Citrus Sinensis ID: 034490

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90---
Protein Sequence
MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDLLHDATRREARGG
Secondary Structure (PSIPRED)
ccHHHHHHHccccEEEEEEccccEEEEEEEEEcccccEEEEEEEEEEcccccEEEcccEEEEEcccEEEEEEccccccHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHccccEEEEEEccEEEEEEEEEcccHEEEEEcEEEEEcccccccEEEccEEEEEccEEEEEEccccHccHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIklentrvvdqdkyphmlsvrncfirgsvvryvqlppdgvdvdllHDATRREARGG
Flexible Loop (DISEMBL)
mlffsyfkdlvgrEVTVELkndlairgtlhsvdQYLNIKlentrvvdqdkyPHMLSVRNCFIRGSVVRYVqlppdgvdvdllhDATRREARGG
Low Complexity Region (SEG)
MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDLLHDATRREARGG
Disordered region (IsUnstruct)
*LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDLL***********
Disordered Region (DISOPRED)
MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDL************
Disordered Region (DISEMBL)
MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDLLHDATRREARGG
Disordered Region (DISPRO)
MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDLLHDATRR*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDLLHDATRREARGG
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	93	2.2.26 [Sep-21-2011]
O35900	95	U6 snRNA-associated Sm-li	yes	no	0.967	0.947	0.744	4e-34
Q9Y333	95	U6 snRNA-associated Sm-li	yes	no	0.967	0.947	0.744	4e-34
Q54TF6	117	Probable U6 snRNA-associa	yes	no	0.978	0.777	0.670	1e-31
P38203	95	U6 snRNA-associated Sm-li	yes	no	0.967	0.947	0.655	4e-28
O94408	96	U6 snRNA-associated Sm-li	yes	no	0.956	0.927	0.640	4e-27
A9CTE0	97	Probable U6 snRNA-associa	N/A	no	0.924	0.886	0.384	4e-13
Q8SQK1	94	Probable U6 snRNA-associa	yes	no	0.795	0.787	0.342	4e-08
Q8QZX5	122	U7 snRNA-associated Sm-li	no	no	0.752	0.573	0.369	2e-06
Q54KX4	177	Probable U6 snRNA-associa	no	no	0.913	0.480	0.311	2e-06
Q9QXA5	137	U6 snRNA-associated Sm-li	no	no	0.956	0.649	0.336	2e-06

>sp|O35900|LSM2_MOUSE U6 snRNA-associated Sm-like protein LSm2 OS=Mus musculus GN=Lsm2 PE=3 SV=1

 Score =  143 bits (360), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 67/90 (74%), Positives = 76/90 (84%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLF+S+FK LVG++V VELKNDL+I GTLHSVDQYLNIKL +  V D +KYPHMLSV+NC
Sbjct: 1  MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREA 90
          FIRGSVVRYVQLP D VD  LL DA R+EA
Sbjct: 61 FIRGSVVRYVQLPADEVDTQLLQDAARKEA 90

Binds specifically to the 3'-terminal U-tract of U6 snRNA. May be involved in pre-mRNA splicing.
Mus musculus (taxid: 10090)

>sp|Q9Y333|LSM2_HUMAN U6 snRNA-associated Sm-like protein LSm2 OS=Homo sapiens GN=LSM2 PE=1 SV=1

 Score =  143 bits (360), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 67/90 (74%), Positives = 76/90 (84%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLF+S+FK LVG++V VELKNDL+I GTLHSVDQYLNIKL +  V D +KYPHMLSV+NC
Sbjct: 1  MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREA 90
          FIRGSVVRYVQLP D VD  LL DA R+EA
Sbjct: 61 FIRGSVVRYVQLPADEVDTQLLQDAARKEA 90

Binds specifically to the 3'-terminal U-tract of U6 snRNA. May be involved in pre-mRNA splicing.

Homo sapiens (taxid: 9606)

>sp|Q54TF6|LSM2_DICDI Probable U6 snRNA-associated Sm-like protein LSm2 OS=Dictyostelium discoideum GN=lsm2 PE=3 SV=1

 Score =  134 bits (338), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 61/91 (67%), Positives = 78/91 (85%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLFFS++K LVG+E+TVELKNDL+I G L SVDQ+LNIKL++ +V ++DKYP+M+SV+NC
Sbjct: 1  MLFFSFYKSLVGKEITVELKNDLSITGLLQSVDQFLNIKLKDIKVNEEDKYPYMISVKNC 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREAR 91
          FIRGSVVRYV LP + VDV+ L D +R EAR
Sbjct: 61 FIRGSVVRYVHLPAEDVDVETLQDHSRLEAR 91

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

Dictyostelium discoideum (taxid: 44689)

>sp|P38203|LSM2_YEAST U6 snRNA-associated Sm-like protein LSm2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM2 PE=1 SV=1

 Score =  123 bits (308), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 59/90 (65%), Positives = 70/90 (77%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLFFS+FK LV +EV VELKND+ I+GTL SVDQ+LN+KL+N    D+ KYPH+ SVRN 
Sbjct: 1  MLFFSFFKTLVDQEVVVELKNDIEIKGTLQSVDQFLNLKLDNISCTDEKKYPHLGSVRNI 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREA 90
          FIRGS VRYV L  + VD +LL DATRRE 
Sbjct: 61 FIRGSTVRYVYLNKNMVDTNLLQDATRREV 90

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

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

>sp|O94408|LSM2_SCHPO U6 snRNA-associated Sm-like protein LSm2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm2 PE=3 SV=1

 Score =  119 bits (299), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 57/89 (64%), Positives = 69/89 (77%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLF+S+FK L+  EVTVELKND++IRG L SVDQ+LN+KLEN  VVD  KYPHM +V++ 
Sbjct: 1  MLFYSFFKTLIDTEVTVELKNDMSIRGILKSVDQFLNVKLENISVVDASKYPHMAAVKDL 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRRE 89
          FIRGSVVRYV +    VD  LL DA RR+
Sbjct: 61 FIRGSVVRYVHMSSAYVDTILLADACRRD 89

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

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

>sp|A9CTE0|LSM2_ENTBH Probable U6 snRNA-associated Sm-like protein LSm2 OS=Enterocytozoon bieneusi (strain H348) GN=LSM2 PE=3 SV=1

 Score = 73.2 bits (178), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/91 (38%), Positives = 59/91 (64%), Gaps = 5/91 (5%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKY----PHMLS 56
          MLFF YFK  +  E+ V LKND++I G L +VD +LNIK+EN   +  +++      + +
Sbjct: 1  MLFFEYFKSQLNNEIIVNLKNDISISGILKNVDPFLNIKIENVIAISTNEFIKINKSITN 60

Query: 57 VRNCFIRGSVVRYVQLPPDGVDVDLLHDATR 87
          ++ C IRGS ++ V+L  +G++  ++ +ATR
Sbjct: 61 IQLCSIRGSAIKSVELKKNGLEEHMV-EATR 90

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. Required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Enterocytozoon bieneusi (strain H348) (taxid: 481877)

>sp|Q8SQK1|LSM2_ENCCU Probable U6 snRNA-associated Sm-like protein LSm2 OS=Encephalitozoon cuniculi (strain GB-M1) GN=LSM2 PE=3 SV=1

 Score = 56.6 bits (135), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLF+ +F+  +G  V+V LK  + + G L  +D YLN+ L + R++    +P + S+  C
Sbjct: 1  MLFYEFFRSSIGSRVSVMLKAGVYVSGRLGGIDPYLNLSLLDVRILSS--HPGLSSISVC 58

Query: 61 FIRGSVVRYVQLPPDG 76
           IRGS ++Y+ +  D 
Sbjct: 59 SIRGSSIKYILVDKDA 74

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. Required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Encephalitozoon cuniculi (strain GB-M1) (taxid: 284813)

>sp|Q8QZX5|LSM10_MOUSE U7 snRNA-associated Sm-like protein LSm10 OS=Mus musculus GN=Lsm10 PE=1 SV=1

 Score = 51.6 bits (122), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 46/73 (63%), Gaps = 3/73 (4%)

Query: 7  FKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSV 66
           + L G+  TV+L+++   RG + +VD ++NI+L N  V   D++ H + + + F+ G  
Sbjct: 21 LQGLQGQITTVDLRDESVARGRIDNVDAFMNIRLAN--VTYTDRWGHQVELDDLFVTGRN 78

Query: 67 VRYVQLPPDGVDV 79
          VRYV + PDGVD+
Sbjct: 79 VRYVHI-PDGVDI 90

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing (By similarity). Increases U7 snRNA levels but not histone 3'-end pre-mRNA processing activity, when overexpressed (By similarity). Required for cell cycle progression from G1 to S phases (By similarity). Binds specifically to U7 snRNA (By similarity). Binds specifically to U7 snRNA (By similarity). Binds to the downstream cleavage product (DCP) of histone pre-mRNA.

Mus musculus (taxid: 10090)

>sp|Q54KX4|LSM4_DICDI Probable U6 snRNA-associated Sm-like protein LSm4 OS=Dictyostelium discoideum GN=lsm4 PE=3 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 5/90 (5%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT--RVVDQDKYPHMLSVR 58
          ML  S  +   G ++ VELKN     G L + D ++NI L+N      D DK+     ++
Sbjct: 1  MLPLSLLRTGQGHQIMVELKNGETYNGLLVNCDNWMNINLKNVIRTSKDSDKF---WKIQ 57

Query: 59 NCFIRGSVVRYVQLPPDGVDVDLLHDATRR 88
          +C+IRG+ ++Y+ +P + +D+    + T R
Sbjct: 58 SCYIRGNTIKYISVPDEIIDLVAEEEQTLR 87

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

Dictyostelium discoideum (taxid: 44689)

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

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/95 (33%), Positives = 48/95 (50%), Gaps = 6/95 (6%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVV--DQDKYPHMLSVR 58
          ML  S  K      + VELKN     G L S D ++NI L        D DK+  M    
Sbjct: 1  MLPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPE-- 58

Query: 59 NCFIRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
           C+IRGS ++Y+++P + +D+ +  +A +   RGG
Sbjct: 59 -CYIRGSTIKYLRIPDEIIDM-VREEAAKGRGRGG 91

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

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	93
255567664	500	Speckle-type POZ protein, putative [Rici	0.989	0.184	0.978	7e-47
296086695	137	unnamed protein product [Vitis vinifera]	1.0	0.678	0.967	1e-46
224073260	93	predicted protein [Populus trichocarpa]	1.0	1.0	0.978	2e-46
359479792	489	PREDICTED: BTB/POZ and MATH domain-conta	0.989	0.188	0.967	2e-46
449436291	93	PREDICTED: U6 snRNA-associated Sm-like p	1.0	1.0	0.978	2e-46
357511085	93	SnRNP core Sm protein Sm-X5-like protein	1.0	1.0	0.967	3e-46
118483945	93	unknown [Populus trichocarpa]	1.0	1.0	0.967	7e-46
388498296	93	unknown [Medicago truncatula]	1.0	1.0	0.946	3e-45
18379085	93	small nuclear ribonucleoprotein-like pro	1.0	1.0	0.967	3e-45
116780108	93	unknown [Picea sitchensis] gi|116790929|	1.0	1.0	0.935	1e-44

>gi|255567664|ref|XP_002524811.1| Speckle-type POZ protein, putative [Ricinus communis] gi|223535995|gb|EEF37654.1| Speckle-type POZ protein, putative [Ricinus communis]

 Score =  191 bits (484), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 90/92 (97%), Positives = 92/92 (100%)

Query: 2   LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCF 61
           LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCF
Sbjct: 409 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCF 468

Query: 62  IRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
           IRGSVVRYVQLPP+GVD+DLLHDATRREARGG
Sbjct: 469 IRGSVVRYVQLPPEGVDIDLLHDATRREARGG 500

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086695|emb|CBI32330.3| unnamed protein product [Vitis vinifera]

 Score =  189 bits (481), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 90/93 (96%), Positives = 93/93 (100%)

Query: 1   MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
           MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC
Sbjct: 45  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 104

Query: 61  FIRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
           FIRGSVVRYVQLPP+GVD++LLHDATRREARGG
Sbjct: 105 FIRGSVVRYVQLPPEGVDIELLHDATRREARGG 137

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073260|ref|XP_002304049.1| predicted protein [Populus trichocarpa] gi|224118384|ref|XP_002331469.1| predicted protein [Populus trichocarpa] gi|118484877|gb|ABK94305.1| unknown [Populus trichocarpa] gi|222841481|gb|EEE79028.1| predicted protein [Populus trichocarpa] gi|222873547|gb|EEF10678.1| predicted protein [Populus trichocarpa]

 Score =  189 bits (480), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/93 (97%), Positives = 93/93 (100%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLFFSYFKDLVG+EVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC
Sbjct: 1  MLFFSYFKDLVGKEVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
          FIRGSVVRYVQLPP+GVDVDLLHDATRREARGG
Sbjct: 61 FIRGSVVRYVQLPPEGVDVDLLHDATRREARGG 93

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359479792|ref|XP_002271534.2| PREDICTED: BTB/POZ and MATH domain-containing protein 2-like [Vitis vinifera]

 Score =  189 bits (479), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 89/92 (96%), Positives = 92/92 (100%)

Query: 2   LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCF 61
           LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCF
Sbjct: 398 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCF 457

Query: 62  IRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
           IRGSVVRYVQLPP+GVD++LLHDATRREARGG
Sbjct: 458 IRGSVVRYVQLPPEGVDIELLHDATRREARGG 489

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449436291|ref|XP_004135926.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm2-like isoform 1 [Cucumis sativus] gi|449436293|ref|XP_004135927.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm2-like isoform 2 [Cucumis sativus] gi|449436295|ref|XP_004135928.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm2-like isoform 3 [Cucumis sativus] gi|449489026|ref|XP_004158193.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm2-like isoform 1 [Cucumis sativus] gi|449489028|ref|XP_004158194.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm2-like isoform 2 [Cucumis sativus] gi|449489032|ref|XP_004158195.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm2-like isoform 3 [Cucumis sativus]

 Score =  189 bits (479), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/93 (97%), Positives = 93/93 (100%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQ+KYPHMLSVRNC
Sbjct: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQEKYPHMLSVRNC 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
          FIRGSVVRYVQLPPDGVDV+LLHDATRREARGG
Sbjct: 61 FIRGSVVRYVQLPPDGVDVELLHDATRREARGG 93

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357511085|ref|XP_003625831.1| SnRNP core Sm protein Sm-X5-like protein [Medicago truncatula] gi|355500846|gb|AES82049.1| SnRNP core Sm protein Sm-X5-like protein [Medicago truncatula] gi|388519597|gb|AFK47860.1| unknown [Lotus japonicus]

 Score =  188 bits (478), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 90/93 (96%), Positives = 93/93 (100%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC
Sbjct: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
          FIRGSVVRYVQLPP+GVD++LLHDATRREARGG
Sbjct: 61 FIRGSVVRYVQLPPEGVDIELLHDATRREARGG 93

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118483945|gb|ABK93861.1| unknown [Populus trichocarpa]

 Score =  187 bits (475), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 90/93 (96%), Positives = 92/93 (98%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLFFSYFKDLVG+EVTVELKNDLAIRG LHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC
Sbjct: 1  MLFFSYFKDLVGKEVTVELKNDLAIRGNLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
          FIRGSVVRYVQLPP+GVDVDLLHDATRREARGG
Sbjct: 61 FIRGSVVRYVQLPPEGVDVDLLHDATRREARGG 93

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388498296|gb|AFK37214.1| unknown [Medicago truncatula]

 Score =  185 bits (470), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 88/93 (94%), Positives = 92/93 (98%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQD+YPHMLSVRNC
Sbjct: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDRYPHMLSVRNC 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
          FIRGSVVRYVQLPP+GVD++LLHDATRREAR G
Sbjct: 61 FIRGSVVRYVQLPPEGVDIELLHDATRREARSG 93

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18379085|ref|NP_563682.1| small nuclear ribonucleoprotein-like protein [Arabidopsis thaliana] gi|297848550|ref|XP_002892156.1| hypothetical protein ARALYDRAFT_470311 [Arabidopsis lyrata subsp. lyrata] gi|98961007|gb|ABF58987.1| At1g03330 [Arabidopsis thaliana] gi|297337998|gb|EFH68415.1| hypothetical protein ARALYDRAFT_470311 [Arabidopsis lyrata subsp. lyrata] gi|332189439|gb|AEE27560.1| small nuclear ribonucleoprotein-like protein [Arabidopsis thaliana]

 Score =  185 bits (470), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 90/93 (96%), Positives = 91/93 (97%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLFFSYFKDLVG+EVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC
Sbjct: 1  MLFFSYFKDLVGQEVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
          FIRGSVVRYVQLP DGVDVDLLHDA RREARGG
Sbjct: 61 FIRGSVVRYVQLPKDGVDVDLLHDAARREARGG 93

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116780108|gb|ABK21554.1| unknown [Picea sitchensis] gi|116790929|gb|ABK25794.1| unknown [Picea sitchensis]

 Score =  183 bits (465), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 87/93 (93%), Positives = 92/93 (98%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          MLFFSYFK+LVG+EVTVELKNDLAIRGTLHSVDQYLNIKLENTRVV+QDKYPHMLSV+NC
Sbjct: 1  MLFFSYFKELVGKEVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVEQDKYPHMLSVKNC 60

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
          FIRGSVVRYV LPPDGVDVD+LHDATRREARGG
Sbjct: 61 FIRGSVVRYVLLPPDGVDVDILHDATRREARGG 93

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

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	93
TAIR|locus:2014480	93	LSM2 "AT1G03330" [Arabidopsis	1.0	1.0	0.967	3.9e-44
UNIPROTKB|A6QQV3	95	LSM2 "LSM2 protein" [Bos tauru	0.967	0.947	0.744	9.8e-32
UNIPROTKB|Q9Y333	95	LSM2 "U6 snRNA-associated Sm-l	0.967	0.947	0.744	9.8e-32
MGI|MGI:90676	95	Lsm2 "LSM2 homolog, U6 small n	0.967	0.947	0.744	9.8e-32
ZFIN|ZDB-GENE-000616-10	95	smx5 "smx5" [Danio rerio (taxi	0.967	0.947	0.744	9.8e-32
WB|WBGene00001808	97	gut-2 [Caenorhabditis elegans	0.956	0.917	0.696	2.1e-29
DICTYBASE|DDB_G0281779	117	lsm2 "putative U6 small nuclea	0.978	0.777	0.670	2.7e-29
ASPGD|ASPL0000065787	98	AN10963 [Emericella nidulans (	0.967	0.918	0.711	1.5e-28
UNIPROTKB|G4NCP9	97	MGG_00355 "U6 snRNA-associated	0.967	0.927	0.666	2.2e-27
SGD|S000000122	95	LSM2 "Lsm (Like Sm) protein" [	0.956	0.936	0.662	2.5e-26

