K FD+  N+IL +  E R    K     E  
Sbjct: 3  VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAERE 62

Query: 55 QQLVLGLYIIRGDNI 69
          ++ VLGL ++RG+N+
Sbjct: 63 EKRVLGLVLLRGENL 77

>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 = 50.6 bits (121), Expect = 6e-10
 Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 9/75 (12%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQL--------- 57
          +   +++ + V     R + G L  +D+  N++L ++ E V    +              
Sbjct: 14 VRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRK 73

Query: 58 VLGLYIIRGDNISIV 72
             +  +RGD++ ++
Sbjct: 74 HYEMLFVRGDSVILI 88

>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 = 49.6 bits (119), Expect = 9e-10
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 7  LESLVEQQISV-ITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIR 65
          ++S+V + I V +  +   +VG L+G D   N+ L  + E     K   +   LG  ++R
Sbjct: 10 VKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAME----CKGEEKVRSLGEIVLR 65

Query: 66 GDNISIVGEVDE 77
          G+N+ ++   +E
Sbjct: 66 GNNVVLIQPQEE 77

>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 = 50.0 bits (119), Expect = 1e-09
 Identities = 16/77 (20%), Positives = 35/77 (45%), Gaps = 11/77 (14%)

Query: 7   LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLV-------- 58
           ++  +  +I V+    +   GVL+GFD+  N++LD+  E  +   E              
Sbjct: 33  IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVM 92

Query: 59  ---LGLYIIRGDNISIV 72
              L   ++ G+N++++
Sbjct: 93  VNRLETILLSGNNVAML 109

>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 = 46.7 bits (111), Expect = 2e-08
 Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L++    Q+ +       I G + GFD+  N++LD++ E ++S  +  +Q  LG  +++G
Sbjct: 25 LQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEE-IHSKTKSRKQ--LGRIMLKG 81

Query: 67 DNISIVGEVD 76
          DNI+++  V 
Sbjct: 82 DNITLLQSVS 91

>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 = 46.0 bits (109), Expect = 3e-08
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          ++  +   + VI    R   G L GFD   NI+L +  E  Y T  GV +      ++ G
Sbjct: 25 IDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTE--YDTVTGVTE-KHSEMLLNG 81

Query: 67 DNISIV 72
          + + ++
Sbjct: 82 NGMCML 87

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

 Score = 41.0 bits (96), Expect = 2e-06
 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 5/72 (6%)

Query: 7  LESLVEQQISVITND-GRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIR 65
          L+ LV  ++ V          G L   D   N+ L+E+ E V     GV    LG   IR
Sbjct: 26 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV----AGVSHGTLGEIFIR 81

Query: 66 GDNISIVGEVDE 77
           +N+  + E+  
Sbjct: 82 CNNVLYIRELPN 93

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

 Score = 41.3 bits (97), Expect = 3e-06
 Identities = 20/77 (25%), Positives = 30/77 (38%), Gaps = 3/77 (3%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L +   + I V   +G    G L+  D   N+ L E      +  +G +   L    IRG
Sbjct: 21 LNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIR---TMPDGDKFFRLPECYIRG 77

Query: 67 DNISIVGEVDEELDSHL 83
          +NI  +   DE L    
Sbjct: 78 NNIKYLRIQDEVLSQVA 94

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

 Score = 41.1 bits (96), Expect = 4e-06
 Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 4/77 (5%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L  L  + +++   +G  + G + G D + N  L         T +  + + L    IRG
Sbjct: 7  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKM----TLKNREPVQLETLSIRG 62

Query: 67 DNISIVGEVDEELDSHL 83
          +NI      D      L
Sbjct: 63 NNIRYFILPDSLPLDTL 79

>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 = 38.0 bits (88), Expect = 5e-05
 Identities = 13/69 (18%), Positives = 31/69 (44%), Gaps = 10/69 (14%)

Query: 14  QISVITNDGRNIVGVLKGFDQATNIILDESHERVYS----------TKEGVQQLVLGLYI 63
           Q+ +   + + ++G +K FD+  N++L+   E              +K   +   +    
Sbjct: 41  QVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMF 100

Query: 64  IRGDNISIV 72
           +RGD++ +V
Sbjct: 101 LRGDSVIVV 109

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

 Score = 37.7 bits (87), Expect = 7e-05
 Identities = 14/77 (18%), Positives = 24/77 (31%), Gaps = 4/77 (5%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L       ++  TN G    G L   +   N  +      +  T    +   L    IRG
Sbjct: 10 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSN----ITVTYRDGRVAQLEQVYIRG 65

Query: 67 DNISIVGEVDEELDSHL 83
            I  +   D   ++ +
Sbjct: 66 SKIRFLILPDMLKNAPM 82

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	98
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.93
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.92
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.91
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.91
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.91
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.91
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.9
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.9
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.9
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.9
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.9
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.89
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.89
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.89
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.89
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.89
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.88
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.88
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.87
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.87
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.87
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.86
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.83
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.8
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.11
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	96.86
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	96.68
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	96.47
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	96.45
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	96.43
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.3
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	96.17
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.16
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	96.12
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	95.91
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	95.89
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	95.43
1ycy_A	71	Conserved hypothetical protein; structural genomic	95.2
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	94.72
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	94.53
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	94.06
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	92.47
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	91.76
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	88.38
1bia_A	321	BIRA bifunctional protein; transcription regulatio	88.18
2xk0_A	69	Polycomb protein PCL; transcription, aromatic CAGE	85.88
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	83.59

>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=99.93  E-value=6.8e-26  Score=145.99  Aligned_cols=82  Identities=22%  Similarity=0.419  Sum_probs=70.2

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCC---CeeEEEecEEEEcCCcEEEEEecCccc
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKE---GVQQLVLGLYIIRGDNISIVGEVDEEL   79 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~---~~~~r~lg~v~irG~~I~~i~~~d~~~   79 (98)
                      |.+.|.+++|++|+|+|+|||+|.|+|.|||+||||+|+||.|++..+++   +...+.+|+++|||++|++|.+.+++.
T Consensus        11 p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d~~~   90 (96)
T 3bw1_A           11 PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPSEDD   90 (96)
T ss_dssp             HHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC---
T ss_pred             HHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecCccc
Confidence            67899999999999999999999999999999999999999999875432   356789999999999999999999988


Q ss_pred             cccCC
Q 034299           80 DSHLD   84 (98)
Q Consensus        80 e~~~~   84 (98)
                      ++.+|
T Consensus        91 d~~~~   95 (96)
T 3bw1_A           91 DGAVE   95 (96)
T ss_dssp             --CCC
T ss_pred             ccccc
Confidence            87776

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

Probab=99.92  E-value=1.5e-24  Score=133.58  Aligned_cols=72  Identities=24%  Similarity=0.350  Sum_probs=65.2

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      .|.+.|.+++|++|+|+|+|||+|.|+|.|||+|||++|+||.|++.    +...+.+|.++|||++|++|.++++
T Consensus         4 ~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~----~~~~~~lg~v~iRG~~I~~i~~~~e   75 (75)
T 1h64_1            4 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQD----GEVVKRYGKIVIRGDNVLAISPTEE   75 (75)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEET----TEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             hHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEee----CCceeECCEEEECCCEEEEEEeCCC
Confidence            37889999999999999999999999999999999999999999874    2567899999999999999998764

>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=99.91  E-value=3.2e-24  Score=132.77  Aligned_cols=73  Identities=25%  Similarity=0.356  Sum_probs=66.6

Q ss_pred             CCChhhHHhhcCCeEEEEECCC-cEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            1 MSGGPGLESLVEQQISVITNDG-RNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~G-r~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      |.|.+.|.++++++|+|+|++| +++.|+|.|||+|||++|+||+|++.    +...+.+|.++|||++|++|.++|+
T Consensus         4 ~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~----~~~~~~lg~v~iRG~nI~~i~~~de   77 (77)
T 1ljo_A            4 VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKG----EEKVRSLGEIVLRGNNVVLIQPQEE   77 (77)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEET----TEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             cchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEec----CCcEeECCeEEEeCCeEEEEEeCCC
Confidence            6788999999999999999999 99999999999999999999999873    3567899999999999999999864

>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=99.91  E-value=1.9e-24  Score=137.41  Aligned_cols=77  Identities=27%  Similarity=0.435  Sum_probs=65.9