TAIR|locus:2014480 LSM2 "AT1G03330" [Arabidopsis thaliana (taxid:3702)]

 Score = 465 (168.7 bits), Expect = 3.9e-44, P = 3.9e-44
 Identities = 90/93 (96%), Positives = 91/93 (97%)

Query:     1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
             MLFFSYFKDLVG+EVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC
Sbjct:     1 MLFFSYFKDLVGQEVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60

Query:    61 FIRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
             FIRGSVVRYVQLP DGVDVDLLHDA RREARGG
Sbjct:    61 FIRGSVVRYVQLPKDGVDVDLLHDAARREARGG 93

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0005829 "cytosol" evidence=IDA

UNIPROTKB|A6QQV3 LSM2 "LSM2 protein" [Bos taurus (taxid:9913)]

 Score = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 67/90 (74%), Positives = 76/90 (84%)

Query:     1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
             MLF+S+FK LVG++V VELKNDL+I GTLHSVDQYLNIKL +  V D +KYPHMLSV+NC
Sbjct:     1 MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query:    61 FIRGSVVRYVQLPPDGVDVDLLHDATRREA 90
             FIRGSVVRYVQLP D VD  LL DA R+EA
Sbjct:    61 FIRGSVVRYVQLPADEVDTQLLQDAARKEA 90

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

GO:0019901 "protein kinase binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|Q9Y333 LSM2 "U6 snRNA-associated Sm-like protein LSm2" [Homo sapiens (taxid:9606)]

 Score = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 67/90 (74%), Positives = 76/90 (84%)

Query:     1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
             MLF+S+FK LVG++V VELKNDL+I GTLHSVDQYLNIKL +  V D +KYPHMLSV+NC
Sbjct:     1 MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query:    61 FIRGSVVRYVQLPPDGVDVDLLHDATRREA 90
             FIRGSVVRYVQLP D VD  LL DA R+EA
Sbjct:    61 FIRGSVVRYVQLPADEVDTQLLQDAARKEA 90

GO:0019901 "protein kinase binding" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

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

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

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0043928 "exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:90676 Lsm2 "LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 67/90 (74%), Positives = 76/90 (84%)

Query:     1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
             MLF+S+FK LVG++V VELKNDL+I GTLHSVDQYLNIKL +  V D +KYPHMLSV+NC
Sbjct:     1 MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query:    61 FIRGSVVRYVQLPPDGVDVDLLHDATRREA 90
             FIRGSVVRYVQLP D VD  LL DA R+EA
Sbjct:    61 FIRGSVVRYVQLPADEVDTQLLQDAARKEA 90

GO:0000244 "assembly of spliceosomal tri-snRNP" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0006402 "mRNA catabolic process" evidence=ISO

GO:0008380 "RNA splicing" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IDA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

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

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

ZFIN|ZDB-GENE-000616-10 smx5 "smx5" [Danio rerio (taxid:7955)]

 Score = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 67/90 (74%), Positives = 76/90 (84%)

Query:     1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
             MLF+S+FK LVG++V VELKNDL+I GTLHSVDQYLNIKL +  V D +KYPHMLSV+NC
Sbjct:     1 MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query:    61 FIRGSVVRYVQLPPDGVDVDLLHDATRREA 90
             FIRGSVVRYVQLP D VD  LL DA R+EA
Sbjct:    61 FIRGSVVRYVQLPADEVDTQLLQDAARKEA 90

GO:0006397 "mRNA processing" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

WB|WBGene00001808 gut-2 [Caenorhabditis elegans (taxid:6239)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 62/89 (69%), Positives = 75/89 (84%)

Query:     1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
             MLFFS+FK LVG++V VELKNDL+I GTLHSVDQYLN+KL +  V D +++PHM+SV+NC
Sbjct:     1 MLFFSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNMKLTDITVSDPERFPHMVSVKNC 60

Query:    61 FIRGSVVRYVQLPPDGVDVDLLHDATRRE 89
             FIRGSVVRYVQLP D VD  LL D+ R+E
Sbjct:    61 FIRGSVVRYVQLPSDQVDTQLLADSCRKE 89

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

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

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0040027 "negative regulation of vulval development" evidence=IMP

GO:0040007 "growth" evidence=IMP

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

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

GO:0008406 "gonad development" evidence=IMP

GO:0016477 "cell migration" evidence=IMP

DICTYBASE|DDB_G0281779 lsm2 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 325 (119.5 bits), Expect = 2.7e-29, P = 2.7e-29
 Identities = 61/91 (67%), Positives = 78/91 (85%)

Query:     1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
             MLFFS++K LVG+E+TVELKNDL+I G L SVDQ+LNIKL++ +V ++DKYP+M+SV+NC
Sbjct:     1 MLFFSFYKSLVGKEITVELKNDLSITGLLQSVDQFLNIKLKDIKVNEEDKYPYMISVKNC 60

Query:    61 FIRGSVVRYVQLPPDGVDVDLLHDATRREAR 91
             FIRGSVVRYV LP + VDV+ L D +R EAR
Sbjct:    61 FIRGSVVRYVHLPAEDVDVETLQDHSRLEAR 91

GO:0006397 "mRNA processing" evidence=IEA

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:0005634 "nucleus" evidence=IEA

ASPGD|ASPL0000065787 AN10963 [Emericella nidulans (taxid:162425)]

 Score = 318 (117.0 bits), Expect = 1.5e-28, P = 1.5e-28
 Identities = 64/90 (71%), Positives = 73/90 (81%)

Query:     1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
             MLFFS+FK L  + VT+ELKND+ IRGTL SVDQYLNIKL++  V+D DKYPH+ SV+N 
Sbjct:     1 MLFFSFFKTLTNQVVTIELKNDIRIRGTLKSVDQYLNIKLDDIDVLDLDKYPHLSSVKNM 60

Query:    61 FIRGSVVRYVQLPPDGVDVDLLHDATRREA 90
             FIRGSVVRYV LP   VDV LL DATRREA
Sbjct:    61 FIRGSVVRYVVLPRSEVDVGLLEDATRREA 90

GO:0005730 "nucleolus" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

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

GO:0005829 "cytosol" evidence=IEA

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

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

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|G4NCP9 MGG_00355 "U6 snRNA-associated Sm-like protein LSm2" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 60/90 (66%), Positives = 72/90 (80%)

Query:     1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
             MLFFS+FK L+  E+TVELKN + IRGTL SVDQYLN+KL++  VV+  KYPH+ +V+N 
Sbjct:     1 MLFFSFFKTLIDVEITVELKNSIQIRGTLKSVDQYLNLKLDDISVVEDIKYPHLSAVKNV 60

Query:    61 FIRGSVVRYVQLPPDGVDVDLLHDATRREA 90
             FIRGSVVRY+ LP   VDV LL DATRREA
Sbjct:    61 FIRGSVVRYIHLPASHVDVPLLEDATRREA 90

GO:0003674 "molecular_function" evidence=ND

SGD|S000000122 LSM2 "Lsm (Like Sm) protein" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 59/89 (66%), Positives = 70/89 (78%)

Query:     1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
             MLFFS+FK LV +EV VELKND+ I+GTL SVDQ+LN+KL+N    D+ KYPH+ SVRN 
Sbjct:     1 MLFFSFFKTLVDQEVVVELKNDIEIKGTLQSVDQFLNLKLDNISCTDEKKYPHLGSVRNI 60

Query:    61 FIRGSVVRYVQLPPDGVDVDLLHDATRRE 89
             FIRGS VRYV L  + VD +LL DATRRE
Sbjct:    61 FIRGSTVRYVYLNKNMVDTNLLQDATRRE 89

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=TAS

GO:0003723 "RNA binding" evidence=IEA;IDA;IPI

GO:0005688 "U6 snRNP" evidence=IDA

GO:0005634 "nucleus" evidence=IEA;IDA

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

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

GO:0005730 "nucleolus" evidence=IDA

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

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

GO:0006364 "rRNA processing" evidence=IEA

GO:0008380 "RNA splicing" 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)
P38203	LSM2_YEAST	No assigned EC number	0.6555	0.9677	0.9473	yes	no
O94408	LSM2_SCHPO	No assigned EC number	0.6404	0.9569	0.9270	yes	no
Q54TF6	LSM2_DICDI	No assigned EC number	0.6703	0.9784	0.7777	yes	no
O35900	LSM2_MOUSE	No assigned EC number	0.7444	0.9677	0.9473	yes	no
Q9Y333	LSM2_HUMAN	No assigned EC number	0.7444	0.9677	0.9473	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_kg.C_LG_III0001	SubName- Full=Putative uncharacterized protein; (93 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	grail3.0053017202	SubName- Full=Putative uncharacterized protein; (99 aa)				•	•		•		0.700
	estExt_Genewise1_v1.C_LG_IX3230	SubName- Full=Putative uncharacterized protein; (99 aa)				•	•	•	•		0.597
	estExt_Genewise1_v1.C_LG_I1870	SubName- Full=Putative uncharacterized protein; (99 aa)				•	•	•	•		0.597
	estExt_fgenesh4_pm.C_LG_V0415	hypothetical protein (98 aa)				•	•	•	•		0.589
	grail3.0003059101	hypothetical protein (98 aa)				•	•	•	•		0.587
	estExt_fgenesh4_kg.C_LG_VII0024	SubName- Full=Putative uncharacterized protein; (143 aa)				•	•	•	•		0.581
	grail3.0053017102	SubName- Full=Putative uncharacterized protein; (88 aa)				•	•	•	•		0.578
	eugene3.00090932	SubName- Full=Putative uncharacterized protein; (88 aa)				•	•	•	•		0.578
	eugene3.00440042	hypothetical protein (2357 aa)					•	•	•		0.573
	gw1.X.1452.1	annotation not avaliable (75 aa)				•	•	•	•		0.572

---

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	93
cd01725	89	cd01725, LSm2, Like-Sm protein 2	8e-63
smart00651	67	smart00651, Sm, snRNP Sm proteins	2e-16
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	2e-15
pfam01423	66	pfam01423, LSM, LSM domain	3e-15
cd01733	78	cd01733, LSm10, Like-Sm protein 10	3e-14
cd01723	76	cd01723, LSm4, Like-Sm protein 4	3e-12
cd00600	63	cd00600, Sm_like, Sm and related proteins	6e-11
cd01726	68	cd01726, LSm6, Like-Sm protein 6	3e-10
cd01724	92	cd01724, Sm_D1, Sm protein D1	2e-07
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	5e-07
cd01721	70	cd01721, Sm_D3, Sm protein D3	7e-07
cd01722	69	cd01722, Sm_F, Sm protein F	3e-06
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	2e-04
cd11679	65	cd11679, archaeal_Sm_like, archaeal Sm-related pro	0.001
pfam14438	113	pfam14438, SM-ATX, SM domain found in Ataxin-2	0.004

>gnl|CDD|212472 cd01725, LSm2, Like-Sm protein 2

 Score =  184 bits (470), Expect = 8e-63
 Identities = 71/89 (79%), Positives = 78/89 (87%)

Query: 2  LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCF 61
          LFFS+FK LVG+EVTVELKNDL+I GTLHSVDQYLNIKL N  V D +KYPH+LSV+NCF
Sbjct: 1  LFFSFFKTLVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNISVNDPEKYPHLLSVKNCF 60

Query: 62 IRGSVVRYVQLPPDGVDVDLLHDATRREA 90
          IRGSVVRYVQLP D VD +LL DATRREA
Sbjct: 61 IRGSVVRYVQLPADEVDTELLQDATRREA 89

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

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

 Score = 66.4 bits (163), Expect = 2e-16
 Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 5  SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRG 64
           + K L+G+ V VELKN    RGTL   DQ++N+ LE+     +D       +   FIRG
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE-KKRKLGLVFIRG 59

Query: 65 SVVRYVQL 72
          + + Y+ L
Sbjct: 60 NNIVYIIL 67

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

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

 Score = 64.2 bits (157), Expect = 2e-15
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT--RVVDQDKYPHMLSVR 58
           L  S+ K L+ + V V+LKN    RGTL   DQY+N+ L++    +    +        
Sbjct: 6  PLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGG 65

Query: 59 NCFIRGSVVRYVQL 72
             IRG  +  +  
Sbjct: 66 EVLIRGDNIVLISP 79

Length = 79

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

 Score = 63.7 bits (156), Expect = 3e-15
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 5  SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRG 64
           + + L+G+ VTVELKN   +RGTL   DQ++N+ L++     +D   + L      IRG
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLG--LVLIRG 58

Query: 65 SVVRYVQL 72
          + +  +  
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|212480 cd01733, LSm10, Like-Sm protein 10

 Score = 61.4 bits (150), Expect = 3e-14
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 10/71 (14%)

Query: 7  FKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD----QDKYPHMLSVRNCFI 62
           + L GR  TVEL+N+ ++RG + +VD ++NI L +    D    Q  +         F+
Sbjct: 14 LQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQHHFDEF------FV 67

Query: 63 RGSVVRYVQLP 73
          +G  +RYV +P
Sbjct: 68 QGRNIRYVHIP 78

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

>gnl|CDD|212470 cd01723, LSm4, Like-Sm protein 4

 Score = 56.0 bits (136), Expect = 3e-12
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVV--DQDKYPHMLSVRNCFIRGSVVRY 69
          G  V VELKN     G L + D ++NI L+N      D D++  M     C+IRG+ ++Y
Sbjct: 11 GHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKM---PECYIRGNTIKY 67

Query: 70 VQLPPDGVD 78
          ++LP + +D
Sbjct: 68 LRLPDEVID 76

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

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

 Score = 52.6 bits (127), Expect = 6e-11
 Identities = 21/64 (32%), Positives = 39/64 (60%), Gaps = 2/64 (3%)

Query: 8  KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVV 67
          KD +G+ V+VELK+   + GTL + D+Y+N+ L++  VV+  +   +  +    IRGS +
Sbjct: 2  KDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDD--VVETGRDGKVRVLGLVLIRGSNI 59

Query: 68 RYVQ 71
            ++
Sbjct: 60 VSIR 63

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

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

 Score = 50.6 bits (122), Expect = 3e-10
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 8/70 (11%)

Query: 4  FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRN---C 60
            + K ++G+ V V+LKN +  RG L  +D Y+N+ LE+T      +      V      
Sbjct: 3  SKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQL-----VAKYGDA 57

Query: 61 FIRGSVVRYV 70
          FIRG+ V Y+
Sbjct: 58 FIRGNNVLYI 67

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

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

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 30/80 (37%), Positives = 47/80 (58%), Gaps = 4/80 (5%)

Query: 10 LVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRY 69
          L    VT+ELKN   + GT+  VD  +N  L+N ++  + K P  +S+    IRG+ +RY
Sbjct: 9  LSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNP--VSLDTLSIRGNNIRY 66

Query: 70 VQLPPDGVDVD-LLHDATRR 88
          + L PD +++D LL D T +
Sbjct: 67 IIL-PDSLNLDTLLVDDTPK 85

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Length = 92

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

 Score = 42.6 bits (101), Expect = 5e-07
 Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 2/60 (3%)

Query: 11 VGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYV 70
          + + V V+LK    +RG L   DQ+LN+ LEN   + + +    L      +RG  V ++
Sbjct: 10 LNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLG--TVLVRGDNVVFI 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|212468 cd01721, Sm_D3, Sm protein D3

 Score = 42.5 bits (101), Expect = 7e-07
 Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 4/64 (6%)

Query: 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQD-KYPHMLSVRNCFIRGSVVRYV 70
          G  VTVELK     RG L   +  +N +L++  V  +D K   +  V   +IRGS +R++
Sbjct: 10 GHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGKVSKLEQV---YIRGSQIRFI 66

Query: 71 QLPP 74
           LP 
Sbjct: 67 ILPD 70

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

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

 Score = 40.7 bits (96), Expect = 3e-06
 Identities = 17/35 (48%), Positives = 24/35 (68%)

Query: 9  DLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT 43
           L G+ V V+LK  +  +GTL SVD Y+N++L NT
Sbjct: 8  GLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANT 42

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|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein

 Score = 35.9 bits (83), Expect = 2e-04
 Identities = 16/37 (43%), Positives = 24/37 (64%), Gaps = 1/37 (2%)

Query: 8  KDLVGREVTVELKNDL-AIRGTLHSVDQYLNIKLENT 43
          K LVG  + VE+K D   ++G L +VD Y+N+ L +T
Sbjct: 6  KSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDT 42

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|212490 cd11679, archaeal_Sm_like, archaeal Sm-related protein

 Score = 34.2 bits (79), Expect = 0.001
 Identities = 19/69 (27%), Positives = 29/69 (42%), Gaps = 7/69 (10%)

Query: 3  FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQY-LNIKLENTRVVDQDKYPHMLSVRNCF 61
          F +    L+ +EV V L N     G L   D   LNI L N +    +K+P +       
Sbjct: 1  FAAELNSLLDKEVIVTLSNGKTYTGQLVGFDPSSLNIVLTNAKDSSGNKFPKV------I 54

Query: 62 IRGSVVRYV 70
          I G+ +  +
Sbjct: 55 INGNRISEI 63

Archaeal Sm-related 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 = 65

>gnl|CDD|222754 pfam14438, SM-ATX, SM domain found in Ataxin-2

 Score = 33.4 bits (77), Expect = 0.004
 Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 15/91 (16%)

Query: 10 LVGREVTVELKNDLAIRGTLHSVD--QYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVV 67
          L+G+ V V LKN     G  H+        + L+  RV+ +       S  +  +RG +V
Sbjct: 10 LIGQRVEVTLKNGSVYEGIFHTASPEDDFGVVLKMARVLPK-------SDASGPLRGKIV 62

Query: 68 RYVQLPPDGV------DVDLLHDATRREARG 92
            + +P   +      DVDL + A+     G
Sbjct: 63 DTLIIPSKDIVQIEAKDVDLSYAASGGAKDG 93

SM domain found in Ataxin-2. Length = 113

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	93
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.95
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.95
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.94
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.94
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.93
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.92
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	99.92
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.91
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.91
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.9
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	99.9
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.88
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.87
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.87
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.86
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.84
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.81
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.81
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	99.81
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.8
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.8
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	99.79
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.79
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.78
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.78
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.73
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.66
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	99.63
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.49
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	99.44
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	99.38
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.28
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	99.0
KOG3168	177	consensus U1 snRNP component [Transcription]	98.97
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	98.42
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	98.37
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.91
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.54
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	97.28
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	96.9
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	96.8
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.61
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	96.58
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.13
COG1923	77	Hfq Uncharacterized host factor I protein [General	96.06
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	96.02
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	95.58
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	95.53
PRK14638	150	hypothetical protein; Provisional	94.75
PRK14639	140	hypothetical protein; Provisional	94.39
PRK14091	165	RNA-binding protein Hfq; Provisional	94.15
PRK14091	165	RNA-binding protein Hfq; Provisional	93.82
PRK02001	152	hypothetical protein; Validated	93.67
PRK14644	136	hypothetical protein; Provisional	92.53
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	92.5
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	92.42
KOG1073	361	consensus Uncharacterized mRNA-associated protein	92.14
PRK14640	152	hypothetical protein; Provisional	91.7
PRK14642	197	hypothetical protein; Provisional	91.15
PRK14633	150	hypothetical protein; Provisional	90.88
PRK14632	172	hypothetical protein; Provisional	90.28
PRK14636	176	hypothetical protein; Provisional	90.2
PRK14643	164	hypothetical protein; Provisional	90.18
PRK14645	154	hypothetical protein; Provisional	90.1
PRK00092	154	ribosome maturation protein RimP; Reviewed	89.58
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	89.56
PRK14634	155	hypothetical protein; Provisional	89.46
PRK14646	155	hypothetical protein; Provisional	88.95
PRK14647	159	hypothetical protein; Provisional	88.3
PRK14637	151	hypothetical protein; Provisional	87.36
PRK09618	142	flgD flagellar basal body rod modification protein	86.79
PRK14631	174	hypothetical protein; Provisional	86.66
PRK14641	173	hypothetical protein; Provisional	86.48
PRK06955	300	biotin--protein ligase; Provisional	84.94
PRK14630	143	hypothetical protein; Provisional	81.11
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	81.08
PF11607	101	DUF3247: Protein of unknown function (DUF3247); In	80.68

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

Probab=99.95  E-value=1.3e-27  Score=149.42  Aligned_cols=86  Identities=27%  Similarity=0.459  Sum_probs=78.3

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCC-cchh
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDG-VDVD   80 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~-~d~~   80 (93)
                      .|+.||+++.|++|+|+|+||.+|+|+|.++|.|||++|+||+++..++.  ...++.+||||++|+||++|+++ +|+.
T Consensus         1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~--~~~~~~v~IRG~nI~yi~lPd~l~~~~~   78 (90)
T cd01724           1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRN--PVPLDTLSIRGNNIRYFILPDSLNLDTL   78 (90)
T ss_pred             CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCc--eeEcceEEEeCCEEEEEEcCCcCCcchh
Confidence            47899999999999999999999999999999999999999999877665  36789999999999999999997 8999


Q ss_pred             hhhHhhhhh
Q 034490           81 LLHDATRRE   89 (93)
Q Consensus        81 ~~~~~~~~~   89 (93)
                      +++++++++
T Consensus        79 l~~~~~~~~   87 (90)
T cd01724          79 LVDSTPKPK   87 (90)
T ss_pred             hhhcCCccc
Confidence            998876644

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=99.95  E-value=2.5e-27  Score=145.52  Aligned_cols=80  Identities=81%  Similarity=1.280  Sum_probs=71.8

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchhh
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDL   81 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~~   81 (93)
                      +|+.||+++.|++|+|+|+||.+|+|+|.++|.|||++|+||+++.+++......++.++|||++|+||++|+..+|...
T Consensus         1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~~~~   80 (81)
T cd01725           1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVDTEL   80 (81)
T ss_pred             ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcCccc
Confidence            68999999999999999999999999999999999999999998876553333567899999999999999999888764

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.

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

Probab=99.94  E-value=8.7e-27  Score=141.47  Aligned_cols=76  Identities=29%  Similarity=0.550  Sum_probs=68.5

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcc
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVD   78 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d   78 (93)
                      +|++||+++.|++|.|+|+||++|+|+|.+||.|||++|+||+++..++.. ...++.+||||++|+||++|++++|
T Consensus         1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~-~~~~~~v~IRG~~I~~i~~p~~~~~   76 (76)
T cd01723           1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDK-FWKMPECYIRGNTIKYLRVPDEIID   76 (76)
T ss_pred             CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcE-eeeCCcEEEeCCEEEEEEcCHHHCC
Confidence            699999999999999999999999999999999999999999998766542 3457899999999999999997654

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=99.94  E-value=2.1e-26  Score=137.92  Aligned_cols=70  Identities=30%  Similarity=0.492  Sum_probs=65.2

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      |+.||+++.|++|+|+|+||.+|+|+|.+||.|||++|+||+++..++.  ..+++.+||||++|+||++||
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 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGR--VSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCc--EeEcCcEEEeCCEEEEEEeCC
Confidence            8899999999999999999999999999999999999999998876654  357899999999999999996

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

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

Probab=99.93  E-value=4.9e-25  Score=134.53  Aligned_cols=69  Identities=32%  Similarity=0.679  Sum_probs=64.4

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP   73 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~   73 (93)
                      +.+||+++.|++|.|+||||.+|+|+|.++|.+||++|+||+++.+++..  .+++.+||||++|+||++|
T Consensus        10 l~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~--~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733          10 LIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQ--VQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             HHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCce--eECCcEEEECCEEEEEEcC
Confidence            67999999999999999999999999999999999999999998876653  4789999999999999998

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.

>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=99.92  E-value=7.2e-25  Score=130.11  Aligned_cols=67  Identities=33%  Similarity=0.546  Sum_probs=61.8

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      |++||++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..++.  ...++.++|||++|+||+
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~--~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQL--KNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCce--eeEeCCEEEECCEEEEEC
Confidence            8999999999999999999999999999999999999999999776543  367899999999999985

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.

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

Probab=99.92  E-value=1.5e-24  Score=133.46  Aligned_cols=92  Identities=75%  Similarity=1.159  Sum_probs=88.8

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchh
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVD   80 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~   80 (93)
                      |+.++|+++++|++|.|+|||+..+.|+|.++|+|+|+.|.|......++.|+..+...+||||+.|+||++|...+|.+
T Consensus         1 mLFysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vdtq   80 (96)
T KOG3448|consen    1 MLFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVDTQ   80 (96)
T ss_pred             CchHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHHHHH
Confidence            89999999999999999999999999999999999999999999999999999899999999999999999999999999


Q ss_pred             hhhHhhhhhhcC
Q 034490           81 LLHDATRREARG   92 (93)
Q Consensus        81 ~~~~~~~~~~~~   92 (93)
                      .++++.|+++..
T Consensus        81 ll~da~R~e~~~   92 (96)
T KOG3448|consen   81 LLQDAARREAIL   92 (96)
T ss_pred             HHHHHHHHHHHh
Confidence            999999988754

>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=99.91  E-value=5.6e-24  Score=126.62  Aligned_cols=68  Identities=34%  Similarity=0.475  Sum_probs=61.7

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      .|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||++...+..  ...+|.++|||++|+||+
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 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKS--TGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCcc--ccCcCcEEEECCEEEEEC
Confidence            48999999999999999999999999999999999999999998865433  257899999999999984

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

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.91  E-value=1.5e-23  Score=126.11  Aligned_cols=68  Identities=25%  Similarity=0.390  Sum_probs=62.5

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      .|+.+|++++|++|.|+|+||++|+|+|.+||+|||++|+||+++.++..  ...++.++|||++|.+|+
T Consensus         4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~~V~~i~   71 (72)
T PRK00737          4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEV--VRKLGKVVIRGDNVVYVS   71 (72)
T ss_pred             chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCe--EeEcCcEEEeCCEEEEEc
Confidence            59999999999999999999999999999999999999999999865532  368899999999999996

>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=99.90  E-value=1.9e-23  Score=124.21  Aligned_cols=67  Identities=30%  Similarity=0.457  Sum_probs=62.3

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      |+.+|++++||+|.|+|+||++|+|+|.+||+|||++|+||+++..+..  ...++.++|||++|.+|+
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~lg~~~iRG~~I~~i~   67 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEP--VRKYGRVVIRGDNVLFIS   67 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCe--EeEcCcEEEeCCEEEEEc
Confidence            8899999999999999999999999999999999999999999876543  367899999999999986

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.

>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=99.90  E-value=2e-23  Score=126.82  Aligned_cols=69  Identities=19%  Similarity=0.410  Sum_probs=63.3

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEc---CCCCCceEeeeeEEEecCeEEEEE
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD---QDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~---~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      |+|+.+|+++++++|.|+|++|+++.|+|.+||+|||++|+||+|..   ++.  ....+|.++|||++|.+|+
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~--~~~~lg~v~iRG~nV~~i~   73 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGR--KITKLDQILLNGNNICMLV   73 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCc--eeeEcCeEEEeCCeEEEEE
Confidence            89999999999999999999999999999999999999999999975   222  2367899999999999998

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.

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

Probab=99.90  E-value=5.7e-24  Score=137.86  Aligned_cols=85  Identities=26%  Similarity=0.479  Sum_probs=77.5

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchh
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVD   80 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~   80 (93)
                      |+|+++|+.+.|+++.||||||.+|.|.|+.||.+|||+|.+++++.+++.. +-.+++++|||++|+|+.+|++++|..
T Consensus         1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdk-f~r~pEcYirGttIkylri~d~iid~v   79 (134)
T KOG3293|consen    1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDK-FFRMPECYIRGTTIKYLRIPDEIIDKV   79 (134)
T ss_pred             CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCc-eeecceeEEecceeEEEeccHHHHHHH
Confidence            8999999999999999999999999999999999999999999999887642 456899999999999999999998887


Q ss_pred             hhhHhh
Q 034490           81 LLHDAT   86 (93)
Q Consensus        81 ~~~~~~   86 (93)
                      .-+-..
T Consensus        80 kee~~~   85 (134)
T KOG3293|consen   80 KEECVS   85 (134)
T ss_pred             HHHHHH
Confidence            776443

>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=99.88  E-value=6.8e-22  Score=118.97  Aligned_cols=70  Identities=16%  Similarity=0.322  Sum_probs=62.8

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      |-++|+++++|+|.|+|++|++|+|+|.+||+|||++|+||+|+..+..  ...+|.++|||++|.+|..-+
T Consensus         1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~--~~~lg~v~IRG~~I~~i~~~~   70 (72)
T cd01719           1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGE--KNNIGMVVIRGNSIVMLEALE   70 (72)
T ss_pred             CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCc--eeEeceEEECCCEEEEEEccc
Confidence            5578999999999999999999999999999999999999999874433  368899999999999998654

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.

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

Probab=99.87  E-value=1.3e-21  Score=115.32  Aligned_cols=67  Identities=39%  Similarity=0.628  Sum_probs=60.9

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL   72 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   72 (93)
                      .+|++++|++|+|+|+||++++|+|.+||+|||++|+||+++..+.. +...++.+||||++|++|++
T Consensus         1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-EKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-EEEEEEEEEEEGGGEEEEEE
T ss_pred             ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-cEeECcEEEEECCEEEEEEC
Confidence            37999999999999999999999999999999999999999976642 24788999999999999984

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

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

Probab=99.87  E-value=1.7e-21  Score=118.82  Aligned_cols=70  Identities=30%  Similarity=0.444  Sum_probs=60.5

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEc--CCCCCceEeeeeEEEecCeEEEEE
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD--QDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~--~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      .|+++|++++|++|.|+|+||++|+|+|.+||+|||++|+||+++.  ++........+.++|||++|++|.
T Consensus         7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~   78 (79)
T COG1958           7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLIS   78 (79)
T ss_pred             CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEe
Confidence            5899999999999999999999999999999999999999999986  332211233449999999999996

>smart00651 Sm snRNP Sm proteins

Probab=99.86  E-value=1.8e-21  Score=114.61  Aligned_cols=67  Identities=37%  Similarity=0.607  Sum_probs=60.4

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL   72 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   72 (93)
                      .+|++++|++|+|+|+||+++.|+|.+||+|||++|+||+++..+.. +..+++.+||||++|++|+.
T Consensus         1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~-~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE-KKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCc-EEeEeCCEEEcCCEEEEEeC
Confidence            37999999999999999999999999999999999999999876522 24789999999999999973

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

>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=99.86  E-value=3.4e-21  Score=118.35  Aligned_cols=69  Identities=26%  Similarity=0.337  Sum_probs=61.3

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC-----------CCceEeeeeEEEecCeEEEEE
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK-----------YPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~-----------~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      |+.+|+.+++|+|.|.|++|+++.|+|.+||.||||+|+||+|.....           ....+.+|.+||||++|.+|+
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            899999999999999999999999999999999999999999975321           112468899999999999986

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

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

Probab=99.85  E-value=1.1e-20  Score=117.50  Aligned_cols=71  Identities=21%  Similarity=0.254  Sum_probs=61.4

Q ss_pred             chhHHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCC-----------CceEeeeeEEEecCeEE
Q 034490            2 LFFSYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKY-----------PHMLSVRNCFIRGSVVR   68 (93)
Q Consensus         2 ~p~~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~-----------~~~~~~~~~~IRG~~I~   68 (93)
                      =|+++|+.++  |++|.|.|++|+.+.|+|.+||.|||++|+||+|......           ...+.+|.+||||++|.
T Consensus         2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv   81 (87)
T cd01720           2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI   81 (87)
T ss_pred             ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence            4999999997  9999999999999999999999999999999999753311           12356899999999999


Q ss_pred             EEEc
Q 034490           69 YVQL   72 (93)
Q Consensus        69 ~I~~   72 (93)
                      +|+-
T Consensus        82 ~Is~   85 (87)
T cd01720          82 LVLR   85 (87)
T ss_pred             EEec
Confidence            9873

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.

>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=99.84  E-value=2.7e-20  Score=108.17  Aligned_cols=63  Identities=35%  Similarity=0.549  Sum_probs=57.5

Q ss_pred             HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490            7 FKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         7 L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      |++++|++|+|+|+||+.|.|+|.+||.+||++|+||.++..+..  ...++.+||||++|++|+
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~--~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGK--KRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCc--EEECCeEEEECCEEEEEC
Confidence            578899999999999999999999999999999999999876533  478999999999999984

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.

>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=99.84  E-value=4.5e-20  Score=113.28  Aligned_cols=70  Identities=20%  Similarity=0.261  Sum_probs=60.1

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCC------CceEeeeeEEEecCeEEEEEcCC
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKY------PHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~------~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      .-|.++++|+|.|.|++|+++.|+|.+||+||||+|++|+|...+..      ...+.+|.++|||++|.+|...+
T Consensus         5 ~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           5 LDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             hhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            45899999999999999999999999999999999999999754311      12467899999999999998553

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.

>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=99.81  E-value=1.7e-19  Score=110.26  Aligned_cols=69  Identities=19%  Similarity=0.338  Sum_probs=60.7

Q ss_pred             chhHHHhhcCCC--EEEEEEc--CCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490            2 LFFSYFKDLVGR--EVTVELK--NDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         2 ~p~~~L~~~~gk--~V~V~L~--~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      +|+..+.++.++  +|.|+|+  +|+++.|+|.+||+|||++|+||+|...... ....+|.++|||++|.+|+
T Consensus         6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~-~~~~lG~iliRGnnV~~I~   78 (79)
T cd01718           6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK-TRKPLGRILLKGDNITLIQ   78 (79)
T ss_pred             CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc-eEeEcCcEEEeCCEEEEEc
Confidence            699999999999  8888887  8999999999999999999999999864222 2367899999999999987

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

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

Probab=99.81  E-value=2.8e-19  Score=109.07  Aligned_cols=68  Identities=16%  Similarity=0.257  Sum_probs=58.5

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC--------CCceEeeeeEEEecCeEEEEEc
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK--------YPHMLSVRNCFIRGSVVRYVQL   72 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~--------~~~~~~~~~~~IRG~~I~~I~~   72 (93)
                      +-|.+++|++|.|.|+||+.+.|+|.+||.|||++|+||+|.....        ..+.+.+|.++|||++|.+|++
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            3478899999999999999999999999999999999999964211        1124689999999999999985

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.

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

Probab=99.81  E-value=1.3e-19  Score=115.20  Aligned_cols=82  Identities=26%  Similarity=0.414  Sum_probs=76.6

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchhh
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDL   81 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~~   81 (93)
                      .|+.+|++..|+-|++|+.+|..|+|+|...|++||++|.|++.+..++.  ...++.+||||++|+|+.+||.+.++|+
T Consensus         5 vpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~--vs~le~V~IRGS~IRFlvlPdmLKnAPm   82 (119)
T KOG3172|consen    5 VPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR--VSQLEQVFIRGSKIRFLVLPDMLKNAPM   82 (119)
T ss_pred             cceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCc--ceeeeeEEEecCeEEEEECchHhhcCcc
Confidence            58899999999999999999999999999999999999999999988775  3678999999999999999999999999


Q ss_pred             hhHh
Q 034490           82 LHDA   85 (93)
Q Consensus        82 ~~~~   85 (93)
                      |..+
T Consensus        83 Fkk~   86 (119)
T KOG3172|consen   83 FKKG   86 (119)
T ss_pred             cccc
Confidence            9744

>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=99.80  E-value=6.7e-19  Score=106.49  Aligned_cols=70  Identities=23%  Similarity=0.165  Sum_probs=60.1

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC-CCceEeeeeEEEecCeEEEEEc
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK-YPHMLSVRNCFIRGSVVRYVQL   72 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~-~~~~~~~~~~~IRG~~I~~I~~   72 (93)
                      +...|.++++|+|.|.|++|++|.|+|.+||+|||++|+||.|..... ....+.+|.++|||++|.+|..
T Consensus         3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728           3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence            467899999999999999999999999999999999999998864221 1123678999999999999874

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.