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEee-cC-----CCeeEEEecEEEEcCCcEEEEEec
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYS-TK-----EGVQQLVLGLYIIRGDNISIVGEV   75 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~-~~-----~~~~~r~lg~v~irG~~I~~i~~~   75 (98)
                      .|.+.|.+++|++|+|+|+|||+|.|+|.|||+||||+|+||+|++.. ++     .+...+.+|+++|||++|++|.+.
T Consensus         4 ~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~~~   83 (91)
T 1d3b_B            4 GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   83 (91)
T ss_dssp             ---CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             ChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEEcC
Confidence            477899999999999999999999999999999999999999998643 21     235688999999999999999988


Q ss_pred             Ccc
Q 034299           76 DEE   78 (98)
Q Consensus        76 d~~   78 (98)
                      +..
T Consensus        84 ~~~   86 (91)
T 1d3b_B           84 GPP   86 (91)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            654

>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=99.91  E-value=3.6e-24  Score=141.75  Aligned_cols=77  Identities=30%  Similarity=0.528  Sum_probs=58.2

Q ss_pred             hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCC---CeeEEEecEEEEcCCcEEEEEecCcccc
Q 034299            4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKE---GVQQLVLGLYIIRGDNISIVGEVDEELD   80 (98)
Q Consensus         4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~---~~~~r~lg~v~irG~~I~~i~~~d~~~e   80 (98)
                      ...|.+|++++|+|.|+|||+|.|+|.|||+||||+|+||.|++..++.   ....+.+|+++|||++|++|.+.|...|
T Consensus        25 i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~ee  104 (113)
T 4emk_C           25 ILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDGSEE  104 (113)
T ss_dssp             -------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC----
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCcccc
Confidence            4689999999999999999999999999999999999999999865321   2468899999999999999999996554

>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=99.91  E-value=8e-24  Score=130.78  Aligned_cols=72  Identities=25%  Similarity=0.356  Sum_probs=66.1

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      .|.+.|.+++|++|+|+|+||++|.|+|.|||+|||++|+||.|++.    +...+.+|.++|||++|++|.++|.
T Consensus         4 ~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~----~~~~~~lg~v~iRG~~I~~i~~~d~   75 (77)
T 1i4k_A            4 RPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQN----GEVVRKVGSVVIRGDTVVFVSPAPG   75 (77)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEET----TEEEEEEEEEEECGGGEEEEEECC-
T ss_pred             cHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEec----CCcEeECCEEEECCCEEEEEEeCCC
Confidence            48889999999999999999999999999999999999999999874    2467899999999999999999875

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

Probab=99.90  E-value=1.4e-23  Score=132.84  Aligned_cols=76  Identities=26%  Similarity=0.307  Sum_probs=65.7

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCccccc
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDS   81 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e~   81 (98)
                      .|.+.|.+++|++|+|+|++|++|.|+|.|||+|||++|+||.|+..    +...+.+|.++|||++|++|.++|++.++
T Consensus         6 ~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~----g~~~~~lg~v~IRG~nI~~i~~~d~~~~~   81 (86)
T 3s6n_F            6 NPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYID----GALSGHLGEVLIRCNNVLYIRGVEEEEED   81 (86)
T ss_dssp             CHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEET----TEEEEEESSEEECGGGEEEEEECC-----
T ss_pred             CcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcC----CceeeEccEEEEeCCeEEEEEeCCccccc
Confidence            47789999999999999999999999999999999999999998752    34678999999999999999999877653

>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=99.90  E-value=4e-23  Score=132.84  Aligned_cols=73  Identities=18%  Similarity=0.215  Sum_probs=65.6

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      .|...|.++++++|+|+|++||+|.|+|.|||+||||+|+||+|++.+   +..++.+|.++|||++|++|.+..+
T Consensus        20 ~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~---~~~~~~lg~v~IRG~nI~~i~p~~~   92 (94)
T 4emk_A           20 LPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTV---TGVTEKHSEMLLNGNGMCMLIPGGK   92 (94)
T ss_dssp             CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETT---TCCEEEEEEEEECSTTEEEEEECC-
T ss_pred             cCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecC---CCcEeEcCEEEEcCCEEEEEEeCCC
Confidence            577899999999999999999999999999999999999999999732   2457899999999999999998754

>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=99.90  E-value=1.1e-23  Score=129.86  Aligned_cols=71  Identities=27%  Similarity=0.410  Sum_probs=64.2

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      .|.+.|.+++|++|+|+|+||++|.|+|.|||+|||++|+||.|++.    +...+.+|.++|||++|++|.+.|
T Consensus         4 ~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~----~~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 4emk_B            4 SPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVN----GKKTNVYGDAFIRGNNVLYVSALD   74 (75)
T ss_dssp             HHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEET----TEEEEEEEEEEEEGGGSSEEEEC-
T ss_pred             chHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEec----CCcccEecEEEEcCCeEEEEEecC
Confidence            36679999999999999999999999999999999999999999862    346789999999999999999875

>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=99.90  E-value=1.1e-23  Score=130.39  Aligned_cols=71  Identities=32%  Similarity=0.623  Sum_probs=52.8

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      +.+.|.+++|++|+|+|+|||+|.|+|.|||+|||++|+||.|++..    .+.+.+|.++|||++|++|.+.|.
T Consensus         5 ~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~----~~~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            5 HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATS----GQQNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             ---------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC--------CBSSEEECSSSEEEEEC---
T ss_pred             chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccC----CcEeEcCEEEECCCeEEEEEeccC
Confidence            45799999999999999999999999999999999999999998642    346789999999999999998863

>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=99.90  E-value=3e-23  Score=129.54  Aligned_cols=71  Identities=24%  Similarity=0.412  Sum_probs=64.1

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      |.+.|.+++|++|+|+|+|||+|.|+|.|||+|||++|+||+|++..    ...+.+|.++|||++|++|.++++
T Consensus        10 P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~----~~~~~lg~v~iRG~~I~~i~~~~~   80 (81)
T 1th7_A           10 AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD----GSGKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             HHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSS----SCEEEEEEEEECGGGEEEEEEC--
T ss_pred             hHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecC----CceeECCEEEECCCEEEEEEecCC
Confidence            66799999999999999999999999999999999999999998742    457899999999999999998864

>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=99.89  E-value=3.9e-23  Score=129.13  Aligned_cols=70  Identities=27%  Similarity=0.489  Sum_probs=64.4

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      .|...|.++++++|+|+|+|||+|.|+|.|||+|||++|+||.|+  .   +...+.+|.++|||++|++|.++|
T Consensus        11 ~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~--~---~~~~~~lg~v~iRG~~I~~i~~~d   80 (81)
T 1i8f_A           11 TLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI--I---DGNVYKRGTMVVRGENVLFISPVP   80 (81)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE--E---TTEEEEEEEEEECGGGEEEEEECC
T ss_pred             chHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE--c---CCcccCCCEEEECCCEEEEEEeCC
Confidence            467899999999999999999999999999999999999999998  2   246789999999999999999875

>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=99.89  E-value=9.4e-23  Score=127.98  Aligned_cols=70  Identities=29%  Similarity=0.411  Sum_probs=64.4

Q ss_pred             CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      +.|...|.+++|++|+|+|+||++|.|+|.|||+|||++|+||+|++.    +...+.+|.++|||++|++|.+
T Consensus        14 ~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~----~~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           14 QRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED----GEVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             TCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEET----TEEEEEEEEEEECGGGEEEEEC
T ss_pred             cChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEec----CCcccCCCEEEECCCEEEEEEC
Confidence            468889999999999999999999999999999999999999999874    2567899999999999999964

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

Probab=99.89  E-value=9.1e-23  Score=130.75  Aligned_cols=74  Identities=18%  Similarity=0.281  Sum_probs=64.2

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecC-CC--------eeEEEecEEEEcCCcEEEE
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTK-EG--------VQQLVLGLYIIRGDNISIV   72 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~-~~--------~~~r~lg~v~irG~~I~~i   72 (98)
                      .|...|.+++|++|+|+|++||+|.|+|.|||+||||+|+||.|++.... ++        ..++.+|+++|||++|++|
T Consensus         9 ~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nVv~I   88 (93)
T 4emg_A            9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVILI   88 (93)
T ss_dssp             CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGEEEE
T ss_pred             CCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeEEEE
Confidence            47788999999999999999999999999999999999999999986421 11        3578999999999999999


Q ss_pred             Eec
Q 034299           73 GEV   75 (98)
Q Consensus        73 ~~~   75 (98)
                      .++
T Consensus        89 ~p~   91 (93)
T 4emg_A           89 APP   91 (93)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            875

>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=99.89  E-value=4.9e-23  Score=134.79  Aligned_cols=80  Identities=26%  Similarity=0.251  Sum_probs=55.5