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

Probab=99.80  E-value=1.3e-19  Score=107.96  Aligned_cols=69  Identities=29%  Similarity=0.368  Sum_probs=62.3

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL   72 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   72 (93)
                      -|-+||+.+.||+|.|+||.|.+|.|+|.++|.|||+.|.+|+|..++...  -.+|+++||.+||.||.-
T Consensus         8 NPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~--g~lGEilIRCNNvlyi~g   76 (79)
T KOG3482|consen    8 NPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVST--GNLGEILIRCNNVLYIRG   76 (79)
T ss_pred             CchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhccccc--ccceeEEEEeccEEEEec
Confidence            367999999999999999999999999999999999999999997665442  578999999999999953

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

Probab=99.79  E-value=1.1e-18  Score=111.13  Aligned_cols=88  Identities=34%  Similarity=0.541  Sum_probs=78.9

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCC-cch
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDG-VDV   79 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~-~d~   79 (93)
                      |..+.||+.+.+.+|+|||+||++++|+|.++|.+||..|.++..+.++ ++  .++..++|||++|+|+.+||+. +|+
T Consensus         1 mklvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~p--v~l~~lsirgnniRy~~lpD~l~ld~   77 (109)
T KOG3428|consen    1 MKLVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EP--VRLDTLSIRGNNIRYYILPDSLNLDT   77 (109)
T ss_pred             ChHHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-Cc--eeEEEEEeecceEEEEEccCCcCcce
Confidence            7789999999999999999999999999999999999999999998875 43  4678999999999999999996 888


Q ss_pred             hhhhHhhhhhhc
Q 034490           80 DLLHDATRREAR   91 (93)
Q Consensus        80 ~~~~~~~~~~~~   91 (93)
                      .+++++++-.++
T Consensus        78 Llvd~~~~~~~~   89 (109)
T KOG3428|consen   78 LLVDDAPRLHLR   89 (109)
T ss_pred             eeeehhhhhhhh
Confidence            888888774443

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

Probab=99.79  E-value=1.8e-20  Score=111.69  Aligned_cols=71  Identities=32%  Similarity=0.523  Sum_probs=65.9

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      .|.+||++.+||+|.|+|.+|..|+|+|.++|.|||+.|+.+++..+++.+  .+++.+||||++|.||+..+
T Consensus         6 ~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~--n~ygdaFirGnnVlyIs~~~   76 (77)
T KOG1783|consen    6 MPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLK--NKYGDAFIRGNNVLYISTQK   76 (77)
T ss_pred             CcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCccc--ccccceeeccccEEEEEecc
Confidence            378999999999999999999999999999999999999999999887764  78899999999999998754

>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=99.78  E-value=2.3e-18  Score=104.34  Aligned_cols=69  Identities=14%  Similarity=0.240  Sum_probs=60.5

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC----CCceEeeeeEEEecCeEEEEEcC
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK----YPHMLSVRNCFIRGSVVRYVQLP   73 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~----~~~~~~~~~~~IRG~~I~~I~~~   73 (93)
                      +-|++++|++|+|.|+||+.+.|+|.+||.+||++|+||.|.....    ....+.+|.++|||++|..|+++
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v~   75 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEVE   75 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEEC
Confidence            4688999999999999999999999999999999999999986431    12357999999999999999853

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.

>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=99.78  E-value=2.9e-18  Score=103.47  Aligned_cols=69  Identities=23%  Similarity=0.259  Sum_probs=59.9

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcC---CCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQ---DKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~---~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      +.|+++++++|.|.|++|+.+.|+|.+||+|||++|++|.|...   .+. ....+|.+++||++|.+|...|
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~-~~~~lG~~~iRG~~I~~i~~~d   73 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGV-EQVVLGLYIIRGDNIAVVGEID   73 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCc-eeeEeceEEECCCEEEEEEccC
Confidence            46889999999999999999999999999999999999998642   122 2467899999999999998654

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.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.73  E-value=3.9e-17  Score=101.84  Aligned_cols=71  Identities=17%  Similarity=0.290  Sum_probs=57.4

Q ss_pred             chhHHHhhcCC--CEEEEEEcCC--cEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490            2 LFFSYFKDLVG--REVTVELKND--LAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP   73 (93)
Q Consensus         2 ~p~~~L~~~~g--k~V~V~L~~g--~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~   73 (93)
                      .|+..+.+++.  .+|.|++.++  +++.|+|.+||.|||++|+||+|...+.. ....+|.++|||++|.+|+..
T Consensus        14 ~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~-~~~~lG~ilIRGnnV~~I~~~   88 (89)
T PTZ00138         14 QPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKN-TRKDLGRILLKGDNITLIMAA   88 (89)
T ss_pred             CCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCc-eeeEcCeEEEcCCEEEEEEcC
Confidence            47777777764  4677787774  89999999999999999999999864332 236889999999999999753

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

Probab=99.66  E-value=2.8e-16  Score=94.04  Aligned_cols=66  Identities=21%  Similarity=0.365  Sum_probs=59.3

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL   72 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   72 (93)
                      +.|+++.+|++.++|..|+.+.|+|.+||.|||++|++++|...+..  ...++.++|||++|..+..
T Consensus         7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~--~~~ig~~vIrgnsiv~~ea   72 (77)
T KOG1780|consen    7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD--KNNIGMVVIRGNSIVMVEA   72 (77)
T ss_pred             chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC--cceeeeEEEeccEEEEEee
Confidence            38999999999999999999999999999999999999999876553  2578999999999998853

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

Probab=99.63  E-value=1e-16  Score=97.83  Aligned_cols=73  Identities=29%  Similarity=0.378  Sum_probs=62.6

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEc------CCC-----CCceEeeeeEEEecCeEEEE
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD------QDK-----YPHMLSVRNCFIRGSVVRYV   70 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~------~~~-----~~~~~~~~~~~IRG~~I~~I   70 (93)
                      -|+++|+-.++.+|+|+|+++++++|+|.+||+|+|++|+|++++-      ++.     ....+.++.+|+||++|.+|
T Consensus         5 ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilv   84 (91)
T KOG3460|consen    5 EPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILV   84 (91)
T ss_pred             ccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEE
Confidence            4999999999999999999999999999999999999999998852      111     01136788999999999999


Q ss_pred             EcCC
Q 034490           71 QLPP   74 (93)
Q Consensus        71 ~~~~   74 (93)
                      +.|-
T Consensus        85 spp~   88 (91)
T KOG3460|consen   85 SPPL   88 (91)
T ss_pred             cCcc
Confidence            9774

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

Probab=99.49  E-value=2.3e-14  Score=86.30  Aligned_cols=69  Identities=19%  Similarity=0.378  Sum_probs=61.7

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEc--CCCCCceEeeeeEEEecCeEEEEE
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD--QDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~--~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      +|++++.+++|.++.|.+++++++.|+|.+||.|.|++|+|++|+.  +++. ...+++.+++.|++|....
T Consensus         7 lPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr-~~tk~~~iLLnGNni~mLv   77 (84)
T KOG1775|consen    7 LPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGR-RMTKLDQILLNGNNITMLV   77 (84)
T ss_pred             ccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcc-eeeeeeeeeecCCcEEEEe
Confidence            7999999999999999999999999999999999999999999864  3332 2568899999999999875

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

Probab=99.44  E-value=1.4e-13  Score=83.85  Aligned_cols=67  Identities=19%  Similarity=0.423  Sum_probs=55.4

Q ss_pred             hHHHhhcCCCEEEEEEcC--CcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490            4 FSYFKDLVGREVTVELKN--DLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP   73 (93)
Q Consensus         4 ~~~L~~~~gk~V~V~L~~--g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~   73 (93)
                      +.||+.  ..+|.|+|..  +..+.|.+.+||+|||++|++|++....... -..+|.++++|++|..|.-.
T Consensus        18 fr~Lq~--~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~-rk~lGRilLKGDnItli~~~   86 (88)
T KOG1774|consen   18 FRFLQN--RTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKS-RKELGRILLKGDNITLIQSA   86 (88)
T ss_pred             HHHHhc--CCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccC-CCccccEEEcCCcEEEEeec
Confidence            577777  4589999997  6889999999999999999999997643322 14789999999999999743

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

Probab=99.38  E-value=6.2e-13  Score=82.50  Aligned_cols=86  Identities=21%  Similarity=0.242  Sum_probs=73.9

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEc--CCCCCceEeeeeEEEecCeEEEEEcCCCCcchhhh
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD--QDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDLL   82 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~--~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~~~   82 (93)
                      +-|.++++++|.|...||+.+.|.|.+||+..||.|+++-+..  ...-.....+|...|||+||..|..-++.+|+.+-
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~~ld   82 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDSRLD   82 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhhhhh
Confidence            3578999999999999999999999999999999999998742  11111136789999999999999999999999999


Q ss_pred             hHhhhhhh
Q 034490           83 HDATRREA   90 (93)
Q Consensus        83 ~~~~~~~~   90 (93)
                      +...|+++
T Consensus        83 ~tkir~ep   90 (96)
T KOG1784|consen   83 LTKIRAEP   90 (96)
T ss_pred             hhhcccCC
Confidence            98888775

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

Probab=99.28  E-value=4.3e-13  Score=84.24  Aligned_cols=76  Identities=16%  Similarity=0.260  Sum_probs=62.5

Q ss_pred             HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC------CCceEeeeeEEEecCeEEEEEcCCCC--cc
Q 034490            7 FKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK------YPHMLSVRNCFIRGSVVRYVQLPPDG--VD   78 (93)
Q Consensus         7 L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~------~~~~~~~~~~~IRG~~I~~I~~~~~~--~d   78 (93)
                      |..+++|+|+|++..|++.+|+|.+||+.||++|+|++|.-.+.      ....+++|.+.+||..+..|+..+..  +.
T Consensus        22 Lsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e~I~  101 (108)
T KOG1781|consen   22 LSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSEEIA  101 (108)
T ss_pred             HHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchhhhc
Confidence            67889999999999999999999999999999999999863221      11248899999999999999977652  44


Q ss_pred             hhhh
Q 034490           79 VDLL   82 (93)
Q Consensus        79 ~~~~   82 (93)
                      .|+.
T Consensus       102 npf~  105 (108)
T KOG1781|consen  102 NPFV  105 (108)
T ss_pred             cchh
Confidence            4444

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

Probab=99.00  E-value=4.1e-11  Score=77.94  Aligned_cols=69  Identities=22%  Similarity=0.245  Sum_probs=57.6

Q ss_pred             HHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEE--cCCCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490            6 YFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVV--DQDKYPHMLSVRNCFIRGSVVRYVQLPPD   75 (93)
Q Consensus         6 ~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~--~~~~~~~~~~~~~~~IRG~~I~~I~~~~~   75 (93)
                      =|-+.+.|++.|-|+||+.+.|.|.+||+|-|++|.+|.|.  ..+.+. .+..|.+.|||.||..+..-+.
T Consensus        13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~-di~~glfiIRGENVvllGeid~   83 (129)
T KOG1782|consen   13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYC-DIPRGLFIIRGENVVLLGEIDL   83 (129)
T ss_pred             HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceec-ccCceEEEEecCcEEEEecCCc
Confidence            36678899999999999999999999999999999999984  233332 2567999999999999975543

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=98.97  E-value=8.5e-11  Score=80.16  Aligned_cols=69  Identities=13%  Similarity=0.225  Sum_probs=58.8

Q ss_pred             HHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcC---------CCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490            6 YFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQ---------DKYPHMLSVRNCFIRGSVVRYVQLPPD   75 (93)
Q Consensus         6 ~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~---------~~~~~~~~~~~~~IRG~~I~~I~~~~~   75 (93)
                      -+-.+++.++.|.+.||+++.|.+.+||.|||++|.||+|...         +++ ..+-++.+++||.+|.+.++.+-
T Consensus         8 kml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~e-Ekr~lgLvllRgenIvs~tVegp   85 (177)
T KOG3168|consen    8 KMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGE-EKRVLGLVLLRGENIVSMTVEGP   85 (177)
T ss_pred             HHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccc-eeeEEEEEEecCCcEEEEeccCC
Confidence            3556789999999999999999999999999999999998531         223 25789999999999999998764

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

Probab=98.42  E-value=3.1e-08  Score=63.45  Aligned_cols=69  Identities=23%  Similarity=0.310  Sum_probs=55.2

Q ss_pred             hhHHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcC-------CCC----CceEeeeeEEEecCeEEE
Q 034490            3 FFSYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQ-------DKY----PHMLSVRNCFIRGSVVRY   69 (93)
Q Consensus         3 p~~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~-------~~~----~~~~~~~~~~IRG~~I~~   69 (93)
                      |++.+.+..  ..+|.|-++|+..+-|...+||.++|++|+++.+...       +..    .+.+.++.+||||++|..
T Consensus        25 pls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~  104 (114)
T KOG3459|consen   25 PLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVIL  104 (114)
T ss_pred             chhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEE
Confidence            556666655  6789999999999999999999999999999988531       111    124678999999999887


Q ss_pred             EE
Q 034490           70 VQ   71 (93)
Q Consensus        70 I~   71 (93)
                      +.
T Consensus       105 v~  106 (114)
T KOG3459|consen  105 VL  106 (114)
T ss_pred             EE
Confidence            75

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

Probab=98.37  E-value=1.6e-06  Score=52.16  Aligned_cols=44  Identities=30%  Similarity=0.442  Sum_probs=36.5

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEecc---ccceEEeeEEEEcC
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQ---YLNIKLENTRVVDQ   48 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~---~mNl~L~~~~~~~~   48 (93)
                      =++..++|++|.|.++||..|+|++.+++.   -+.++|+.+.....
T Consensus         5 ~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~   51 (77)
T PF14438_consen    5 YLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPK   51 (77)
T ss_dssp             HHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS
T ss_pred             HHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccc
Confidence            367889999999999999999999999998   89999999998764

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

Probab=97.91  E-value=1.1e-05  Score=47.58  Aligned_cols=37  Identities=19%  Similarity=0.225  Sum_probs=31.8

Q ss_pred             CCEEEEEEcCC----cEEEEEEEEeccccceEEeeEEEEcC
Q 034490           12 GREVTVELKND----LAIRGTLHSVDQYLNIKLENTRVVDQ   48 (93)
Q Consensus        12 gk~V~V~L~~g----~~~~G~L~~~D~~mNl~L~~~~~~~~   48 (93)
                      +++|.|.++.-    -.++|.|.+||.|+|+.|.|+.|+..
T Consensus         8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~   48 (66)
T cd01739           8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR   48 (66)
T ss_pred             CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence            67888888863    47889999999999999999999754

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

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

Probab=97.54  E-value=0.00085  Score=42.36  Aligned_cols=68  Identities=22%  Similarity=0.323  Sum_probs=53.8

Q ss_pred             hhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCCC-------CceEeeeeEEEecCeEEEEEcCCC
Q 034490            8 KDLVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDKY-------PHMLSVRNCFIRGSVVRYVQLPPD   75 (93)
Q Consensus         8 ~~~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~~-------~~~~~~~~~~IRG~~I~~I~~~~~   75 (93)
                      ..++|++|.+..+++..|+|+|..+|. .-.+.|.+|.....+..       +....++.+..||+.|.-+.+-+.
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~   79 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEP   79 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcC
Confidence            468999999999999999999999996 77999999998642110       011246789999999999987654

>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=97.28  E-value=0.0044  Score=37.94  Aligned_cols=64  Identities=17%  Similarity=0.254  Sum_probs=49.1

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP   73 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~   73 (93)
                      .+.+|.++.||+|.+.|.++.++.|+..++|. ..|+..++-.-  +=     -..++..+|.+-|..++++
T Consensus        15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~T--Pl-----Gv~~eAlLR~~DVi~~~f~   79 (80)
T PF11095_consen   15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQT--PL-----GVQPEALLRCSDVISISFD   79 (80)
T ss_dssp             HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEET--TT-----TEEEEEEEEGGGEEEEEE-
T ss_pred             HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCC--Cc-----ccChhheeecCCEEEEEec
Confidence            36788999999999999999999999999995 55887776541  11     1247899999999999875

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=96.90  E-value=0.0034  Score=36.60  Aligned_cols=37  Identities=19%  Similarity=0.356  Sum_probs=30.2

Q ss_pred             HHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEee
Q 034490            6 YFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLEN   42 (93)
Q Consensus         6 ~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~   42 (93)
                      ||+.+.  ..+|+|-|.||-.++|.+.+||.|+=+.-.+
T Consensus         3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716           3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence            344443  6789999999999999999999999776554

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=96.80  E-value=0.0038  Score=36.39  Aligned_cols=31  Identities=26%  Similarity=0.353  Sum_probs=27.8

Q ss_pred             CCEEEEEEcCCcEEEEEEEEeccccceEEee
Q 034490           12 GREVTVELKNDLAIRGTLHSVDQYLNIKLEN   42 (93)
Q Consensus        12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~   42 (93)
                      +.+|+|-|.||-.++|.+.+||.|+=+.-.+
T Consensus        15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383        15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            7899999999999999999999998776544

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.

>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=96.61  E-value=0.024  Score=34.20  Aligned_cols=62  Identities=21%  Similarity=0.326  Sum_probs=46.5

Q ss_pred             hhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCCC--------CceEeeeeEEEecCeEEE
Q 034490            8 KDLVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDKY--------PHMLSVRNCFIRGSVVRY   69 (93)
Q Consensus         8 ~~~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~~--------~~~~~~~~~~IRG~~I~~   69 (93)
                      ..++|+++.+.-+.+.-|.|+|.++|. .--+.|+|+...-.++.        +...-++.+.-||+.|.-
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            368999999999999999999999995 45788999987632110        112345778888887753

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.

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=96.58  E-value=0.006  Score=37.25  Aligned_cols=32  Identities=22%  Similarity=0.384  Sum_probs=28.6

Q ss_pred             CCEEEEEEcCCcEEEEEEEEeccccceEEeeE
Q 034490           12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENT   43 (93)
Q Consensus        12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~   43 (93)
                      +.+|+|-|.||-.++|.+.+||.|+=+.-.+.
T Consensus        19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g   50 (79)
T PRK00395         19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG   50 (79)
T ss_pred             CCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence            78999999999999999999999997776554

>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=96.13  E-value=0.027  Score=30.78  Aligned_cols=34  Identities=26%  Similarity=0.335  Sum_probs=29.3

Q ss_pred             CCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEE
Q 034490           11 VGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRV   45 (93)
Q Consensus        11 ~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~   45 (93)
                      +|++|+|++ ++..++|+..++|+.-.|+++....
T Consensus         2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g   35 (48)
T PF02237_consen    2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG   35 (48)
T ss_dssp             TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred             CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence            699999999 6677799999999999999876443

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 ....

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

Probab=96.06  E-value=0.015  Score=35.24  Aligned_cols=35  Identities=23%  Similarity=0.431  Sum_probs=28.9

Q ss_pred             HHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceE
Q 034490            5 SYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIK   39 (93)
Q Consensus         5 ~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~   39 (93)
                      .||+++.  +.+|.|-|.||-.++|.+.+||.|.=+.
T Consensus        10 ~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~VlL   46 (77)
T COG1923          10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVLL   46 (77)
T ss_pred             HHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence            3555544  7899999999999999999999997544

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

Probab=96.02  E-value=0.041  Score=37.95  Aligned_cols=62  Identities=27%  Similarity=0.348  Sum_probs=43.6

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPD   75 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~   75 (93)
                      ..+..++||.|.|.+.| +++.|.|..+|+ .-|++|-+-.+   ++.   .  ..-+|-|.+|..|..-++
T Consensus        10 ~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~---~--sv~~I~ghaVk~vevl~~   72 (166)
T PF06372_consen   10 LEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGK---R--SVKVIMGHAVKSVEVLSE   72 (166)
T ss_dssp             HHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS----E--EEEEE-GGGEEEEEEEE-
T ss_pred             HHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCc---e--eEEEEEccceEEEEEccC
Confidence            35788999999999999 999999999996 67999885544   222   1  246799999999976654

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.