Q ss_pred             CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcccc
Q 034299            1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELD   80 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e   80 (98)
                      +.|...|.+++|++|+|+|++|++|.|+|.+||+||||+|+||+|+..   ++...+.+|.++|||++|.+|..+|+.++
T Consensus        15 ~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~---dg~~~~~lg~v~IRG~nI~~I~~pd~l~d   91 (105)
T 4emh_A           15 MLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMP---DGDKFFRLPECYIRGNNIKYLRIQDEVLS   91 (105)
T ss_dssp             -----------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECT---TSCEEEEEEEEEECGGGEEEEEC------
T ss_pred             CcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEcc---CCceeeEcCeEEEeCCeEEEEecCHHHhh
Confidence            467889999999999999999999999999999999999999999743   23457889999999999999999998877


Q ss_pred             ccC
Q 034299           81 SHL   83 (98)
Q Consensus        81 ~~~   83 (98)
                      ++.
T Consensus        92 ~p~   94 (105)
T 4emh_A           92 QVA   94 (105)
T ss_dssp             ---
T ss_pred             hhh
Confidence            644

>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=99.89  E-value=7.4e-23  Score=131.27  Aligned_cols=72  Identities=29%  Similarity=0.361  Sum_probs=61.5

Q ss_pred             CCChhhHHhhcCCeEEEEECCC-cEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            1 MSGGPGLESLVEQQISVITNDG-RNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~G-r~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      |.|.+.|.+++|++|+|+|++| ++|.|+|.|||+|||++|+||+|++.    +...+.+|.++|||++|++|.+++
T Consensus        20 ~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~----~~~~~~lg~v~IRG~nI~~I~~~~   92 (93)
T 1n9r_A           20 VNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVA----GVSHGTLGEIFIRCNNVLYIRELP   92 (93)
T ss_dssp             ------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEET----TEEEEECCSEEECGGGEEEEEECC
T ss_pred             CChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcC----CCeEeEcCEEEEcCCeEEEEEeCC
Confidence            4578899999999999999999 99999999999999999999999862    356789999999999999999875

>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=99.88  E-value=2e-23  Score=139.33  Aligned_cols=82  Identities=18%  Similarity=0.340  Sum_probs=66.5

Q ss_pred             CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeec--C----CCee-----EEEecEEEEcCCcE
Q 034299            1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYST--K----EGVQ-----QLVLGLYIIRGDNI   69 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~--~----~~~~-----~r~lg~v~irG~~I   69 (98)
                      +.|...|.++++++|+|+|++||+|.|+|+|||+||||+|+||+|++...  +    ++..     .+.+|+++|||++|
T Consensus        27 ~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~nV  106 (121)
T 2fwk_A           27 ILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNV  106 (121)
T ss_dssp             CCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGE
T ss_pred             cCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCEE
Confidence            35778899999999999999999999999999999999999999998541  1    1223     68899999999999


Q ss_pred             EEEEecCcccccc
Q 034299           70 SIVGEVDEELDSH   82 (98)
Q Consensus        70 ~~i~~~d~~~e~~   82 (98)
                      ++|.+.+++.+..
T Consensus       107 v~I~~~~~~~~~~  119 (121)
T 2fwk_A          107 AMLVPGGDPDSFN  119 (121)
T ss_dssp             EEEESSSCC----
T ss_pred             EEEEecCCCCCcC
Confidence            9999987765543

>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=99.88  E-value=2e-22  Score=124.52  Aligned_cols=72  Identities=18%  Similarity=0.057  Sum_probs=65.3

Q ss_pred             CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      |.|...|++++|++|+|+|++|++|+|+|.+||+|||++|+||+|+..   + ...+.+|.++|||++|.+|..+|
T Consensus         4 ~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~---~-~~~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            4 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYR---D-GRVAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECT---T-SCEEEEEEEEECGGGEEEEEECC
T ss_pred             cCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECC---C-CcEEEcCeEEEeCCEEEEEEcCC
Confidence            568889999999999999999999999999999999999999999852   2 24789999999999999999875

>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=99.87  E-value=1.7e-22  Score=129.40  Aligned_cols=72  Identities=22%  Similarity=0.349  Sum_probs=65.1

Q ss_pred             CChhhHHhhcCCeEEEEE----CCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            2 SGGPGLESLVEQQISVIT----NDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l----~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      .|...|.++++++++|++    ++||+|.|+|.|||+|||++|+||+|++.+   +..++.+|.++|||+||++|.+.+
T Consensus        16 ~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~---~~~~~~lg~v~iRG~nV~~i~~~~   91 (92)
T 3s6n_E           16 QPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSK---TKSRKQLGRIMLKGDNITLLQSVS   91 (92)
T ss_dssp             CHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSS---SCCEEEEEEEEECGGGEEEEEEC-
T ss_pred             CCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecC---CCceeEcCeEEEeCCEEEEEEeCC
Confidence            577899999999999999    999999999999999999999999998743   245789999999999999999875

>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=99.87  E-value=7.3e-22  Score=143.91  Aligned_cols=76  Identities=28%  Similarity=0.451  Sum_probs=66.6

Q ss_pred             CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEe-ecC-----CCeeEEEecEEEEcCCcEEEEEec
Q 034299            2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVY-STK-----EGVQQLVLGLYIIRGDNISIVGEV   75 (98)
Q Consensus         2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~-~~~-----~~~~~r~lg~v~irG~~I~~i~~~   75 (98)
                      .+...|++|++|+|+|+|+|||+|+|+|+|||+||||+|+||+|++. +++     +..+++++|++||||+||++|...
T Consensus         4 ~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isve   83 (231)
T 3pgw_B            4 GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   83 (231)
T ss_pred             CchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEec
Confidence            45679999999999999999999999999999999999999999974 221     235789999999999999999876


Q ss_pred             Cc
Q 034299           76 DE   77 (98)
Q Consensus        76 d~   77 (98)
                      +.
T Consensus        84 ~p   85 (231)
T 3pgw_B           84 GP   85 (231)
T ss_pred             CC
Confidence            53

>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=99.87  E-value=7.4e-22  Score=131.46  Aligned_cols=73  Identities=22%  Similarity=0.257  Sum_probs=66.6

Q ss_pred             CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      |.|..+|.++++++|+|+|++|++|.|+|.+||+||||+|+||+|+..    +...+.+|.++|||+||++|.++|.
T Consensus         1 M~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~----~~~~~~lg~v~IRG~nI~~I~~pd~   73 (119)
T 1b34_A            1 MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLK----NREPVQLETLSIRGNNIRYFILPDS   73 (119)
T ss_dssp             -CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECT----TSCCEEEEEEEECGGGEEEEECCTT
T ss_pred             CChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecC----CCceeEcceEEEcCCeEEEEEeccc
Confidence            889999999999999999999999999999999999999999999852    2345789999999999999999886

>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=99.86  E-value=1.1e-21  Score=130.37  Aligned_cols=76  Identities=21%  Similarity=0.331  Sum_probs=62.6

Q ss_pred             CChhhHHhhc--CCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeec-CC--C-------eeEEEecEEEEcCCcE
Q 034299            2 SGGPGLESLV--EQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYST-KE--G-------VQQLVLGLYIIRGDNI   69 (98)
Q Consensus         2 ~~~~~L~~~i--~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~-~~--~-------~~~r~lg~v~irG~~I   69 (98)
                      .|...|.+++  +++|+|.|++||+|.|+|.|||+||||+|+||.|++... +.  +       ..++.+|.+||||++|
T Consensus        27 ~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~nV  106 (118)
T 1b34_B           27 GPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSV  106 (118)
T ss_dssp             CHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGE
T ss_pred             ChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCCEE
Confidence            5778999999  599999999999999999999999999999999987542 11  1       1367899999999999


Q ss_pred             EEEEecCc
Q 034299           70 SIVGEVDE   77 (98)
Q Consensus        70 ~~i~~~d~   77 (98)
                      ++|.+.+.
T Consensus       107 v~I~~~~~  114 (118)
T 1b34_B          107 IVVLRNPL  114 (118)
T ss_dssp             EEEEECCC
T ss_pred             EEEEeCch
Confidence            99998764

>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=99.83  E-value=3.6e-20  Score=124.58  Aligned_cols=75  Identities=19%  Similarity=0.084  Sum_probs=66.6