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

Probab=95.58  E-value=0.034  Score=32.84  Aligned_cols=53  Identities=28%  Similarity=0.426  Sum_probs=39.6

Q ss_pred             hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490            4 FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         4 ~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      +..|++++|++|.|++-.|+. +|+|.++-... ++|+..      +       ..+|||=.+|.+|.
T Consensus        13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDh-Ivl~~~------~-------~~~~IR~~~IV~v~   65 (66)
T PF10842_consen   13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDH-IVLEEN------G-------TPFFIRIAQIVWVM   65 (66)
T ss_pred             HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCE-EEEEeC------C-------cEEEEEeeeEEEEc
Confidence            578999999999999988776 99999987532 233222      1       35688988888875

>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=95.53  E-value=0.15  Score=29.67  Aligned_cols=36  Identities=14%  Similarity=0.161  Sum_probs=30.8

Q ss_pred             cCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEE
Q 034490           10 LVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRV   45 (93)
Q Consensus        10 ~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~   45 (93)
                      .+|..|.+++..|.+++|.+.+||...++.+-.+..
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s   39 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS   39 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence            479999999999999999999999888777555443

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

>PRK14638 hypothetical protein; Provisional

Probab=94.75  E-value=0.068  Score=36.08  Aligned_cols=36  Identities=14%  Similarity=0.234  Sum_probs=29.9

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEe
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLE   41 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~   41 (93)
                      .-+..++|++|.|.+++++.++|+|.++|.. ++.|.
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            3467889999999999999999999999964 34443

>PRK14639 hypothetical protein; Provisional

Probab=94.39  E-value=0.094  Score=35.00  Aligned_cols=35  Identities=29%  Similarity=0.418  Sum_probs=29.8

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L   40 (93)
                      .-++.++|+.|.|++.+++.+.|+|.++|.. ++.|
T Consensus        81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l  115 (140)
T PRK14639         81 EHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL  115 (140)
T ss_pred             HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            3467899999999999999999999999983 4444

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=94.15  E-value=0.12  Score=35.65  Aligned_cols=32  Identities=22%  Similarity=0.369  Sum_probs=28.3

Q ss_pred             CCEEEEEEcCCcEEEEEEEEeccccceEEeeE
Q 034490           12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENT   43 (93)
Q Consensus        12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~   43 (93)
                      ..+|+|-|.||-.++|.+.+||.|.=+...+.
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            67899999999999999999999987766554

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=93.82  E-value=0.16  Score=35.01  Aligned_cols=38  Identities=16%  Similarity=0.282  Sum_probs=31.0

Q ss_pred             HHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEeeE
Q 034490            6 YFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLENT   43 (93)
Q Consensus         6 ~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~   43 (93)
                      ||+.+.  ..+|+|-|.||-.++|.+.+||+|.=+.-.+.
T Consensus        16 fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g   55 (165)
T PRK14091         16 FLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG   55 (165)
T ss_pred             HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            444444  67899999999999999999999987776554

>PRK02001 hypothetical protein; Validated

Probab=93.67  E-value=0.55  Score=31.84  Aligned_cols=34  Identities=41%  Similarity=0.597  Sum_probs=29.2

Q ss_pred             HHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490            6 YFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         6 ~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L   40 (93)
                      -+..++|+.|.|.|.++..+.|+|.++|+. ++.|
T Consensus        84 ~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l  117 (152)
T PRK02001         84 QYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL  117 (152)
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence            467889999999999999999999999975 3444

>PRK14644 hypothetical protein; Provisional

Probab=92.53  E-value=0.28  Score=32.64  Aligned_cols=35  Identities=23%  Similarity=0.348  Sum_probs=29.1

Q ss_pred             HHhhcCCCEEEEEEcCC----cEEEEEEEEeccccceEEe
Q 034490            6 YFKDLVGREVTVELKND----LAIRGTLHSVDQYLNIKLE   41 (93)
Q Consensus         6 ~L~~~~gk~V~V~L~~g----~~~~G~L~~~D~~mNl~L~   41 (93)
                      -+..++|+.|.|.|++.    ..++|.|.++|.. ++.|.
T Consensus        79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            36788999999999987    9999999999973 45554

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.50  E-value=0.44  Score=32.43  Aligned_cols=32  Identities=25%  Similarity=0.434  Sum_probs=28.9

Q ss_pred             HHHhhcCCCEEEEEE----cCCcEEEEEEEEecccc
Q 034490            5 SYFKDLVGREVTVEL----KNDLAIRGTLHSVDQYL   36 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L----~~g~~~~G~L~~~D~~m   36 (93)
                      .-+..++|+.|.|+|    .+.+.++|+|.++|..+
T Consensus        92 ~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~  127 (153)
T COG0779          92 EHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET  127 (153)
T ss_pred             HHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence            457788999999999    78899999999999877

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

Probab=92.42  E-value=0.35  Score=29.22  Aligned_cols=35  Identities=34%  Similarity=0.493  Sum_probs=27.9

Q ss_pred             HHHhhcCCCEEEEEEc---CC-cEEEEEEEEeccccceEE
Q 034490            5 SYFKDLVGREVTVELK---ND-LAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~---~g-~~~~G~L~~~D~~mNl~L   40 (93)
                      .-+..++|+.|.|+++   +| +.+.|.|.++|.. ++.|
T Consensus        18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l   56 (83)
T cd01734          18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL   56 (83)
T ss_pred             HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence            3467889999999998   55 6899999999984 3444

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.

>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.14  E-value=0.57  Score=35.96  Aligned_cols=67  Identities=21%  Similarity=0.327  Sum_probs=51.6

Q ss_pred             hhcCCCEEEEEEcCCcEEEEEEEEec-cccceEEeeEEEEcCCC-------CC-ceEeeeeEEEecCeEEEEEcCC
Q 034490            8 KDLVGREVTVELKNDLAIRGTLHSVD-QYLNIKLENTRVVDQDK-------YP-HMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         8 ~~~~gk~V~V~L~~g~~~~G~L~~~D-~~mNl~L~~~~~~~~~~-------~~-~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      ..++|++|.+.=+++.-|+|+|.-+| +..=|-|.+|..+-.++       .+ ...-++.++-||+.|+-+.+-+
T Consensus         5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~   80 (361)
T KOG1073|consen    5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQE   80 (361)
T ss_pred             cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeecc
Confidence            46899999999999999999999999 56689999986642111       01 1114578999999999777655

>PRK14640 hypothetical protein; Provisional

Probab=91.70  E-value=0.4  Score=32.34  Aligned_cols=36  Identities=31%  Similarity=0.501  Sum_probs=28.7

Q ss_pred             HHHhhcCCCEEEEEE----cCCcEEEEEEEEeccccceEEe
Q 034490            5 SYFKDLVGREVTVEL----KNDLAIRGTLHSVDQYLNIKLE   41 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L----~~g~~~~G~L~~~D~~mNl~L~   41 (93)
                      .-++.++|+.|.|.|    .+.+.++|+|.++|.. ++.|.
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            346788999999999    4679999999999874 44443

>PRK14642 hypothetical protein; Provisional

Probab=91.15  E-value=0.46  Score=33.62  Aligned_cols=34  Identities=26%  Similarity=0.467  Sum_probs=28.2

Q ss_pred             HHhhcCCCEEEEEEc-------------CCcEEEEEEEEeccccceEE
Q 034490            6 YFKDLVGREVTVELK-------------NDLAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         6 ~L~~~~gk~V~V~L~-------------~g~~~~G~L~~~D~~mNl~L   40 (93)
                      =+..++|+.|.|.|+             +.+.++|+|.++|.. ++.|
T Consensus        94 df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         94 DFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             HHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            356789999999998             679999999999974 4444

>PRK14633 hypothetical protein; Provisional

Probab=90.88  E-value=0.53  Score=31.69  Aligned_cols=36  Identities=25%  Similarity=0.311  Sum_probs=28.6

Q ss_pred             HHHhhcCCCEEEEEEc----CCcEEEEEEEEeccccceEEe
Q 034490            5 SYFKDLVGREVTVELK----NDLAIRGTLHSVDQYLNIKLE   41 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~----~g~~~~G~L~~~D~~mNl~L~   41 (93)
                      .-++.++|++|.|.++    +.+.++|+|.++++. ++.|.
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            3467889999999994    569999999999874 44453

>PRK14632 hypothetical protein; Provisional

Probab=90.28  E-value=0.61  Score=32.12  Aligned_cols=36  Identities=25%  Similarity=0.425  Sum_probs=28.8

Q ss_pred             HHHhhcCCCEEEEEEcC-------CcEEEEEEEEeccccceEEe
Q 034490            5 SYFKDLVGREVTVELKN-------DLAIRGTLHSVDQYLNIKLE   41 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~-------g~~~~G~L~~~D~~mNl~L~   41 (93)
                      .-++.++|+.|.|.|++       .+.++|+|.++|.. ++.|.
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            34678899999999986       57999999999864 44553

>PRK14636 hypothetical protein; Provisional

Probab=90.20  E-value=0.59  Score=32.35  Aligned_cols=35  Identities=26%  Similarity=0.511  Sum_probs=27.9

Q ss_pred             HHHhhcCCCEEEEEEc---CC-cEEEEEEEEeccccceEE
Q 034490            5 SYFKDLVGREVTVELK---ND-LAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~---~g-~~~~G~L~~~D~~mNl~L   40 (93)
                      .-+..++|++|.|+|+   +| +.++|+|.++|.. ++.|
T Consensus        91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            3467889999999998   55 7999999999873 3444

>PRK14643 hypothetical protein; Provisional

Probab=90.18  E-value=0.62  Score=31.91  Aligned_cols=30  Identities=17%  Similarity=0.140  Sum_probs=26.1

Q ss_pred             HHhhcCCCEEEEEEcC----CcEEEEEEEEeccc
Q 034490            6 YFKDLVGREVTVELKN----DLAIRGTLHSVDQY   35 (93)
Q Consensus         6 ~L~~~~gk~V~V~L~~----g~~~~G~L~~~D~~   35 (93)
                      -++.++|++|.|.|+.    .+.++|+|.++|..
T Consensus        98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         98 ELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             HHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            4678899999999976    59999999999964

>PRK14645 hypothetical protein; Provisional

Probab=90.10  E-value=0.63  Score=31.58  Aligned_cols=33  Identities=15%  Similarity=0.272  Sum_probs=26.9

Q ss_pred             HHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490            6 YFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         6 ~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L   40 (93)
                      -+..++|++|.|.+ +++.++|+|.++|.. .+.|
T Consensus        96 df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l  128 (154)
T PRK14645         96 HFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF  128 (154)
T ss_pred             HHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence            46788999999986 789999999999974 3444

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=89.58  E-value=0.79  Score=30.77  Aligned_cols=31  Identities=35%  Similarity=0.567  Sum_probs=26.5

Q ss_pred             HHHhhcCCCEEEEEE----cCCcEEEEEEEEeccc
Q 034490            5 SYFKDLVGREVTVEL----KNDLAIRGTLHSVDQY   35 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L----~~g~~~~G~L~~~D~~   35 (93)
                      .-++.++|+.|.|++    .++..++|+|.++|..
T Consensus        91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~  125 (154)
T PRK00092         91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE  125 (154)
T ss_pred             HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence            456789999999998    5678999999999983

>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=89.56  E-value=0.55  Score=30.95  Aligned_cols=30  Identities=37%  Similarity=0.623  Sum_probs=23.7

Q ss_pred             HHHhhcCCCEEEEEEc----CCcEEEEEEEEecc
Q 034490            5 SYFKDLVGREVTVELK----NDLAIRGTLHSVDQ   34 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~----~g~~~~G~L~~~D~   34 (93)
                      .-+..++|+.|.|+++    +.+.+.|+|.++|.
T Consensus        80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~  113 (141)
T PF02576_consen   80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE  113 (141)
T ss_dssp             HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred             HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence            4577899999999994    45799999999998

; PDB: 1IB8_A.

>PRK14634 hypothetical protein; Provisional

Probab=89.46  E-value=0.79  Score=31.03  Aligned_cols=35  Identities=20%  Similarity=0.373  Sum_probs=27.6

Q ss_pred             HHHhhcCCCEEEEEEcCC----cEEEEEEEEeccccceEE
Q 034490            5 SYFKDLVGREVTVELKND----LAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g----~~~~G~L~~~D~~mNl~L   40 (93)
                      .-++.++|+.|.|+|.+.    +.++|+|.++|.. ++.|
T Consensus        93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l  131 (155)
T PRK14634         93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI  131 (155)
T ss_pred             HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence            346788999999999743    7999999999974 3444

>PRK14646 hypothetical protein; Provisional

Probab=88.95  E-value=0.9  Score=30.76  Aligned_cols=35  Identities=26%  Similarity=0.331  Sum_probs=27.9

Q ss_pred             HHHhhcCCCEEEEEEcCC----cEEEEEEEEeccccceEE
Q 034490            5 SYFKDLVGREVTVELKND----LAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g----~~~~G~L~~~D~~mNl~L   40 (93)
                      .-++.++|++|.|+|++.    +.++|+|.++|+. .+.|
T Consensus        93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l  131 (155)
T PRK14646         93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI  131 (155)
T ss_pred             HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence            346788999999999653    7889999999985 4544

>PRK14647 hypothetical protein; Provisional

Probab=88.30  E-value=1.1  Score=30.46  Aligned_cols=30  Identities=20%  Similarity=0.303  Sum_probs=25.7

Q ss_pred             HHHhhcCCCEEEEEEc---------CCcEEEEEEEEecc
Q 034490            5 SYFKDLVGREVTVELK---------NDLAIRGTLHSVDQ   34 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~---------~g~~~~G~L~~~D~   34 (93)
                      .-++.++|+.|.|.|+         +.+.++|+|.++|.
T Consensus        92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~  130 (159)
T PRK14647         92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD  130 (159)
T ss_pred             HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence            3467889999999996         35999999999996

>PRK14637 hypothetical protein; Provisional

Probab=87.36  E-value=1.3  Score=29.96  Aligned_cols=36  Identities=25%  Similarity=0.268  Sum_probs=26.8

Q ss_pred             HHHhhcCCCEEEEEEcCCcEE-EEEEEEeccccceEEe
Q 034490            5 SYFKDLVGREVTVELKNDLAI-RGTLHSVDQYLNIKLE   41 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~-~G~L~~~D~~mNl~L~   41 (93)
                      .-+..++|+.|.|++.+...+ +|+|.++|+. ++.|.
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            346788999999999544455 7999999875 44443

>PRK09618 flgD flagellar basal body rod modification protein; Provisional

Probab=86.79  E-value=1.3  Score=29.89  Aligned_cols=26  Identities=35%  Similarity=0.542  Sum_probs=23.9

Q ss_pred             hhcCCCEEEEEEcCCcEEEEEEEEec
Q 034490            8 KDLVGREVTVELKNDLAIRGTLHSVD   33 (93)
Q Consensus         8 ~~~~gk~V~V~L~~g~~~~G~L~~~D   33 (93)
                      .+++||.|.+...+|..++|++.++-
T Consensus        88 ~slVGk~V~~~~~~g~~~tG~V~~V~  113 (142)
T PRK09618         88 SELIGKEVEWEGEDGEIVSGTVTSVK  113 (142)
T ss_pred             HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence            47899999999999999999999986

>PRK14631 hypothetical protein; Provisional

Probab=86.66  E-value=1.5  Score=30.30  Aligned_cols=29  Identities=24%  Similarity=0.442  Sum_probs=25.3

Q ss_pred             HHHhhcCCCEEEEEEc----CCcEEEEEEEEec
Q 034490            5 SYFKDLVGREVTVELK----NDLAIRGTLHSVD   33 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~----~g~~~~G~L~~~D   33 (93)
                      .-++.++|+.|.|+|.    +.+.++|+|.++|
T Consensus       110 ~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~  142 (174)
T PRK14631        110 EQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD  142 (174)
T ss_pred             HHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence            3467889999999996    4599999999998

>PRK14641 hypothetical protein; Provisional

Probab=86.48  E-value=1.3  Score=30.59  Aligned_cols=29  Identities=24%  Similarity=0.471  Sum_probs=24.7

Q ss_pred             HHHhhcCCCEEEEEEcC----CcEEEEEEEEec
Q 034490            5 SYFKDLVGREVTVELKN----DLAIRGTLHSVD   33 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~----g~~~~G~L~~~D   33 (93)
                      .-++.++|+.|.|.|.+    .+.++|+|.++|
T Consensus        97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            34678899999999976    468999999996

>PRK06955 biotin--protein ligase; Provisional

Probab=84.94  E-value=5  Score=29.62  Aligned_cols=33  Identities=27%  Similarity=0.384  Sum_probs=28.8

Q ss_pred             hcCCCEEEEEEcCCcEEEEEEEEeccccceEEe
Q 034490            9 DLVGREVTVELKNDLAIRGTLHSVDQYLNIKLE   41 (93)
Q Consensus         9 ~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~   41 (93)
                      ...|++|.|...++..++|+..++|+.-.|.+.
T Consensus       246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~  278 (300)
T PRK06955        246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLD  278 (300)
T ss_pred             hcCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence            367999999766778899999999999999885

>PRK14630 hypothetical protein; Provisional

Probab=81.11  E-value=3.3  Score=27.66  Aligned_cols=29  Identities=24%  Similarity=0.332  Sum_probs=23.8

Q ss_pred             HHhhcCCCEEEEEEcCCcEEEEEEEEeccc
Q 034490            6 YFKDLVGREVTVELKNDLAIRGTLHSVDQY   35 (93)
Q Consensus         6 ~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~   35 (93)
                      -++.++|++|.|.|... ..+|+|.++|+.
T Consensus        91 df~r~~G~~v~V~l~~~-~~~G~L~~~~d~  119 (143)
T PRK14630         91 EFKIFEGKKIKLMLDND-FEEGFILEAKAD  119 (143)
T ss_pred             HHHHhCCCEEEEEEcCc-ceEEEEEEEeCC
Confidence            46788999999999664 459999999873

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

Probab=81.08  E-value=9.8  Score=28.04  Aligned_cols=31  Identities=32%  Similarity=0.502  Sum_probs=27.3