Q ss_pred             CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCccc
Q 034299            1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEEL   79 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~   79 (98)
                      |.|..+|.+++|++|+|+|++|++|.|+|.+||+||||+|+||+|+..   ++ +...++.+||||++|.+|..+|.-.
T Consensus         4 ~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~---~g-~~~~l~~v~IRGnnI~~I~lpd~l~   78 (126)
T 2y9a_D            4 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYR---DG-RVAQLEQVYIRGSKIRFLILPDMLK   78 (126)
T ss_dssp             CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECT---TS-CCEEEEEEEECGGGEEEEECCSSCS
T ss_pred             ccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcC---CC-cEeecccEEEeCCEEEEEEcccccc
Confidence            468899999999999999999999999999999999999999999742   22 3678999999999999999887543

>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=99.80  E-value=7.8e-20  Score=123.50  Aligned_cols=69  Identities=20%  Similarity=0.348  Sum_probs=62.6

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCccccc
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDS   81 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e~   81 (98)
                      +.|.+++|++|+|+|++|++|.|+|.|||+|||++|+||.|+.        .+.+|.++|||++|++|.++++..+.
T Consensus         3 ~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~--------~~~lg~v~IRG~nI~~I~~~d~~~d~   71 (130)
T 1m5q_A            3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA--------GEKFNRVFIMYRYIVHIDSTERRIDM   71 (130)
T ss_dssp             HHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT--------CCEEEEEEECGGGEEEEEECCCCCCH
T ss_pred             hHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc--------CCEeceEEEeCCeEEEEEcCCcccCH
Confidence            5899999999999999999999999999999999999999962        24789999999999999999876443

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

Probab=99.11  E-value=1.6e-10  Score=72.95  Aligned_cols=67  Identities=18%  Similarity=0.253  Sum_probs=57.7

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCccccc
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDS   81 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e~   81 (98)
                      ..|++|+||+|.|.+.||++|+|.|.+|| ...|++|.|+.+      ++    ....++|.|..|..|...++..++
T Consensus        10 ~el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~~------~~----~~~~~iI~G~aI~eI~v~~~~~~~   77 (86)
T 1y96_A           10 LEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLE------DG----SMSVTGIMGHAVQTVETMNEGDHR   77 (86)
T ss_dssp             HHHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEECT------TS----CEEEEEECGGGEEEEEEEECCCHH
T ss_pred             HHHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeeccc------CC----eEEEEEEecceEEEEEEecchhHH
Confidence            58999999999999999999999999999 999999999822      11    247899999999999988765543

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

Probab=96.86  E-value=0.0022  Score=38.99  Aligned_cols=54  Identities=24%  Similarity=0.305  Sum_probs=41.3

Q ss_pred             hHHhhc--CCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            6 GLESLV--EQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         6 ~L~~~i--~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      .|+++.  ..+|.|.|.+|..+.|.+.+||+|+ +.|++.                ...+|--..|..|.+..
T Consensus        13 ~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~-vlL~~~----------------~~~LIYKhAIsTI~p~~   68 (74)
T 2ylb_A           13 FLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLKNT----------------VSQMVYKHAISTVVPSR   68 (74)
T ss_dssp             HHHHHHHHTCCEEEEETTSCEEEEEEEEECSSE-EEEESS----------------SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEECC----------------ceEEEEeeeEEEEeEcc
Confidence            456666  7899999999999999999999999 555431                23467777777777653

>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A

Probab=96.68  E-value=0.0035  Score=38.85  Aligned_cols=36  Identities=28%  Similarity=0.460  Sum_probs=29.2

Q ss_pred             hHHhhc--CCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299            6 GLESLV--EQQISVITNDGRNIVGVLKGFDQATNIILDE   42 (98)
Q Consensus         6 ~L~~~i--~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~   42 (98)
                      .|+++.  ..+|+|-|.+|-.+.|.+.+||+|+ +.|++
T Consensus        11 fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ft-VlL~~   48 (82)
T 1u1s_A           11 YLNTLRKERVPVSIYLVNGIKLQGQIESFDQFV-ILLKN   48 (82)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEES
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceE-EEEec
Confidence            444444  6889999999999999999999999 55543

>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387, stronGly BENT five-stranded antiparallel beta- sheet, structural genomics, PSI; NMR {Danio rerio} SCOP: b.38.1.5 PDB: 2vxf_A

Probab=96.47  E-value=0.0097  Score=37.75  Aligned_cols=75  Identities=16%  Similarity=0.245  Sum_probs=53.1

Q ss_pred             hhhHHhhcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeecC--CC---eeEEEecEEEEcCCcEEEEEecCc
Q 034299            4 GPGLESLVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYSTK--EG---VQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~~--~~---~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      ...-.+|+|+++.+..+.+-.|+|+|...| +..-+.|+|+.-+=+...  ++   .......-++.||+.|.-+...+.
T Consensus        11 ~~~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e~   90 (95)
T 2fb7_A           11 PSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEP   90 (95)
T ss_dssp             -----CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESCC
T ss_pred             CCccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEecC
Confidence            345678999999999999999999999999 666788999855432211  10   123345788999999999887654


Q ss_pred             c
Q 034299           78 E   78 (98)
Q Consensus        78 ~   78 (98)
                      +
T Consensus        91 p   91 (95)
T 2fb7_A           91 P   91 (95)
T ss_dssp             S
T ss_pred             C
Confidence            3

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

Probab=96.45  E-value=0.0039  Score=40.21  Aligned_cols=36  Identities=28%  Similarity=0.445  Sum_probs=29.0

Q ss_pred             hHHhhcC--CeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299            6 GLESLVE--QQISVITNDGRNIVGVLKGFDQATNIILDE   42 (98)
Q Consensus         6 ~L~~~i~--k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~   42 (98)
                      .|+.+..  .+|.|.|.+|-.+.|.+.+||+|+ +.|++
T Consensus        13 fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~-VlL~~   50 (104)
T 2y90_A           13 FLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLKN   50 (104)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEES
T ss_pred             HHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEEC
Confidence            4555554  489999999999999999999999 55543

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

Probab=96.43  E-value=0.025  Score=35.41  Aligned_cols=70  Identities=20%  Similarity=0.242  Sum_probs=53.1

Q ss_pred             HhhcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeecCCC-----eeEEEecEEEEcCCcEEEEEecCc
Q 034299            8 ESLVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYSTKEG-----VQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         8 ~~~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~~~~-----~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      ..|+|+++.+..+.+-.|+|+|...| +..-+.|+|+..+=+.....     .......-++.||+.|.-+...+.
T Consensus         9 ~~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~~~   84 (88)
T 2vxe_A            9 LPELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVNN   84 (88)
T ss_dssp             SCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEECCC
T ss_pred             CcccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEEecc
Confidence            56899999999999999999999999 66678899986653321111     122345788999999999887643

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

Probab=96.30  E-value=0.0069  Score=37.23  Aligned_cols=54  Identities=22%  Similarity=0.297  Sum_probs=39.1

Q ss_pred             hHHhhc--CCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            6 GLESLV--EQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         6 ~L~~~i--~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      .|+.+.  ..+|.|.|.+|..+.|.+.+||+|+ +.|++-                ...+|--.-|..|.+..
T Consensus        12 fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~-VlL~~g----------------~~qLIYKhAISTI~P~~   67 (79)
T 3sb2_A           12 FLNALRKEHVPVSIYLVNGIKLQGHVESFDQYV-VLLRNT----------------VTQMVYKHAISTVVPAR   67 (79)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEESS----------------SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcE-EEEECC----------------ceEEEEeeeEEEEeecC
Confidence            445554  4669999999999999999999999 445321                12356677777777653

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

Probab=96.17  E-value=0.012  Score=35.90  Aligned_cols=35  Identities=23%  Similarity=0.509  Sum_probs=29.4

Q ss_pred             hHHhhc--CCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299            6 GLESLV--EQQISVITNDGRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         6 ~L~~~i--~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      .|+++.  ..+|.|.|.+|-.+.|.+.+||+|+ +.|.
T Consensus        11 fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~-VlL~   47 (77)
T 1kq1_A           11 ALENFKANQTEVTVFFLNGFQMKGVIEEYDKYV-VSLN   47 (77)
T ss_dssp             HHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcE-EEEE
Confidence            455666  7899999999999999999999999 4443

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

Probab=96.16  E-value=0.0092  Score=39.54  Aligned_cols=58  Identities=19%  Similarity=0.318  Sum_probs=45.0

Q ss_pred             hHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEe--cceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcc
Q 034299            6 GLESLVEQQISVITNDGRNIVGVLKGFDQATNIIL--DESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEE   78 (98)
Q Consensus         6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL--~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~   78 (98)
                      .+.+|+|+.|.|+|+||..+.|++..+|.. +|.|  ++|...+.              -|+.+.|.-+..++.+
T Consensus         6 ~~sqFlGy~V~v~LkDgs~~qG~I~~vd~k-~LtL~~~~a~~s~~--------------~I~asdI~DLkVl~~~   65 (125)
T 4a53_A            6 SVADFYGSNVEVLLNNDSKARGVITNFDSS-NSILQLRLANDSTK--------------SIVTKDIKDLRILPKN   65 (125)
T ss_dssp             CHHHHTTCEEEEEETTSCEEEEEEEEEETT-TTEEEEEETTTEEE--------------EEEGGGEEEEEECCSC
T ss_pred             cHHHhcCceEEEEECCCCEeeEEEEeecCC-eeEEeccccccccc--------------eeecccccceeeeecc
Confidence            368999999999999999999999999854 4777  88844321              5777777777666543

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

Probab=96.12  E-value=0.012  Score=36.09  Aligned_cols=35  Identities=29%  Similarity=0.511  Sum_probs=28.9

Q ss_pred             hHHhhc--CCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299            6 GLESLV--EQQISVITNDGRNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         6 ~L~~~i--~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~   41 (98)
                      .|+++.  ..+|+|-|.+|..+.|.+.+||+|+ +.|+
T Consensus        15 fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~-VlL~   51 (78)
T 3ahu_A           15 FLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFT-VLLE   51 (78)
T ss_dssp             HHHHHHHHTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceE-EEEE
Confidence            445555  7899999999999999999999999 4443

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

Probab=95.91  E-value=0.016  Score=34.89  Aligned_cols=29  Identities=7%  Similarity=0.256  Sum_probs=25.5

Q ss_pred             cCCeEEEEECCCcEEEEEEEEEcCCCceE
Q 034299           11 VEQQISVITNDGRNIVGVLKGFDQATNII   39 (98)
Q Consensus        11 i~k~V~V~l~~Gr~i~G~L~~~D~~~Nlv   39 (98)
                      -..+|+|-|.+|-.+.|.+.+||+|+=++
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll   52 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSNYEIMV   52 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            36789999999999999999999999444

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

Probab=95.89  E-value=0.025  Score=35.02  Aligned_cols=64  Identities=17%  Similarity=0.238  Sum_probs=49.4

Q ss_pred             HhhcCCeEEEEECCCc-EEEEEEEEEcC-CCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcc
Q 034299            8 ESLVEQQISVITNDGR-NIVGVLKGFDQ-ATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEE   78 (98)
Q Consensus         8 ~~~i~k~V~V~l~~Gr-~i~G~L~~~D~-~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~   78 (98)
                      .+|+|+.|.+..+++- .|.|.+..+|. ..||.|.++..      ++. +.....+.+++..|..+...+.+
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f~------NG~-~~~s~eVtls~~DI~~L~ii~~~   70 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPFH------NGV-KCLVPEVTFRAGDITELKILEIP   70 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEEE------TTE-ECSSSEEEEEGGGCSEEEEEECC
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhhh------CCC-CCCCcEEEEEecChhheEEEecC
Confidence            4899999999999998 99999999995 46899999942      122 22334588888888777765543

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

Probab=95.43  E-value=0.11  Score=31.28  Aligned_cols=56  Identities=14%  Similarity=0.199  Sum_probs=40.7

Q ss_pred             hhHHhhc--CCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEec
Q 034299            5 PGLESLV--EQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV   75 (98)
Q Consensus         5 ~~L~~~i--~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~   75 (98)
                      ..|+.|+  .++|.|.|.+|..+.|++.-+|.++ +.|.+..+              ..++|.-..|++|.+.
T Consensus        14 R~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~c-l~L~~~~~--------------~~~LI~R~AI~~Ikp~   71 (72)
T 3hfn_A           14 RQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTC-VCIADENS--------------RQTTIWKQAIAYLQPK   71 (72)
T ss_dssp             HHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSE-EEEEC-----------------CEEEEEGGGEEEEEEC
T ss_pred             HHHHHHHhhCceEEEEecCCCEEEEEEEEECCCE-EEEEcCCC--------------CeEEEEeeeeEEEEeC
Confidence            3567777  4788999999999999999999998 44444311              1356777777777653

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

Probab=95.20  E-value=0.14  Score=30.34  Aligned_cols=41  Identities=20%  Similarity=0.413  Sum_probs=33.5

Q ss_pred             hHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEE
Q 034299            6 GLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERV   47 (98)
Q Consensus         6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~   47 (98)
                      .|++|-|++|-+..-+...|+|.|.-||.-. +.|+|++.+.
T Consensus        10 tL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~   50 (71)
T 1ycy_A           10 VLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI   50 (71)
T ss_dssp             HHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT
T ss_pred             HHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHh
Confidence            5789999999999999999999999999887 8899998864

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

Probab=94.72  E-value=0.28  Score=30.34  Aligned_cols=60  Identities=18%  Similarity=0.249  Sum_probs=47.2

Q ss_pred             hHHhhcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            6 GLESLVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      .|....|++|.+.+.++-++.|++.++| ...|+..++-    ..|- |    .....++|++.|.++..
T Consensus        23 ~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L----~TPi-G----v~~eAlLR~~Dii~~sF   83 (85)
T 1y96_B           23 SLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQL----QTPI-G----VQAEALLRCSDIISYTF   83 (85)
T ss_dssp             HHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEE----CCTT-C----CEEEEEEEGGGEEEEEE
T ss_pred             HHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhc----CCCc-c----cchhhhhhcCCEEEEEe
Confidence            4566789999999999999999999999 6778776663    1121 1    25678999999999875

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

Probab=94.53  E-value=0.14  Score=30.58  Aligned_cols=55  Identities=16%  Similarity=0.248  Sum_probs=39.2

Q ss_pred             hhHHhhc--CCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            5 PGLESLV--EQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         5 ~~L~~~i--~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      ..|+.|+  ..+|.|.|.+|..+.|.+.-+|.++ +.|.+...              -.++|.-..|++|.+
T Consensus        12 R~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~c-l~L~~~~~--------------~~~LI~r~AI~~I~p   68 (70)
T 3hfo_A           12 RQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDG-LGLVDDSE--------------RSTIVRLAAIAYITP   68 (70)
T ss_dssp             HHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE-EEEECTTC--------------CEEEEEGGGEEEEEE
T ss_pred             HHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCE-EEEEcCCC--------------CeEEEEeeeeEEEee
Confidence            3566666  5889999999999999999999998 44444211              123566666776654

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

Probab=94.06  E-value=0.35  Score=30.68  Aligned_cols=63  Identities=8%  Similarity=0.154  Sum_probs=47.9

Q ss_pred             HhhcCCeEEEEECCCc-EEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            8 ESLVEQQISVITNDGR-NIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         8 ~~~i~k~V~V~l~~Gr-~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      ++|+|+-|.|.+.+-- .|.|.+..+|+ .+|.|.+|...-..     -+.....|.++-..|..+...+
T Consensus         8 edwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaFrNGip-----lk~~~~EVtLsa~DI~~L~IIe   71 (103)
T 2rm4_A            8 QDWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAFRNGVP-----LRKQNAEVVLKCTDIRSIDLIE   71 (103)
T ss_dssp             GGGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEEETTEE-----CSCSSSCEEEETTTEEEEEEEE
T ss_pred             cceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhhhcCcC-----cCCCCceEEEEecchhheeeec
Confidence            5899999999999986 99999999996 44999888653110     1234567778888888777754

>3rux_A BIRA bifunctional protein; biotin-protein ligase, ligase-ligase inhibitor complex; HET: BS5; 1.70A {Mycobacterium tuberculosis} PDB: 3l1a_A 3l2z_A 2cgh_A

Probab=92.47  E-value=0.19  Score=36.53  Aligned_cols=34  Identities=21%  Similarity=0.460  Sum_probs=30.8

Q ss_pred             hcCCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299           10 LVEQQISVITNDGRNIVGVLKGFDQATNIILDES   43 (98)
Q Consensus        10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~   43 (98)
                      ++|++|++...+|..+.|+..++|....|+|+..
T Consensus       222 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~  255 (270)
T 3rux_A          222 TIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVG  255 (270)
T ss_dssp             STTSEEEEECTTSCEEEEEEEEECTTSCEEEEET
T ss_pred             ccCCEEEEEECCCeEEEEEEEEECCCCeEEEEEC
Confidence            4689999998889999999999999999999764

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

Probab=91.76  E-value=0.2  Score=34.06  Aligned_cols=35  Identities=17%  Similarity=0.262  Sum_probs=28.8