Q ss_pred             cCCCEEEEEEcCCcEEEEEEEEeccccceEEe
Q 034490           10 LVGREVTVELKNDLAIRGTLHSVDQYLNIKLE   41 (93)
Q Consensus        10 ~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~   41 (93)
                      +.|++|.+... +..++|++.++|+.-.|++.
T Consensus       270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~  300 (319)
T PRK11886        270 FLGREVKLIIG-DKEISGIARGIDEQGALLLE  300 (319)
T ss_pred             ccCCeEEEEeC-CcEEEEEEEEECCCceEEEE
Confidence            57999999874 46799999999999999996

>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris

Probab=80.68  E-value=2.6  Score=26.60  Aligned_cols=19  Identities=32%  Similarity=0.532  Sum_probs=15.4

Q ss_pred             CCEEEEEEcCCcEEEEEEE
Q 034490           12 GREVTVELKNDLAIRGTLH   30 (93)
Q Consensus        12 gk~V~V~L~~g~~~~G~L~   30 (93)
                      ..+|.++|+||+.+.|++.
T Consensus        28 e~~V~l~L~DGs~l~Gtv~   46 (101)
T PF11607_consen   28 EERVELELDDGSMLRGTVA   46 (101)
T ss_dssp             T-EEEEEETTS-EEEEEEC
T ss_pred             cceEEEEEcCCCeeeeeec
Confidence            4689999999999999974

The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	93
4emh_A	105	Crystal Structure Of Splsm4 Length = 105		9e-05
1b34_A	119	Crystal Structure Of The D1d2 Sub-Complex From The		2e-04

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 12  GREVTVELKNDLAIRGTLHSVDQYLNIKLENT--RVVDQDKYPHMLSVRNCFIRGSVVRY 69
           GR + VELKN     G L + D Y N+ L        D DK+     +  C+IRG+ ++Y
Sbjct: 26  GRPILVELKNGETFNGHLENCDNYXNLTLREVIRTXPDGDKF---FRLPECYIRGNNIKY 82
Query: 70  VQLPPDGVDVDLLHDATRREARG 92
           +++  + +       A +RE RG
Sbjct: 83  LRIQDEVLSQVAKQQAQQRENRG 105

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 3/82 (3%)
Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          M    +   L    VT+ELKN   + GT+  VD  +N  L+  ++  +++ P  + +   
Sbjct: 1  MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREP--VQLETL 58
Query: 61 FIRGSVVRYVQLPPDGVDVDLL 82
           IRG+ +RY  L PD + +D L
Sbjct: 59 SIRGNNIRYFIL-PDSLPLDTL 79

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	93
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	3e-34
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	3e-28
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	2e-24
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	3e-22
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	9e-18
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	1e-17
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	1e-15
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	1e-10
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	6e-10
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	7e-10
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	3e-09
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	1e-08
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	2e-08
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	3e-06
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	3e-06
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	5e-06
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	2e-05
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	5e-05
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	7e-05
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	8e-04

>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 =  112 bits (282), Expect = 3e-34
 Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 1/92 (1%)

Query: 1   MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
           ML  +      GR + VELKN     G L + D Y+N+ L        D       +  C
Sbjct: 15  MLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDG-DKFFRLPEC 73

Query: 61  FIRGSVVRYVQLPPDGVDVDLLHDATRREARG 92
           +IRG+ ++Y+++  + +       A +RE RG
Sbjct: 74  YIRGNNIKYLRIQDEVLSQVAKQQAQQRENRG 105

>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 = 97.7 bits (243), Expect = 3e-28
 Identities = 26/93 (27%), Positives = 40/93 (43%), Gaps = 2/93 (2%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60
          M    +   L    VT+ELKN   + GT+  VD  +N  L+  ++  +++ P  L     
Sbjct: 1  MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLE--TL 58

Query: 61 FIRGSVVRYVQLPPDGVDVDLLHDATRREARGG 93
           IRG+ +RY  LP       LL D   +     
Sbjct: 59 SIRGNNIRYFILPDSLPLDTLLVDVEPKVKSKK 91

>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 = 88.2 bits (218), Expect = 2e-24
 Identities = 21/89 (23%), Positives = 34/89 (38%), Gaps = 2/89 (2%)

Query: 5  SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRG 64
              +  G  VT E       RG L   +  +N ++ N  V  +D     L     +IRG
Sbjct: 8  KVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQL--EQVYIRG 65

Query: 65 SVVRYVQLPPDGVDVDLLHDATRREARGG 93
          S +R++ LP    +  +L     +    G
Sbjct: 66 SKIRFLILPDMLKNAPMLKSMKNKNQGSG 94

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

 Score = 80.9 bits (200), Expect = 3e-22
 Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 5  SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRG 64
              +  G  VT E       RG L   +  +N ++ N  V  +D     L     +IRG
Sbjct: 8  KVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLE--QVYIRG 65

Query: 65 SVVRYVQLP 73
            +R++ LP
Sbjct: 66 CKIRFLILP 74

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

 Score = 70.2 bits (172), Expect = 9e-18
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 6  YFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGS 65
          +   L G+ V V+LK  +  +G L SVD Y+N++L NT           L      IR +
Sbjct: 10 FLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG--EVLIRCN 67

Query: 66 VVRYVQLPPDGVDVDLLHD 84
           V Y++   +  +   + +
Sbjct: 68 NVLYIRGVEEEEEDGEMRE 86

>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 = 69.9 bits (171), Expect = 1e-17
 Identities = 24/71 (33%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 6  YFKDLVGREVTVELK-NDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRG 64
          + K LV   V V+LK N    RGTL S D Y N++L              L     FIR 
Sbjct: 25 FLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLG--EIFIRC 82

Query: 65 SVVRYVQLPPD 75
          + V Y++  P+
Sbjct: 83 NNVLYIRELPN 93

>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 = 64.7 bits (158), Expect = 1e-15
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 6  YFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGS 65
          +   ++G++V + L + +  +G L  +D Y+N+ LE T      K  ++    + FIRG+
Sbjct: 8  FLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYG--DAFIRGN 65

Query: 66 VVRYVQLPPD 75
           V YV    D
Sbjct: 66 NVLYVSALDD 75

>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 = 51.5 bits (124), Expect = 1e-10
 Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 2/68 (2%)

Query: 8  KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVV 67
             + ++V V LK     RG L   D +LN+ L +  ++   +           IRG  V
Sbjct: 10 HRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYG--KIVIRGDNV 67

Query: 68 RYVQLPPD 75
            +    +
Sbjct: 68 LAISPTEE 75

>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 = 50.1 bits (120), Expect = 6e-10
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 6/70 (8%)

Query: 8  KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT-RVVDQDKYPHMLSVRNCFIRGSV 66
          +D +G++V V+L++   IRG L S DQ++N+ LE+   ++D + Y          +RG  
Sbjct: 17 QDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGT----MVVRGEN 72

Query: 67 VRYVQLPPDG 76
          V ++  P  G
Sbjct: 73 VLFIS-PVPG 81

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

 Score = 49.6 bits (119), Expect = 7e-10
 Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 8  KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVV 67
             +   V V LK     RGTL   D ++N+ L +   +   +    +   +  IRG  V
Sbjct: 10 NRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVG--SVVIRGDTV 67

Query: 68 RYVQLPPDG 76
           +V   P G
Sbjct: 68 VFVSPAPGG 76

>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 = 48.1 bits (115), Expect = 3e-09
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 8  KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVV 67
           + +   V ++LK D   RG L S D ++N+ L +   ++  +    L      IRG  +
Sbjct: 21 GNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLG--TVLIRGDNI 78

Query: 68 RYV 70
           Y+
Sbjct: 79 VYI 81

>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 = 46.5 bits (111), Expect = 1e-08
 Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 3/69 (4%)

Query: 8  KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVV 67
           + +   V V+LK +  +RG L S DQ++N+ L ++  +  D     L      IRG  V
Sbjct: 15 AESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGT--IVIRGDNV 72

Query: 68 RYVQLPPDG 76
            +  P   
Sbjct: 73 ILIS-PLQT 80

>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 = 45.8 bits (109), Expect = 2e-08
 Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 3/65 (4%)

Query: 8  KDLVGREVTVELKND-LAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSV 66
          K +VG+ + VE+K +   + G L  VD Y+N+ L N      ++    L      +RG+ 
Sbjct: 11 KSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLG--EIVLRGNN 68

Query: 67 VRYVQ 71
          V  +Q
Sbjct: 69 VVLIQ 73

>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 = 41.1 bits (96), Expect = 3e-06
 Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 6/74 (8%)

Query: 8   KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT--RVVDQDKYPHMLSVRN---CFI 62
                + +         I G L   DQ +N+ L++   ++ + +      ++R      +
Sbjct: 29  SRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVV 88

Query: 63  RGSVVRYVQLPPDG 76
           RG+ +  +  P DG
Sbjct: 89  RGTTLVLIA-PMDG 101

>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 = 40.6 bits (95), Expect = 3e-06
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 11/83 (13%)

Query: 4  FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT--------RVVDQDKYPHML 55
              +  +   V V+L+ D  + G LH+ D++LN+ L +                     
Sbjct: 11 LDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKT 70

Query: 56 SVRN---CFIRGSVVRYVQLPPD 75
            ++    F+RG  V  +  P +
Sbjct: 71 IRKHYEMLFVRGDSVILIAPPRN 93

>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 = 40.1 bits (94), Expect = 5e-06
 Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 5/80 (6%)

Query: 4  FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT--RVVDQDKYPHMLSVRNC- 60
              K  +   V ++L+    + GTL + D + NI L +    +   +      S R C 
Sbjct: 12 LDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCE 71

Query: 61 --FIRGSVVRYVQLPPDGVD 78
            FIRG  V  +  P +  D
Sbjct: 72 MVFIRGDTVTLISTPSEDDD 91

>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 = 38.5 bits (90), Expect = 2e-05
 Identities = 9/65 (13%), Positives = 28/65 (43%), Gaps = 6/65 (9%)

Query: 8  KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT--RVVDQDKYPHMLSVRNCFIRGS 65
          K  + ++++++L     ++G L   D ++N+ ++          +    +      IRG+
Sbjct: 10 KKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM----VVIRGN 65

Query: 66 VVRYV 70
           +  +
Sbjct: 66 SIIML 70

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

 Score = 37.5 bits (87), Expect = 5e-05
 Identities = 12/40 (30%), Positives = 20/40 (50%)

Query: 11 VGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK 50
          +G  + V +K++    GTL   D Y+NI L++    D   
Sbjct: 29 IGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVT 68

>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 = 37.7 bits (87), Expect = 7e-05
 Identities = 14/69 (20%), Positives = 29/69 (42%)

Query: 2  LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCF 61
          L  +     +G  + V +K D    G L   D+Y+N+ L++ +          +S  N  
Sbjct: 28 LPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKK 87

Query: 62 IRGSVVRYV 70
          ++  +V  +
Sbjct: 88 LKRVMVNRL 96

>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 Length = 130

 Score = 35.1 bits (80), Expect = 8e-04
 Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 6/77 (7%)

Query: 3  FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFI 62
          F +   +L+GREV V L N    +G LH+VD  LNI L N      +K+  +      FI
Sbjct: 1  FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRV------FI 54

Query: 63 RGSVVRYVQLPPDGVDV 79
              + ++      +D+
Sbjct: 55 MYRYIVHIDSTERRIDM 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	93
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.96
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.96
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.95
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.95
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.93
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.93
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.92
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.92
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.91
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.91
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.91
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.91
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.91
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.9
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.9
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.89
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.89
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.87
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.87
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.87
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.86
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.86
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.85
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.8
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.15
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	97.17
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.14
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	97.12
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	97.07
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	96.99
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	96.94
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.86
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.78
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.73
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	96.55
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	96.51
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	96.03
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	96.02
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	95.59
1ycy_A	71	Conserved hypothetical protein; structural genomic	94.77
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	90.89
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	90.08
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	87.29
1bia_A	321	BIRA bifunctional protein; transcription regulatio	84.75
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	83.88
2e12_A	101	SM-like motif, hypothetical protein XCC3642; novel	81.62
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	81.49

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

Probab=99.96  E-value=7.8e-30  Score=162.44  Aligned_cols=91  Identities=29%  Similarity=0.531  Sum_probs=55.7

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchh
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVD   80 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~   80 (93)
                      +.|++||++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..++. ....++.+||||++|+||++|++++|++
T Consensus        15 ~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~-~~~~lg~v~IRG~nI~~I~~pd~l~d~p   93 (105)
T 4emh_A           15 MLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGD-KFFRLPECYIRGNNIKYLRIQDEVLSQV   93 (105)
T ss_dssp             -----------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSC-EEEEEEEEEECGGGEEEEEC--------
T ss_pred             CcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCc-eeeEcCeEEEeCCeEEEEecCHHHhhhh
Confidence            469999999999999999999999999999999999999999999876553 2478999999999999999999999999


Q ss_pred             hhhHhhhhhhcC
Q 034490           81 LLHDATRREARG   92 (93)
Q Consensus        81 ~~~~~~~~~~~~   92 (93)
                      +|+....+++||
T Consensus        94 ~~~~~~~~~~~~  105 (105)
T 4emh_A           94 AKQQAQQRENRG  105 (105)
T ss_dssp             ------------
T ss_pred             hhhhhccccCCC
Confidence            999988888887

>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=99.96  E-value=1e-28  Score=160.23  Aligned_cols=86  Identities=28%  Similarity=0.465  Sum_probs=74.2

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCC-cch
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDG-VDV   79 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~-~d~   79 (93)
                      |+|++||++++|++|+|+|+||++|+|+|.+||+|||++|+||+|+..+++.  .+++.+||||++|+||++|+++ +|+
T Consensus         1 M~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~--~~lg~v~IRG~nI~~I~~pd~l~~d~   78 (119)
T 1b34_A            1 MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREP--VQLETLSIRGNNIRYFILPDSLPLDT   78 (119)
T ss_dssp             -CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCC--EEEEEEEECGGGEEEEECCTTCCHHH
T ss_pred             CChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCce--eEcceEEEcCCeEEEEEeccccccch
Confidence            9999999999999999999999999999999999999999999999766543  7899999999999999999995 888


Q ss_pred             hhhhHhhhh
Q 034490           80 DLLHDATRR   88 (93)
Q Consensus        80 ~~~~~~~~~   88 (93)
                      .+.++++|+
T Consensus        79 ~l~~~~pK~   87 (119)
T 1b34_A           79 LLVDVEPKV   87 (119)
T ss_dssp             HTC------
T ss_pred             hHhhhcccc
Confidence            888888873

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

Probab=99.95  E-value=5.5e-28  Score=158.17  Aligned_cols=86  Identities=22%  Similarity=0.354  Sum_probs=78.6

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchh
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVD   80 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~   80 (93)
                      |.|++||++++|++|+|+|+||++|+|+|.+||.|||++|+||+++..++.  ..+++.+||||++|+||++|+++.+++
T Consensus         4 ~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~--~~~l~~v~IRGnnI~~I~lpd~l~~~~   81 (126)
T 2y9a_D            4 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR--VAQLEQVYIRGSKIRFLILPDMLKNAP   81 (126)
T ss_dssp             CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSC--CEEEEEEEECGGGEEEEECCSSCSSSS
T ss_pred             ccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCc--EeecccEEEeCCEEEEEEccccccchH
Confidence            579999999999999999999999999999999999999999999976654  378999999999999999999998888


Q ss_pred             hhhHhhhh
Q 034490           81 LLHDATRR   88 (93)
Q Consensus        81 ~~~~~~~~   88 (93)
                      +|++..++
T Consensus        82 ~l~~~~~k   89 (126)
T 2y9a_D           82 MLKSMKNK   89 (126)
T ss_dssp             HHHHHHHH
T ss_pred             Hhhhhhhc
Confidence            88866553

>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=99.95  E-value=1.6e-27  Score=143.43  Aligned_cols=72  Identities=24%  Similarity=0.399  Sum_probs=67.8

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      |.|++||++++|++|+|+|++|++|+|+|.+||+|||++|+||+++.+++.  ..+++.+||||++|+||++||
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 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR--VAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSC--EEEEEEEEECGGGEEEEEECC
T ss_pred             cCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCc--EEEcCeEEEeCCEEEEEEcCC
Confidence            679999999999999999999999999999999999999999999986654  478999999999999999996

>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=99.93  E-value=9.1e-26  Score=136.07  Aligned_cols=73  Identities=27%  Similarity=0.437  Sum_probs=66.7

Q ss_pred             CchhHHHhhcCCCEEEEEEcCC-cEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490            1 MLFFSYFKDLVGREVTVELKND-LAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPD   75 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g-~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~   75 (93)
                      |.|+++|++++|++|+|+|+|| ++|+|+|.+||+|||++|+||+++..++.  ..++|.++|||++|++|+.|++
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 VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEK--VRSLGEIVLRGNNVVLIQPQEE   77 (77)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEEEC--
T ss_pred             cchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCc--EeECCeEEEeCCeEEEEEeCCC
Confidence            6899999999999999999999 99999999999999999999999876543  4789999999999999999874

>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=99.93  E-value=2.8e-25  Score=133.73  Aligned_cols=73  Identities=25%  Similarity=0.340  Sum_probs=67.1

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPD   75 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~   75 (93)
                      +.|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..+..  .+++|.++|||++|++|+.|+.
T Consensus         3 ~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~~I~~i~~~d~   75 (77)
T 1i4k_A            3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEV--VRKVGSVVIRGDTVVFVSPAPG   75 (77)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEEECC-
T ss_pred             ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCc--EeECCEEEECCCEEEEEEeCCC
Confidence            469999999999999999999999999999999999999999999876543  4789999999999999999874

>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=3.8e-25  Score=132.67  Aligned_cols=73  Identities=21%  Similarity=0.287  Sum_probs=65.9

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPD   75 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~   75 (93)
                      +.|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..+..  ..++|.++|||++|++|+.+++
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~~I~~i~~~~e   75 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEV--VKRYGKIVIRGDNVLAISPTEE   75 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEEEC--
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCc--eeECCEEEECCCEEEEEEeCCC
Confidence            359999999999999999999999999999999999999999999876543  4789999999999999998863

>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=99.92  E-value=1.1e-24  Score=134.13  Aligned_cols=74  Identities=27%  Similarity=0.343  Sum_probs=65.9

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCc
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGV   77 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~   77 (93)
                      .|++||++++||+|+|+|+||++|+|+|.+||+|||++|+||++...+..  ...++.++|||++|+||+.|++..
T Consensus         6 ~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~--~~~lg~v~IRG~nI~~i~~~d~~~   79 (86)
T 3s6n_F            6 NPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGAL--SGHLGEVLIRCNNVLYIRGVEEEE   79 (86)
T ss_dssp             CHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEESSEEECGGGEEEEEECC---
T ss_pred             CcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCce--eeEccEEEEeCCeEEEEEeCCccc
Confidence            69999999999999999999999999999999999999999998765432  468999999999999999998643