Q ss_pred             hhHHhhcCCeEEEEEC----CCcEEEEEEEEEcCCCceEe
Q 034299            5 PGLESLVEQQISVITN----DGRNIVGVLKGFDQATNIIL   40 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~----~Gr~i~G~L~~~D~~~NlvL   40 (98)
                      .++.+++|+.|.|+++    +.+.++|+|.++|... +.|
T Consensus        97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~-v~l  135 (164)
T 1ib8_A           97 DAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE-LTM  135 (164)
T ss_dssp             HHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE-EEE
T ss_pred             HHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCCE-EEE
Confidence            4678999999999993    4589999999999753 555

>2eay_A Biotin [acetyl-COA-carboxylase] ligase; biotin biosynthesis, dimer, X-RAY diffraction, structural genomics, NPPSFA; 1.95A {Aquifex aeolicus} PDB: 3efs_A* 3fjp_A 3efr_A*

Probab=88.38  E-value=0.38  Score=34.07  Aligned_cols=32  Identities=13%  Similarity=0.343  Sum_probs=27.0

Q ss_pred             hcCCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299           10 LVEQQISVITNDGRNIVGVLKGFDQATNIILDES   43 (98)
Q Consensus        10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~   43 (98)
                      ++|++|++...++  +.|+..++|.+..|+|+..
T Consensus       186 ~~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~  217 (233)
T 2eay_A          186 YLGEEVKLLGEGK--ITGKLVGLSEKGGALILTE  217 (233)
T ss_dssp             TTTSEEEETTEEE--EEEEEEEECTTSCEEEEET
T ss_pred             ccCCEEEEEECCe--EEEEEEEECCCCeEEEEEC
Confidence            4689999876544  9999999999999999753

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=88.18  E-value=1.2  Score=32.65  Aligned_cols=34  Identities=18%  Similarity=0.606  Sum_probs=28.8

Q ss_pred             hhcCCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299            9 SLVEQQISVITNDGRNIVGVLKGFDQATNIILDES   43 (98)
Q Consensus         9 ~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~   43 (98)
                      .++|++|++... +..+.|+..++|..+.|+++..
T Consensus       270 ~~~g~~V~v~~~-~~~~~G~~~gid~~G~L~v~~~  303 (321)
T 1bia_A          270 NFINRPVKLIIG-DKEIFGISRGIDKQGALLLEQD  303 (321)
T ss_dssp             TTTTSEEEEEET-TEEEEEEEEEECTTSCEEEEET
T ss_pred             hhcCCEEEEEEC-CcEEEEEEEEECCCCeEEEEEC
Confidence            347999999875 4589999999999999999753

>2xk0_A Polycomb protein PCL; transcription, aromatic CAGE; NMR {Drosophila melanogaster}

Probab=85.88  E-value=3.7  Score=24.30  Aligned_cols=40  Identities=20%  Similarity=0.335  Sum_probs=29.7

Q ss_pred             hcCCeEEEEECCCcEEEEEEEEEcCCCc-eEecceEEEEee
Q 034299           10 LVEQQISVITNDGRNIVGVLKGFDQATN-IILDESHERVYS   49 (98)
Q Consensus        10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~N-lvL~~~~e~~~~   49 (98)
                      .+|..|.++.+||+.|-|++....+..= +..+|-.+.|..
T Consensus        17 ~~geDVL~rw~DG~fYLGtIVd~~~~~ClV~FeD~S~~Wv~   57 (69)
T 2xk0_A           17 ALQEDVFIKCNDGRFYLGTIIDQTSDQYLIRFDDQSEQWCE   57 (69)
T ss_dssp             CTTCEEEEECTTSCEEEEEEEEECSSCEEEEETTCCEEEEC
T ss_pred             ccCCeEEEEecCCCEEEEEEEecCCceEEEEecCCcceeee
Confidence            4689999999999999999976664433 344666666654

>2ej9_A Putative biotin ligase; biotin biosynthesis, monomer, X-RAY diffraction, structural genomics, NPPSFA; HET: BTN; 2.00A {Methanocaldococcus jannaschii}

Probab=83.59  E-value=1.6  Score=30.79  Aligned_cols=32  Identities=13%  Similarity=0.289  Sum_probs=28.6

Q ss_pred             hcCCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299           10 LVEQQISVITNDGRNIVGVLKGFDQATNIILDE   42 (98)
Q Consensus        10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~   42 (98)
                      ++|++|++...++..+.|+..++|....|+ +.
T Consensus       190 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~-~~  221 (237)
T 2ej9_A          190 TIGKQVKILLSNNEIITGKVYDIDFDGIVL-GT  221 (237)
T ss_dssp             STTCEEEEEETTSCEEEEEEEEECSSEEEE-EE
T ss_pred             ccCCEEEEEECCCeEEEEEEEEECCCCeEE-Ec
Confidence            479999999888877999999999999998 64

---

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	98
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	4e-16
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	6e-14
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-13
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	4e-13
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	8e-13
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	1e-12
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	1e-12
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	3e-12
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-11
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	5e-11
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	1e-08
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	3e-06
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	6e-06

>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 = 64.8 bits (158), Expect = 4e-16
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 6/69 (8%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERV------YSTKEGVQQLVLG 60
          +   ++ ++  I  DGR  +G  K FD+  N+IL +  E            E  ++ VLG
Sbjct: 3  MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 62

Query: 61 LYIIRGDNI 69
          L ++RG+N+
Sbjct: 63 LVLLRGENL 71

>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 = 59.5 bits (144), Expect = 6e-14
 Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 11/77 (14%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYS-----------TKEGVQ 55
          ++  +  +I V+    +   GVL+GFD+  N++LD+  E  +              + V 
Sbjct: 10 IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVM 69

Query: 56 QLVLGLYIIRGDNISIV 72
             L   ++ G+N++++
Sbjct: 70 VNRLETILLSGNNVAML 86

>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 = 57.8 bits (140), Expect = 1e-13
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L+  + +Q+ V   D   I G+L+ FDQ  N++L+++ E +            G  ++RG
Sbjct: 7  LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYK-----RGTMVVRG 61

Query: 67 DNISIVGEV 75
          +N+  +  V
Sbjct: 62 ENVLFISPV 70

>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 = 57.0 bits (138), Expect = 4e-13
 Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 4/69 (5%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L   +   + V     + + G+L+ +DQ  N++L +S E     +       LG  +IRG
Sbjct: 12 LAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEE----IQSDGSGKKLGTIVIRG 67

Query: 67 DNISIVGEV 75
          DN+ ++  +
Sbjct: 68 DNVILISPL 76

>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 = 55.9 bits (135), Expect = 8e-13
 Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 4/66 (6%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L   ++  + V    GR   G L G+D   N++L ++ E     + G     +G  +IRG
Sbjct: 8  LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEE----IQNGEVVRKVGSVVIRG 63

Query: 67 DNISIV 72
          D +  V
Sbjct: 64 DTVVFV 69

>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 = 55.9 bits (135), Expect = 1e-12
 Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 4/66 (6%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          +   +++ + VI   G    G L G+D   N++L ++       ++G      G  +IRG
Sbjct: 7  IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEM----IQDGEVVKRYGKIVIRG 62

Query: 67 DNISIV 72
          DN+  +
Sbjct: 63 DNVLAI 68

>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 = 55.5 bits (134), Expect = 1e-12
 Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 5/72 (6%)

Query: 7  LESLVEQQISV-ITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIR 65
          L+ LV  ++ V +  +     G L   D   N+ L+E+ E V     G     LG   IR
Sbjct: 1  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHG----TLGEIFIR 56

Query: 66 GDNISIVGEVDE 77
           +N+  + E+  
Sbjct: 57 CNNVLYIRELPN 68

>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 = 54.7 bits (132), Expect = 3e-12
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 4/66 (6%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L + +   + +     R   GVLK FD   N++L+++ E     ++G     LG  +IRG
Sbjct: 11 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE----LEDGEVTRRLGTVLIRG 66

Query: 67 DNISIV 72
          DNI  +
Sbjct: 67 DNIVYI 72

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

 Score = 52.4 bits (126), Expect = 2e-11
 Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 5/67 (7%)

Query: 7  LESLVEQQISV-ITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIR 65
          ++S+V + I V +  +   +VG L+G D   N+ L  + E     K   +   LG  ++R
Sbjct: 10 VKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAME----CKGEEKVRSLGEIVLR 65

Query: 66 GDNISIV 72
          G+N+ ++
Sbjct: 66 GNNVVLI 72

>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 = 52.2 bits (125), Expect = 5e-11
 Identities = 12/70 (17%), Positives = 30/70 (42%), Gaps = 10/70 (14%)

Query: 13 QQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEG----------VQQLVLGLY 62
           Q+ +   + + ++G +K FD+  N++L+   E      +            +   +   
Sbjct: 15 TQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKM 74

Query: 63 IIRGDNISIV 72
           +RGD++ +V
Sbjct: 75 FLRGDSVIVV 84

>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 = 47.0 bits (112), Expect = 1e-08
 Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 8/77 (10%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L +L+ +++ V+ ++G    GVL   D   NI+L  +  +     E   ++      I  
Sbjct: 5  LNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA---GEKFNRVF-----IMY 56

Query: 67 DNISIVGEVDEELDSHL 83
            I  +   +  +D   
Sbjct: 57 RYIVHIDSTERRIDMRE 73

>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 = 39.0 bits (91), Expect = 3e-06
 Identities = 12/66 (18%), Positives = 18/66 (27%), Gaps = 4/66 (6%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L       ++  TN G    G L   +   N  +              +   L    IRG
Sbjct: 7  LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY----RDGRVAQLEQVYIRG 62

Query: 67 DNISIV 72
            I  +
Sbjct: 63 CKIRFL 68

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (90), Expect = 6e-06
 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 5/78 (6%)

Query: 7  LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRG 66
          L  L  + +++   +G  + G + G D + N  L         T +  + + L    IRG
Sbjct: 6  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKM----TLKNREPVQLETLSIRG 61

Query: 67 DNISIVGEVDE-ELDSHL 83
          +NI      D   LD+ L
Sbjct: 62 NNIRYFILPDSLPLDTLL 79

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	98
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.91
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.89
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.89
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.89
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.88
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.88
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.87
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.87
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.86
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.86
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.84
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.77
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.73
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	96.97
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	96.88
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	95.77
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	95.49
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	95.01
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	93.59

>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=99.91  E-value=3.3e-24  Score=132.74  Aligned_cols=70  Identities=27%  Similarity=0.452  Sum_probs=61.8

Q ss_pred             hHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCC------CeeEEEecEEEEcCCcEEEEEec
Q 034299            6 GLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKE------GVQQLVLGLYIIRGDNISIVGEV   75 (98)
Q Consensus         6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~------~~~~r~lg~v~irG~~I~~i~~~   75 (98)
                      .|.+|++++|+|.++|||.|.|+|.|||+||||+|++|.|++.....      ...+|.+|+++|||++|++|...
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEcc
Confidence            58899999999999999999999999999999999999998753211      23578999999999999999754

>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=99.89  E-value=2e-23  Score=126.46  Aligned_cols=67  Identities=28%  Similarity=0.538  Sum_probs=61.4

Q ss_pred             hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEec
Q 034299            4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV   75 (98)
Q Consensus         4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~   75 (98)
                      .+.|++++|++|+|+|+||++|.|+|.+||+|||++|+||.|++.     .+.+.+|.++|||++|.+|++.
T Consensus         4 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~-----~~~~~~g~v~iRG~~I~~I~~~   70 (71)
T d1i8fa_           4 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID-----GNVYKRGTMVVRGENVLFISPV   70 (71)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEET-----TEEEEEEEEEECGGGEEEEEEC
T ss_pred             hHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEEC-----CCEEEcceEEEeCCeEEEEeCC
Confidence            468999999999999999999999999999999999999999853     2567899999999999999865

>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=99.89  E-value=5e-24  Score=134.56  Aligned_cols=75  Identities=23%  Similarity=0.405  Sum_probs=64.9

Q ss_pred             CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCC-----------CeeEEEecEEEEcCCcE
Q 034299            1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKE-----------GVQQLVLGLYIIRGDNI   69 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~-----------~~~~r~lg~v~irG~~I   69 (98)
                      |.|...|+++++++|+|.++|||+|.|+|.|||+||||+|+||.|++.....           ...+|.+|++||||++|
T Consensus         4 ~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~V   83 (92)
T d2fwka1           4 ILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNV   83 (92)
T ss_dssp             CCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGE
T ss_pred             cChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEE
Confidence            5688899999999999999999999999999999999999999998754311           13467899999999999


Q ss_pred             EEEEec
Q 034299           70 SIVGEV   75 (98)
Q Consensus        70 ~~i~~~   75 (98)
                      ++|.+.
T Consensus        84 v~I~p~   89 (92)
T d2fwka1          84 AMLVPG   89 (92)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            999874

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

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

Probab=99.89  E-value=5.4e-23  Score=124.18  Aligned_cols=68  Identities=24%  Similarity=0.340  Sum_probs=62.6

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      |...|++++|++|+|+|+||++|.|+|.+||++||++|+||.|...    +.+.+.+|.+||||++|.+|++
T Consensus         3 Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~----~~~~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           3 PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQD----GEVVKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             HHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEET----TEEEEEEEEEEECGGGEEEEEE
T ss_pred             chHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEec----CCcEeEcCcEEEECCeEEEEeC
Confidence            6778999999999999999999999999999999999999999752    3467889999999999999976

>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=99.88  E-value=4.9e-23  Score=124.81  Aligned_cols=68  Identities=26%  Similarity=0.384  Sum_probs=62.0

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      |...|.+++|++|+|+|+||++|.|+|.+||+|||++|+||+|+..    +...+.+|.++|||++|.+|.+
T Consensus         4 Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~----~~~~~~~g~~~IRG~~I~~Isp   71 (72)
T d1i4k1_           4 PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQN----GEVVRKVGSVVIRGDTVVFVSP   71 (72)
T ss_dssp             HHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESS----SSEEEEEEEEEECGGGEEEEEC
T ss_pred             hHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEec----CCeEeEcceEEEeCCeEEEEEc
Confidence            5678999999999999999999999999999999999999999843    2467889999999999999975

>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=99.88  E-value=1.1e-22  Score=123.75  Aligned_cols=68  Identities=29%  Similarity=0.429  Sum_probs=62.7

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      |...|++++|++|.|+|+||++|.|+|.|||++||++|+||.|++.    +...+.+|.++|||++|.+|.+
T Consensus         7 Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~----~~~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           7 PLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED----GEVTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             TTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEET----TEEEEEEEEEEECGGGEEEEEC
T ss_pred             cHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeC----CCeEeEcceEEEeCCEEEEEeC
Confidence            7889999999999999999999999999999999999999999853    3467889999999999999975

>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=99.87  E-value=2.9e-22  Score=122.51  Aligned_cols=70  Identities=24%  Similarity=0.348  Sum_probs=63.1

Q ss_pred             CCChhhHHhhcCCeEEEEECCC-cEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299            1 MSGGPGLESLVEQQISVITNDG-RNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE   74 (98)
Q Consensus         1 m~~~~~L~~~i~k~V~V~l~~G-r~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~   74 (98)
                      +.|...|++++|++|+|++++| ++|.|+|.+||+|||++|+||+|+..    +.+.+.+|.++|||++|.+|.+
T Consensus         4 ~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~----~~~~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           4 VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKG----EEKVRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEET----TEEEEEEEEEEECGGGEEEEEE
T ss_pred             cccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcC----CCcEeEcceEEEeCCEEEEEEC
Confidence            3578899999999999999965 89999999999999999999999853    2467899999999999999976

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

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

Probab=99.87  E-value=1.9e-22  Score=123.41  Aligned_cols=69  Identities=25%  Similarity=0.420  Sum_probs=62.2

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEec
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV   75 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~   75 (98)
                      |...|.+++|++|+|+|+||++|.|+|.|||++||++|+||+|+...    .+++.+|.++|||++|.+|++.
T Consensus         8 ~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----~~~~~~~~v~iRG~~I~~I~~~   76 (76)
T d1th7a1           8 AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD----GSGKKLGTIVIRGDNVILISPL   76 (76)
T ss_dssp             HHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSS----SCEEEEEEEEECGGGEEEEEEC
T ss_pred             HHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecC----CcccCcceEEEECCEEEEEEeC
Confidence            45689999999999999999999999999999999999999997532    3567899999999999999874

>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=99.86  E-value=3.4e-22  Score=126.65  Aligned_cols=74  Identities=19%  Similarity=0.310  Sum_probs=60.5