>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=99.91  E-value=9.4e-25  Score=136.23  Aligned_cols=72  Identities=31%  Similarity=0.403  Sum_probs=61.3

Q ss_pred             CchhHHHhhcCCCEEEEEEcCC-cEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            1 MLFFSYFKDLVGREVTVELKND-LAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g-~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      |.|+++|++++|++|+|+|+|| ++|+|+|.+||+|||++|+||+++..++.  ..++|.+||||++|+||..++
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 VNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVS--HGTLGEIFIRCNNVLYIRELP   92 (93)
T ss_dssp             ------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEE--EEECCSEEECGGGEEEEEECC
T ss_pred             CChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCe--EeEcCEEEEcCCeEEEEEeCC
Confidence            5799999999999999999999 99999999999999999999999865443  478999999999999999886

>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=99.91  E-value=3.5e-24  Score=130.28  Aligned_cols=72  Identities=24%  Similarity=0.299  Sum_probs=65.8

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPD   75 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~   75 (93)
                      .|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..+..  ...+|.++|||++|++|+.+++
T Consensus         9 ~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~~I~~i~~~~~   80 (81)
T 1th7_A            9 TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGS--GKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             HHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSC--EEEEEEEEECGGGEEEEEEC--
T ss_pred             chHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCc--eeECCEEEECCCEEEEEEecCC
Confidence            58999999999999999999999999999999999999999999986654  4789999999999999998873

>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=99.91  E-value=1.1e-24  Score=130.81  Aligned_cols=72  Identities=26%  Similarity=0.428  Sum_probs=65.0

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      +.|+++|++++||+|+|+|+||++|+|+|.+||+|||++|+||++...+..  ..++|.++|||++|+||+..+
T Consensus         3 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 4emk_B            3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKK--TNVYGDAFIRGNNVLYVSALD   74 (75)
T ss_dssp             SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEE--EEEEEEEEEEGGGSSEEEEC-
T ss_pred             CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCc--ccEecEEEEcCCeEEEEEecC
Confidence            469999999999999999999999999999999999999999999875443  478999999999999998654

>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=99.91  E-value=3.5e-24  Score=140.73  Aligned_cols=83  Identities=27%  Similarity=0.353  Sum_probs=76.8

Q ss_pred             hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchhhhh
Q 034490            4 FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDLLH   83 (93)
Q Consensus         4 ~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~~~~   83 (93)
                      +++|++++||+|+|+|+||++|+|+|.+||+|||++|+||+++..      .++|.++|||++|++|+.+++.+|++.|+
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~~------~~lg~v~IRG~nI~~I~~~d~~~d~~~f~   75 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAG------EKFNRVFIMYRYIVHIDSTERRIDMREFA   75 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTTC------CEEEEEEECGGGEEEEEECCCCCCHHHHH
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEcC------CEeceEEEeCCeEEEEEcCCcccCHHHHH
Confidence            689999999999999999999999999999999999999999841      46899999999999999999999999999


Q ss_pred             HhhhhhhcC
Q 034490           84 DATRREARG   92 (93)
Q Consensus        84 ~~~~~~~~~   92 (93)
                      ++.+++++|
T Consensus        76 ~~~~r~~pg   84 (130)
T 1m5q_A           76 KQAEKIFPG   84 (130)
T ss_dssp             HHHHHHSTT
T ss_pred             HHHhhcCCC
Confidence            999887544

>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=99.91  E-value=8.1e-24  Score=128.70  Aligned_cols=71  Identities=28%  Similarity=0.472  Sum_probs=65.2

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      +.|+.+|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|+ ++.  ..+.+|.++|||++|++|+.++
T Consensus        10 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~--~~~~lg~v~iRG~~I~~i~~~d   80 (81)
T 1i8f_A           10 ATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDG--NVYKRGTMVVRGENVLFISPVP   80 (81)
T ss_dssp             CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETT--EEEEEEEEEECGGGEEEEEECC
T ss_pred             cchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCC--cccCCCEEEECCCEEEEEEeCC
Confidence            3699999999999999999999999999999999999999999999 333  2478999999999999999886

>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=99.90  E-value=1.3e-23  Score=128.44  Aligned_cols=69  Identities=22%  Similarity=0.381  Sum_probs=64.2

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      +.|+.+|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|+..+..  ...+|.++|||++|++|+
T Consensus        14 ~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~IRG~~I~~i~   82 (83)
T 1mgq_A           14 QRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEV--TRRLGTVLIRGDNIVYIS   82 (83)
T ss_dssp             TCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEE
T ss_pred             cChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCc--ccCCCEEEECCCEEEEEE
Confidence            479999999999999999999999999999999999999999999876543  478999999999999997

>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=3.1e-23  Score=129.60  Aligned_cols=72  Identities=19%  Similarity=0.271  Sum_probs=64.9

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEc-CCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD-QDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~-~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      +.|+.+|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|+. ++..  ...+|.++|||++|++|+...
T Consensus        19 ~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~--~~~lg~v~IRG~nI~~i~p~~   91 (94)
T 4emk_A           19 ILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGV--TEKHSEMLLNGNGMCMLIPGG   91 (94)
T ss_dssp             -CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCC--EEEEEEEEECSTTEEEEEECC
T ss_pred             ccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCc--EeEcCEEEEcCCEEEEEEeCC
Confidence            47999999999999999999999999999999999999999999987 4333  478999999999999998653

>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=99.89  E-value=3.5e-23  Score=129.63  Aligned_cols=79  Identities=22%  Similarity=0.244  Sum_probs=65.7

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC-----CCceEeeeeEEEecCeEEEEEcCCCC
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK-----YPHMLSVRNCFIRGSVVRYVQLPPDG   76 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~-----~~~~~~~~~~~IRG~~I~~I~~~~~~   76 (93)
                      -|+.+|++++||+|+|+|+||++|.|+|.+||+|||++|+||+|.....     ....+.+|.++|||++|.+|..+++.
T Consensus        10 ~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d~~   89 (96)
T 3bw1_A           10 TPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPSED   89 (96)
T ss_dssp             CHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC--
T ss_pred             hHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecCcc
Confidence            4899999999999999999999999999999999999999999975321     12347899999999999999999876


Q ss_pred             cchh
Q 034490           77 VDVD   80 (93)
Q Consensus        77 ~d~~   80 (93)
                      .|..
T Consensus        90 ~d~~   93 (96)
T 3bw1_A           90 DDGA   93 (96)
T ss_dssp             ---C
T ss_pred             cccc
Confidence            6643

>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=99.89  E-value=3.2e-23  Score=124.79  Aligned_cols=71  Identities=13%  Similarity=0.290  Sum_probs=53.0

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPD   75 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~   75 (93)
                      |.++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|+..++.  ...+|.++|||++|++|+..|.
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 HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQ--QNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             ---------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC------CBSSEEECSSSEEEEEC---
T ss_pred             chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCc--EeEcCEEEECCCeEEEEEeccC
Confidence            5789999999999999999999999999999999999999999876544  3689999999999999997653

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

Probab=99.87  E-value=9.2e-22  Score=122.60  Aligned_cols=73  Identities=22%  Similarity=0.271  Sum_probs=64.3

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCC----CC-------CceEeeeeEEEecCeEEEE
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQD----KY-------PHMLSVRNCFIRGSVVRYV   70 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~----~~-------~~~~~~~~~~IRG~~I~~I   70 (93)
                      .|+.+|+.++|++|+|+|++|++|+|+|.+||.|||++|+||+|+...    +.       ...+.+|.+||||++|.+|
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            699999999999999999999999999999999999999999997542    11       2357899999999999999


Q ss_pred             EcCC
Q 034490           71 QLPP   74 (93)
Q Consensus        71 ~~~~   74 (93)
                      +.|.
T Consensus        89 ~p~~   92 (93)
T 4emg_A           89 APPR   92 (93)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9763

>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=3.4e-22  Score=124.41  Aligned_cols=73  Identities=11%  Similarity=0.287  Sum_probs=65.3

Q ss_pred             CchhHHHhhcCCCEEEEEE----cCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            1 MLFFSYFKDLVGREVTVEL----KNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L----~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      +.|+.||.++++++|+|++    ++|++|+|+|.+||+|||++|+||+|+..+... ..++|.++|||++|.+|+.++
T Consensus        15 ~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~-~~~lg~v~iRG~nV~~i~~~~   91 (92)
T 3s6n_E           15 VQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKS-RKQLGRIMLKGDNITLLQSVS   91 (92)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCC-EEEEEEEEECGGGEEEEEEC-
T ss_pred             cCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCc-eeEcCeEEEeCCEEEEEEeCC
Confidence            3699999999999999999    999999999999999999999999998744332 478999999999999999765

>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=99.87  E-value=2.4e-22  Score=124.34  Aligned_cols=74  Identities=12%  Similarity=0.108  Sum_probs=62.4

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcC---C-----CCCceEeeeeEEEecCeEEEEEcC
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQ---D-----KYPHMLSVRNCFIRGSVVRYVQLP   73 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~---~-----~~~~~~~~~~~~IRG~~I~~I~~~   73 (93)
                      -|.++|++++|++|+|+|+||++|.|+|.+||.|||++|+||+|+..   .     .....+.+|.++|||++|.+|+++
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            36789999999999999999999999999999999999999999631   1     111357899999999999999988


Q ss_pred             CC
Q 034490           74 PD   75 (93)
Q Consensus        74 ~~   75 (93)
                      +.
T Consensus        84 ~~   85 (91)
T 1d3b_B           84 GP   85 (91)
T ss_dssp             EC
T ss_pred             CC
Confidence            64

>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=99.86  E-value=2e-21  Score=124.95  Aligned_cols=81  Identities=11%  Similarity=0.187  Sum_probs=56.4

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC-----CCceEeeeeEEEecCeEEEEEcCCC--
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK-----YPHMLSVRNCFIRGSVVRYVQLPPD--   75 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~-----~~~~~~~~~~~IRG~~I~~I~~~~~--   75 (93)
                      |...|.+++|++|+|+|+||++|.|+|.+||.||||+|+||+|+..+.     ....+.+|.++|||++|.+|+.++.  
T Consensus        24 ~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~e  103 (113)
T 4emk_C           24 SILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDGSE  103 (113)
T ss_dssp             --------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC---
T ss_pred             hHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCccc
Confidence            467899999999999999999999999999999999999999986431     1135789999999999999998875  


Q ss_pred             Ccchhhhh
Q 034490           76 GVDVDLLH   83 (93)
Q Consensus        76 ~~d~~~~~   83 (93)
                      .++.++.+
T Consensus       104 e~~~p~~~  111 (113)
T 4emk_C          104 EIPNPFVQ  111 (113)
T ss_dssp             --------
T ss_pred             cccCcccc
Confidence            36666654

>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=99.86  E-value=4e-22  Score=129.40  Aligned_cols=75  Identities=19%  Similarity=0.338  Sum_probs=64.8

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCC---------CCC----ceEeeeeEEEecCeE
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQD---------KYP----HMLSVRNCFIRGSVV   67 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~---------~~~----~~~~~~~~~IRG~~I   67 (93)
                      +.|+.||+.++|++|+|+|+||++|+|+|.+||.||||+|+||+|+..+         +..    ..+.+|.+||||++|
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            4799999999999999999999999999999999999999999997632         110    036799999999999


Q ss_pred             EEEEcCCC
Q 034490           68 RYVQLPPD   75 (93)
Q Consensus        68 ~~I~~~~~   75 (93)
                      .+|...++
T Consensus       107 v~I~~~~~  114 (121)
T 2fwk_A          107 AMLVPGGD  114 (121)
T ss_dssp             EEEESSSC
T ss_pred             EEEEecCC
Confidence            99997763

>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=99.85  E-value=3.7e-21  Score=124.33  Aligned_cols=75  Identities=21%  Similarity=0.245  Sum_probs=63.2

Q ss_pred             CchhHHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC------C------CceEeeeeEEEecCe
Q 034490            1 MLFFSYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK------Y------PHMLSVRNCFIRGSV   66 (93)
Q Consensus         1 m~p~~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~------~------~~~~~~~~~~IRG~~   66 (93)
                      +.|+.+|+.++  |++|.|+|+||+.|.|+|.+||.|||++|+||+++....      .      ...+.+|.+||||++
T Consensus        26 ~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~n  105 (118)
T 1b34_B           26 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDS  105 (118)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGG
T ss_pred             cChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCCE
Confidence            46999999999  599999999999999999999999999999999975211      0      013569999999999


Q ss_pred             EEEEEcCCC
Q 034490           67 VRYVQLPPD   75 (93)
Q Consensus        67 I~~I~~~~~   75 (93)
                      |.+|+.++.
T Consensus       106 Vv~I~~~~~  114 (118)
T 1b34_B          106 VIVVLRNPL  114 (118)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEeCch
Confidence            999998875

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A

Probab=99.80  E-value=1.8e-19  Score=127.46  Aligned_cols=73  Identities=12%  Similarity=0.138  Sum_probs=63.8

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcC----C----CCCceEeeeeEEEecCeEEEEEcCC
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQ----D----KYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~----~----~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      +-.+|++++||+|+|+|+||++|+|+|.+||.||||+|+||+|+..    +    ...+.+.++.+||||+||.+|++++
T Consensus         5 k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isve~   84 (231)
T 3pgw_B            5 KSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEG   84 (231)
T ss_pred             chHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEecC
Confidence            4678999999999999999999999999999999999999999742    1    0113588999999999999999876


Q ss_pred             C
Q 034490           75 D   75 (93)
Q Consensus        75 ~   75 (93)
                      .
T Consensus        85 p   85 (231)
T 3pgw_B           85 P   85 (231)
T ss_pred             C
Confidence            4

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

Probab=99.15  E-value=3.6e-10  Score=69.17  Aligned_cols=63  Identities=25%  Similarity=0.227  Sum_probs=54.4

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEec-cccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVD-QYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPD   75 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D-~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~   75 (93)
                      ..|++++||+|.|.|.||++|+|.|.+|| ...|++|.|+   ..+.     ....++|.|..|..|.+.++
T Consensus        10 ~el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~---~~~~-----~~~~~iI~G~aI~eI~v~~~   73 (86)
T 1y96_A           10 LEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF---LEDG-----SMSVTGIMGHAVQTVETMNE   73 (86)
T ss_dssp             HHHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE---CTTS-----CEEEEEECGGGEEEEEEEEC
T ss_pred             HHHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec---ccCC-----eEEEEEEecceEEEEEEecc
Confidence            47899999999999999999999999999 8999999999   2222     24689999999999976653

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

Probab=97.17  E-value=0.00048  Score=40.70  Aligned_cols=55  Identities=16%  Similarity=0.289  Sum_probs=40.6

Q ss_pred             HHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            5 SYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         5 ~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      .||+.+.  +.+|+|.|.||..++|++.+||.|+=+.-.+        .       ..+|-=..|.+|....
T Consensus        12 ~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL~~~--------~-------~~LIYKhAIsTI~p~~   68 (74)
T 2ylb_A           12 PFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNT--------V-------SQMVYKHAISTVVPSR   68 (74)
T ss_dssp             HHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEESS--------S-------EEEEEGGGEEEEEESS
T ss_pred             HHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEECC--------c-------eEEEEeeeEEEEeEcc
Confidence            4666666  8899999999999999999999998655421        1       2345556777776443

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

Probab=97.14  E-value=0.0078  Score=36.56  Aligned_cols=66  Identities=21%  Similarity=0.331  Sum_probs=52.5

Q ss_pred             hcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCCC-------CceEeeeeEEEecCeEEEEEcCC
Q 034490            9 DLVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDKY-------PHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         9 ~~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~~-------~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      .++|+++.+.-+.+..|+|+|..+|. .--+.|+||..+-.++.       +...-++.+.-||+.|.-+++-+
T Consensus        10 ~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~~   83 (88)
T 2vxe_A           10 PELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVN   83 (88)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEECC
T ss_pred             cccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEEec
Confidence            46899999999999999999999995 56899999998642210       11234578999999999998765

>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=97.12  E-value=0.00098  Score=39.66  Aligned_cols=37  Identities=22%  Similarity=0.344  Sum_probs=32.1

Q ss_pred             HHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEe
Q 034490            5 SYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLE   41 (93)
Q Consensus         5 ~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~   41 (93)
                      .||+.+.  ..+|.|.|.||..++|.+.+||.|+=+.-.
T Consensus        10 ~fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~~   48 (77)
T 1kq1_A           10 KALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNS   48 (77)
T ss_dssp             HHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEE
T ss_pred             HHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEEE
Confidence            4677776  899999999999999999999999866643

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

Probab=97.07  E-value=0.00086  Score=40.02  Aligned_cols=36  Identities=22%  Similarity=0.392  Sum_probs=31.1

Q ss_pred             HHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490            5 SYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         5 ~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L   40 (93)
                      .||+.+.  +.+|+|-|.||..++|.+.+||.|+=+.-
T Consensus        14 ~fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~   51 (78)
T 3ahu_A           14 QFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLE   51 (78)
T ss_dssp             HHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEEE
Confidence            4666666  89999999999999999999999986654

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

Probab=96.99  E-value=0.0088  Score=36.11  Aligned_cols=64  Identities=13%  Similarity=0.207  Sum_probs=51.8

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP   73 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~   73 (93)
                      .+.+|.++.|++|.+.|..+.++.|+..++|. ..|+..++-. +.-      --+++..+|++-|..+++.
T Consensus        20 fLr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TPi------Gv~~eAlLR~~Dii~~sF~   84 (85)
T 1y96_B           20 YLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQ-TPI------GVQAEALLRCSDIISYTFK   84 (85)
T ss_dssp             HHHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEC-CTT------CCEEEEEEEGGGEEEEEEC
T ss_pred             HHHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcC-CCc------ccchhhhhhcCCEEEEEec
Confidence            36788999999999999999999999999995 5587776643 111      1257899999999999874

>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=96.94  E-value=0.0012  Score=39.67  Aligned_cols=36  Identities=25%  Similarity=0.463  Sum_probs=30.6

Q ss_pred             HHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490            5 SYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         5 ~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L   40 (93)
                      .||+.+.  +.+|+|-|.||..++|.+.+||.|+=+.-
T Consensus        10 ~fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~   47 (82)
T 1u1s_A           10 PYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK   47 (82)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEe
Confidence            4566555  88999999999999999999999986653

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

Probab=96.86  E-value=0.0013  Score=39.26  Aligned_cols=56  Identities=18%  Similarity=0.296  Sum_probs=40.1