Q ss_pred             ChhhHHhhc--CCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCC----------eeEEEecEEEEcCCcEE
Q 034299            3 GGPGLESLV--EQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEG----------VQQLVLGLYIIRGDNIS   70 (98)
Q Consensus         3 ~~~~L~~~i--~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~----------~~~r~lg~v~irG~~I~   70 (98)
                      |...|.+++  +++|+|.+++||.+.|+|.|||+||||+|+||.|++..++++          ..+|.+|++||||+||+
T Consensus         3 Pl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnVv   82 (93)
T d1b34b_           3 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVI   82 (93)
T ss_dssp             HHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEE
T ss_pred             cHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEEE
Confidence            567888888  899999999999999999999999999999999998653211          24678999999999999


Q ss_pred             EEEecC
Q 034299           71 IVGEVD   76 (98)
Q Consensus        71 ~i~~~d   76 (98)
                      +|...+
T Consensus        83 ~I~~~p   88 (93)
T d1b34b_          83 VVLRNP   88 (93)
T ss_dssp             EEEECC
T ss_pred             EEEcCh
Confidence            997754

>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=99.86  E-value=7e-22  Score=118.73  Aligned_cols=66  Identities=30%  Similarity=0.416  Sum_probs=58.5

Q ss_pred             HHhhcCCeEEEEEC-CCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            7 LESLVEQQISVITN-DGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         7 L~~~i~k~V~V~l~-~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      |+++++++|.|+|+ +|++|.|+|.+||+|||++|+||+|+..    +...+.+|.++|||++|.+|...+
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~----~~~~~~lg~~~IRG~nI~~I~~~p   67 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVA----GVSHGTLGEIFIRCNNVLYIRELP   67 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEET----TEEEEECCSEEECGGGEEEEEECC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEec----CCcccCcCeEEEECCEEEEEEeCC
Confidence            67899999999999 5688999999999999999999999753    346778999999999999998553

>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=99.84  E-value=7.1e-21  Score=115.25  Aligned_cols=70  Identities=19%  Similarity=0.067  Sum_probs=62.9

Q ss_pred             ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299            3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD   76 (98)
Q Consensus         3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d   76 (98)
                      |...|.++.|++|+|+|+||++|+|+|.+||.|||++|+||.+...    +.+.+.++.+||||++|.+|..+|
T Consensus         3 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~----~~~~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           3 PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYR----DGRVAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             HHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECT----TSCEEEEEEEEECGGGEEEEEECC
T ss_pred             chHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcC----CCcEeEcCeEEEECCEEEEEEcCC
Confidence            6678999999999999999999999999999999999999988642    235677999999999999999875

>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=99.77  E-value=1.1e-18  Score=107.44  Aligned_cols=69  Identities=22%  Similarity=0.287  Sum_probs=61.1

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE   77 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~   77 (98)
                      ..|+++.|++|.|+|++|.+|+|+|.++|.+||+.|+||.+...    +.+...++.+||||++|.+|..+|.
T Consensus         4 ~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~----~~~~~~~~~v~IRG~~Ir~i~lPd~   72 (80)
T d1b34a_           4 RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLK----NREPVQLETLSIRGNNIRYFILPDS   72 (80)
T ss_dssp             HHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECT----TSCCEEEEEEEECGGGEEEEECCTT
T ss_pred             HHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcC----CCCEEEcccEEEcCCEEEEEECCCC
Confidence            36899999999999999999999999999999999999988632    2345689999999999999998764

>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=99.73  E-value=2.5e-18  Score=114.10  Aligned_cols=66  Identities=21%  Similarity=0.376  Sum_probs=58.7

Q ss_pred             hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcc
Q 034299            5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEE   78 (98)
Q Consensus         5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~   78 (98)
                      +.|++++|++|.|+|+||+++.|+|.+||++||++|+||++..     +.   ..+.++|||++|.+|..+++.
T Consensus         3 ~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~-----~~---k~~~v~IRG~~I~~I~~~e~~   68 (127)
T d1m5q1_           3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA-----GE---KFNRVFIMYRYIVHIDSTERR   68 (127)
T ss_dssp             HHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETT-----CC---EEEEEEECGGGEEEEEECSCC
T ss_pred             hHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECC-----CC---cccEEEEeCCeEEEEEcchhh
Confidence            5899999999999999999999999999999999999998741     11   478899999999999998653

>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: C-terminal domain of transcriptional repressors
family: Biotin repressor (BirA)
domain: Biotin repressor/biotin holoenzyme synthetase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.97  E-value=0.0018  Score=34.49  Aligned_cols=33  Identities=18%  Similarity=0.613  Sum_probs=28.9

Q ss_pred             hcCCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299           10 LVEQQISVITNDGRNIVGVLKGFDQATNIILDES   43 (98)
Q Consensus        10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~   43 (98)
                      |+|++|+|.. .++++.|+..++|....|+|+..
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t~   33 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQD   33 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEET
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEEC
Confidence            6899999875 56889999999999999999754

>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: LSM14 N-terminal domain-like
domain: LSM14 homolog A (Lsm14a)
species: Zebrafish (Danio rerio) [TaxId: 7955]

Probab=96.88  E-value=0.0047  Score=36.60  Aligned_cols=69  Identities=16%  Similarity=0.244  Sum_probs=52.3

Q ss_pred             hcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeecCC--C---eeEEEecEEEEcCCcEEEEEecCcc
Q 034299           10 LVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYSTKE--G---VQQLVLGLYIIRGDNISIVGEVDEE   78 (98)
Q Consensus        10 ~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~~~--~---~~~r~lg~v~irG~~I~~i~~~d~~   78 (98)
                      |+|+++.+..+.+-.|+|+|...| +..-+.|+|+.-+=+....  .   ........++.||+.|.-+...+..
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e~p   76 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEPP   76 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESSCC
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEeccCC
Confidence            799999999999999999999999 5555889998665322111  0   1233567899999999999887543

>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.77  E-value=0.0087  Score=34.17  Aligned_cols=30  Identities=23%  Similarity=0.428  Sum_probs=25.7

Q ss_pred             CCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299           12 EQQISVITNDGRNIVGVLKGFDQATNIILDE   42 (98)
Q Consensus        12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~   42 (98)
                      ..+|.|-|.+|-.+.|.+.+||+|.= .|++
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftv-LL~~   43 (66)
T d1u1sa1          14 RVPVSIYLVNGIKLQGQIESFDQFVI-LLKN   43 (66)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSEE-EEES
T ss_pred             CCcEEEEEEcCcEEEEEEEEEcceEE-EEEC
Confidence            57889999999999999999999984 4544

>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: PF1955-like
domain: Hypothetical protein PF1955
species: Pyrococcus furiosus [TaxId: 2261]

Probab=95.49  E-value=0.011  Score=33.19  Aligned_cols=41  Identities=20%  Similarity=0.413  Sum_probs=33.7

Q ss_pred             hHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEE
Q 034299            6 GLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERV   47 (98)
Q Consensus         6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~   47 (98)
                      .|++|-|++|-|...+...|+|+|.-||.-. |.|+|++.+.
T Consensus         6 tL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~   46 (66)
T d1ycya1           6 VLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI   46 (66)
T ss_dssp             HHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT
T ss_pred             HHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHh
Confidence            5889999999999999999999999999987 8899998864

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

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

Probab=95.01  E-value=0.035  Score=30.98  Aligned_cols=33  Identities=15%  Similarity=0.361  Sum_probs=27.8

Q ss_pred             CCeEEEEECCCcEEEEEEEEEcCCCceEecceE
Q 034299           12 EQQISVITNDGRNIVGVLKGFDQATNIILDESH   44 (98)
Q Consensus        12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~   44 (98)
                      ..+|.|-|.+|-.+.|.+.+||+|.=+.-.+..
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~~~   46 (60)
T d1kq1a_          14 QTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGK   46 (60)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEEEETTE
T ss_pred             CCcEEEEEECCcEEEEEEEEEcceEEEEEeCCc
Confidence            578999999999999999999999966555543

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

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

Probab=93.59  E-value=0.052  Score=30.75  Aligned_cols=37  Identities=19%  Similarity=0.299  Sum_probs=30.0

Q ss_pred             hhhHHhhcCCeEEEEEC---CC-cEEEEEEEEEcCCCceEec
Q 034299            4 GPGLESLVEQQISVITN---DG-RNIVGVLKGFDQATNIILD   41 (98)
Q Consensus         4 ~~~L~~~i~k~V~V~l~---~G-r~i~G~L~~~D~~~NlvL~   41 (98)
                      ..++..|+|+.|.|+|+   +| +.+.|.|.++|+.. +.|.
T Consensus         6 ~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~-i~l~   46 (74)
T d1ib8a1           6 KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE-LTME   46 (74)
T ss_dssp             HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE-EEEE
T ss_pred             HHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCCe-EEEE
Confidence            35789999999999985   35 79999999999864 4443