Q ss_pred             HHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490            5 SYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPD   75 (93)
Q Consensus         5 ~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~   75 (93)
                      .||+.+.  ..+|.|.|.||..++|.+.+||+|+=+. +      .++        ..+|-=..|.+|.....
T Consensus        11 ~fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL-~------~g~--------~qLIYKhAISTI~P~~~   68 (79)
T 3sb2_A           11 PFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL-R------NTV--------TQMVYKHAISTVVPARA   68 (79)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE-E------SSS--------EEEEEGGGEEEEEESSC
T ss_pred             HHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE-E------CCc--------eEEEEeeeEEEEeecCc
Confidence            3555554  6679999999999999999999998665 2      111        12456667888875543

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

Probab=96.78  E-value=0.0031  Score=36.97  Aligned_cols=32  Identities=19%  Similarity=0.290  Sum_probs=28.1

Q ss_pred             CCCEEEEEEcCCcEEEEEEEEeccccceEEee
Q 034490           11 VGREVTVELKNDLAIRGTLHSVDQYLNIKLEN   42 (93)
Q Consensus        11 ~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~   42 (93)
                      .+.+|+|-|.||..++|.+.+||.|+=+.-.+
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   55 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSNYEIMVKVG   55 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceEEEEEeC
Confidence            38899999999999999999999999766543

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

Probab=96.73  E-value=0.0024  Score=41.12  Aligned_cols=55  Identities=25%  Similarity=0.303  Sum_probs=42.0

Q ss_pred             HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEE--eeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            7 FKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKL--ENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         7 L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L--~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      +..++|..|.|+|+||..++|++..+|. -+|+|  ++|...            ..-|+.+.|.-+.+-+
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd~-k~LtL~~~~a~~s------------~~~I~asdI~DLkVl~   63 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFDS-SNSILQLRLANDS------------TKSIVTKDIKDLRILP   63 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEET-TTTEEEEEETTTE------------EEEEEGGGEEEEEECC
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeecC-CeeEEeccccccc------------cceeecccccceeeee
Confidence            3567899999999999999999999984 45666  888321            1268888887776554

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

Probab=96.55  E-value=0.0023  Score=40.07  Aligned_cols=36  Identities=22%  Similarity=0.435  Sum_probs=30.3

Q ss_pred             HHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490            5 SYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         5 ~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L   40 (93)
                      .||+.+.  ..+|.|.|.||..++|++.+||.|+=++-
T Consensus        12 ~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~   49 (104)
T 2y90_A           12 PFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK   49 (104)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE
Confidence            4666666  45999999999999999999999986654

>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=96.51  E-value=0.0094  Score=36.67  Aligned_cols=68  Identities=16%  Similarity=0.288  Sum_probs=52.2

Q ss_pred             HhhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCCC-------CceEeeeeEEEecCeEEEEEcCC
Q 034490            7 FKDLVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDKY-------PHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         7 L~~~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~~-------~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      -..++|+++.+.-+.+..|.|+|..+|. .--+.|+||..+-.++.       +...-++.+.-||+.|.-+.+-+
T Consensus        14 ~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e   89 (95)
T 2fb7_A           14 GTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   89 (95)
T ss_dssp             --CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESC
T ss_pred             cCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEec
Confidence            4578999999999999999999999994 66889999987632110       11234578999999999998754

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

Probab=96.03  E-value=0.013  Score=34.17  Aligned_cols=37  Identities=16%  Similarity=0.051  Sum_probs=31.0

Q ss_pred             hHHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490            4 FSYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         4 ~~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L   40 (93)
                      +..||.++  ..+|.|+|.+|..++|.+.-+|+++=+.-
T Consensus        11 vR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L~   49 (70)
T 3hfo_A           11 VRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLV   49 (70)
T ss_dssp             HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEEE
Confidence            45666666  78999999999999999999999875543

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

Probab=96.02  E-value=0.016  Score=34.83  Aligned_cols=61  Identities=20%  Similarity=0.278  Sum_probs=47.2

Q ss_pred             hhcCCCEEEEEEcCCc-EEEEEEEEeccc-cceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490            8 KDLVGREVTVELKNDL-AIRGTLHSVDQY-LNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP   73 (93)
Q Consensus         8 ~~~~gk~V~V~L~~g~-~~~G~L~~~D~~-mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~   73 (93)
                      .+++|+.|.+..+++. .|+|.|..+|.. -+|.|.++.  .++- +  ....++.+++.-|.-+.+.
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f--~NG~-~--~~s~eVtls~~DI~~L~ii   67 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF--HNGV-K--CLVPEVTFRAGDITELKIL   67 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE--ETTE-E--CSSSEEEEEGGGCSEEEEE
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh--hCCC-C--CCCcEEEEEecChhheEEE
Confidence            4689999999999999 999999999965 589999994  2221 1  2335788999877666543

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

Probab=95.59  E-value=0.021  Score=33.43  Aligned_cols=37  Identities=19%  Similarity=0.182  Sum_probs=31.0

Q ss_pred             hHHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490            4 FSYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKL   40 (93)
Q Consensus         4 ~~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L   40 (93)
                      ++.||.++  ..+|.|+|.+|..++|++.-.|+++=..-
T Consensus        13 vR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L~   51 (72)
T 3hfn_A           13 IRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIA   51 (72)
T ss_dssp             HHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEEE
Confidence            46677776  77899999999999999999999875444

>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=94.77  E-value=0.15  Score=29.15  Aligned_cols=61  Identities=23%  Similarity=0.354  Sum_probs=43.5

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL   72 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   72 (93)
                      .-|..-.|++|-+..-....++|+|..||.-. +.|+|++....++      -..+.++=+.|.+|-+
T Consensus         9 ktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~GNk------~k~liv~idDinWimL   69 (71)
T 1ycy_A            9 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGNR------GKQMLIGLEDINWIML   69 (71)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEEE------EEEEEEEGGGEEEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHhccc------cceeEEEeccceEEEe
Confidence            45777889999999999999999999999864 7789999875432      2355677667766654

>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=90.89  E-value=0.44  Score=33.68  Aligned_cols=34  Identities=24%  Similarity=0.336  Sum_probs=30.6

Q ss_pred             cCCCEEEEEEcCCcEEEEEEEEeccccceEEeeE
Q 034490           10 LVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT   43 (93)
Q Consensus        10 ~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~   43 (93)
                      ..|++|.|.+.++..++|+..++|+.-.|.++..
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            4699999999889999999999999999998753

>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=90.08  E-value=0.29  Score=32.37  Aligned_cols=30  Identities=23%  Similarity=0.322  Sum_probs=25.5

Q ss_pred             HHhhcCCCEEEEEEc----CCcEEEEEEEEeccc
Q 034490            6 YFKDLVGREVTVELK----NDLAIRGTLHSVDQY   35 (93)
Q Consensus         6 ~L~~~~gk~V~V~L~----~g~~~~G~L~~~D~~   35 (93)
                      -+..++|+.|.|+|+    +.+.++|+|.++|..
T Consensus        98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T 1ib8_A           98 AVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED  131 (164)
T ss_dssp             HHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             HHHHhCCcEEEEEEecccCCceEEEEEEEEEeCC
Confidence            356789999999994    459999999999975

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

Probab=87.29  E-value=3.6  Score=25.24  Aligned_cols=62  Identities=15%  Similarity=0.248  Sum_probs=46.3

Q ss_pred             hhcCCCEEEEEEcCCc-EEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490            8 KDLVGREVTVELKNDL-AIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP   73 (93)
Q Consensus         8 ~~~~gk~V~V~L~~g~-~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~   73 (93)
                      ++.+|+.|.|.-.+.- .|+|.+..+|. -++.|.++....-   +-.....++.++..-|..+.+-
T Consensus         8 edwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaFrNGi---plk~~~~EVtLsa~DI~~L~II   70 (103)
T 2rm4_A            8 QDWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAFRNGV---PLRKQNAEVVLKCTDIRSIDLI   70 (103)
T ss_dssp             GGGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEEETTE---ECSCSSSCEEEETTTEEEEEEE
T ss_pred             cceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhhhcCc---CcCCCCceEEEEecchhheeee
Confidence            3689999999999996 99999999995 4499988876321   0002346788888888777653

>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=84.75  E-value=2.6  Score=30.12  Aligned_cols=49  Identities=16%  Similarity=0.245  Sum_probs=34.8

Q ss_pred             hcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEec
Q 034490            9 DLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRG   64 (93)
Q Consensus         9 ~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG   64 (93)
                      ...|++|.|...+ ..++|+..++|+.-.|.+......      +....|++.+|+
T Consensus       270 ~~~g~~V~v~~~~-~~~~G~~~gid~~G~L~v~~~~g~------~~~~~Gev~~r~  318 (321)
T 1bia_A          270 NFINRPVKLIIGD-KEIFGISRGIDKQGALLLEQDGII------KPWMGGEISLRS  318 (321)
T ss_dssp             TTTTSEEEEEETT-EEEEEEEEEECTTSCEEEEETTEE------EEESSCEEEEC-
T ss_pred             hhcCCEEEEEECC-cEEEEEEEEECCCCeEEEEECCCE------EEEEeeeEEEec
Confidence            3469999998765 579999999999999998643211      123346777764

>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=83.88  E-value=1  Score=30.98  Aligned_cols=48  Identities=15%  Similarity=0.129  Sum_probs=33.9

Q ss_pred             hcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEec
Q 034490            9 DLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRG   64 (93)
Q Consensus         9 ~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG   64 (93)
                      ...|++|.+...++  ++|+..++|+.-.|.+......      +....|++.+|+
T Consensus       185 ~~~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~~G~------~~~~~Gev~~r~  232 (233)
T 2eay_A          185 LYLGEEVKLLGEGK--ITGKLVGLSEKGGALILTEEGI------KEILSGEFSLRR  232 (233)
T ss_dssp             TTTTSEEEETTEEE--EEEEEEEECTTSCEEEEETTEE------EEECSCCEEEC-
T ss_pred             cccCCEEEEEECCe--EEEEEEEECCCCeEEEEECCCe------EEEEEeEEEEec
Confidence            34699999987665  9999999999999999643211      113346777764

>2e12_A SM-like motif, hypothetical protein XCC3642; novel SM-like motif, LSM motif, X- RAY crystallography, translation; 1.70A {Xanthomonas campestris PV}

Probab=81.62  E-value=1.5  Score=26.56  Aligned_cols=19  Identities=32%  Similarity=0.478  Sum_probs=16.9

Q ss_pred             CCEEEEEEcCCcEEEEEEE
Q 034490           12 GREVTVELKNDLAIRGTLH   30 (93)
Q Consensus        12 gk~V~V~L~~g~~~~G~L~   30 (93)
                      ..+|.++|.||+.+.||+.
T Consensus        28 q~~v~i~l~DGs~l~GTva   46 (101)
T 2e12_A           28 QERVRIELDDGSMIAGTVA   46 (101)
T ss_dssp             TCEEEEEETTSCEEEEEES
T ss_pred             eeEEEEEEcCCCeEeeeec
Confidence            4689999999999999974

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

Probab=81.49  E-value=3.1  Score=28.55  Aligned_cols=32  Identities=22%  Similarity=0.310  Sum_probs=28.5

Q ss_pred             cCCCEEEEEEcCCcEEEEEEEEeccccceEEee
Q 034490           10 LVGREVTVELKNDLAIRGTLHSVDQYLNIKLEN   42 (93)
Q Consensus        10 ~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~   42 (93)
                      ..|++|.|...++..++|+..++|+.-.|. .+
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            479999999988877999999999999998 53

---

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	93
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	7e-23
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	4e-19
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	2e-18
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	4e-16
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-15
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	3e-15
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	5e-15
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	6e-15
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	2e-14
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	5e-14
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	4e-09
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	6e-06
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	0.004

>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 = 82.8 bits (205), Expect = 7e-23
 Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 3  FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFI 62
          F +   +L+GREV V L N    +G LH+VD  LNI L N      +K+  +      FI
Sbjct: 1  FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRV------FI 54

Query: 63 RGSVVRYVQLPPDGVDVDLL 82
              + ++      +D+   
Sbjct: 55 MYRYIVHIDSTERRIDMREF 74

>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 = 72.4 bits (178), Expect = 4e-19
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 6  YFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGS 65
          +   L    VT+ELKN   + GT+  VD  +N  L+  ++  +++ P  L      IRG+
Sbjct: 5  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQL--ETLSIRGN 62

Query: 66 VVRYVQLPPDGVDVDLL 82
           +RY  L PD + +D L
Sbjct: 63 NIRYFIL-PDSLPLDTL 78

>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 = 70.2 bits (172), Expect = 2e-18
 Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 2/66 (3%)

Query: 8  KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVV 67
           +  G  VT E       RG L   +  +N ++ N  +    +   +  +   +IRG  +
Sbjct: 8  HEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSN--ITVTYRDGRVAQLEQVYIRGCKI 65

Query: 68 RYVQLP 73
          R++ LP
Sbjct: 66 RFLILP 71

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 64.0 bits (156), Expect = 4e-16
 Identities = 24/69 (34%), Positives = 31/69 (44%), Gaps = 3/69 (4%)

Query: 8  KDLVGREVTVELK-NDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSV 66
          K LV   V V+LK N    RGTL S D Y N++L              L     FIR + 
Sbjct: 2  KGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLG--EIFIRCNN 59

Query: 67 VRYVQLPPD 75
          V Y++  P+
Sbjct: 60 VLYIRELPN 68

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

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

 Score = 62.4 bits (152), Expect = 2e-15
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 8  KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT-RVVDQDKYPHMLSVRNCFIRGSV 66
          +D +G++V V+L++   IRG L S DQ++N+ LE+   ++D + Y          +RG  
Sbjct: 8  QDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGT----MVVRGEN 63

Query: 67 VRYVQLPP 74
          V ++   P
Sbjct: 64 VLFISPVP 71

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

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

 Score = 62.0 bits (151), Expect = 3e-15
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 2/67 (2%)

Query: 4  FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIR 63
               + +   V V+LK +  +RG L S DQ++N+ L +    +         +    IR
Sbjct: 9  HKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSD--SEEIQSDGSGKKLGTIVIR 66

Query: 64 GSVVRYV 70
          G  V  +
Sbjct: 67 GDNVILI 73

>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 = 61.6 bits (150), Expect = 5e-15
 Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 2/67 (2%)

Query: 4  FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIR 63
                 +   V V LK     RGTL   D ++N+ L +   +   +    +   +  IR
Sbjct: 5  LDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVG--SVVIR 62

Query: 64 GSVVRYV 70
          G  V +V
Sbjct: 63 GDTVVFV 69

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score = 61.3 bits (149), Expect = 6e-15
 Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 4  FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIR 63
               + +   V ++LK D   RG L S D ++N+ L +   ++  +    L      IR
Sbjct: 8  LDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLG--TVLIR 65

Query: 64 GSVVRYV 70
          G  + Y+
Sbjct: 66 GDNIVYI 72

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71

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

 Score = 59.7 bits (145), Expect = 2e-14
 Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 2/67 (2%)

Query: 4  FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIR 63
                 + ++V V LK     RG L   D +LN+ L +  ++   +           IR
Sbjct: 4  LDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYG--KIVIR 61

Query: 64 GSVVRYV 70
          G  V  +
Sbjct: 62 GDNVLAI 68

>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 = 59.0 bits (143), Expect = 5e-14
 Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 3/65 (4%)

Query: 8  KDLVGREVTVELKND-LAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSV 66
          K +VG+ + VE+K +   + G L  VD Y+N+ L N   ++      + S+    +RG+ 
Sbjct: 11 KSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTN--AMECKGEEKVRSLGEIVLRGNN 68

Query: 67 VRYVQ 71
          V  +Q
Sbjct: 69 VVLIQ 73

>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 = 47.2 bits (112), Expect = 4e-09
 Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 13/83 (15%)

Query: 1  MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT--RVVDQDKYPHMLSVR 58
          +L  +     +G  + V +K D    G L   D+Y+N+ L++        D+       +
Sbjct: 4  ILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNK 63

Query: 59 N-----------CFIRGSVVRYV 70
                        + G+ V  +
Sbjct: 64 KLKRVMVNRLETILLSGNNVAML 86

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

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

 Score = 38.6 bits (90), Expect = 6e-06
 Identities = 7/39 (17%), Positives = 17/39 (43%)

Query: 5  SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT 43
          S     +   +   L++     GT  + D+++N+ L + 
Sbjct: 1  SKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDC 39

>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 = 31.4 bits (71), Expect = 0.004
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 12/75 (16%)

Query: 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENT--RVVDQDKYPHMLSVRN---------- 59
            +V +  +N+  + G + + D++ N+ LEN      +  K                   
Sbjct: 14 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISK 73

Query: 60 CFIRGSVVRYVQLPP 74
           F+RG  V  V   P
Sbjct: 74 MFLRGDSVIVVLRNP 88

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	93
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.95
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.94
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.92
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.91
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.91
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.91
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.91
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.9
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.9
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.9
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.86
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.8
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.8
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	97.23
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	96.71
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	96.39
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	96.12
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	95.07
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	93.11
d2grea1	113	Deblocking aminopeptidase YhfE {Bacillus cereus [T	80.27

>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=99.95  E-value=2.7e-27  Score=140.11  Aligned_cols=71  Identities=24%  Similarity=0.421  Sum_probs=66.9

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      +|+.+|++++|++|+|+|+||++|+|+|.+||.|||++|+||+++..++.  ..+++.+||||++|+||++||
T Consensus         2 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~--~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           2 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR--VAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSC--EEEEEEEEECGGGEEEEEECC
T ss_pred             CchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCc--EeEcCeEEEECCEEEEEEcCC
Confidence            69999999999999999999999999999999999999999999987765  367899999999999999996

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

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

Probab=99.94  E-value=2.1e-26  Score=138.81  Aligned_cols=73  Identities=29%  Similarity=0.499  Sum_probs=68.0

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCc
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGV   77 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~   77 (93)
                      .++||+++.|++|+|+|+||.+|+|+|.++|.|||++|+||+++.+++..  .+++.+||||++|+||++|+++-
T Consensus         2 lv~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~--~~~~~v~IRG~~Ir~i~lPd~l~   74 (80)
T d1b34a_           2 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREP--VQLETLSIRGNNIRYFILPDSLP   74 (80)
T ss_dssp             HHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCC--EEEEEEEECGGGEEEEECCTTCC
T ss_pred             HHHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCE--EEcccEEEcCCEEEEEECCCCcc
Confidence            57999999999999999999999999999999999999999999887764  68999999999999999998763

>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=99.92  E-value=7.5e-25  Score=128.93  Aligned_cols=69  Identities=22%  Similarity=0.302  Sum_probs=64.1

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL   72 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   72 (93)
                      .|+.+|++++|++|+|+|+||++|+|+|.+||+|||++|+||++..++..  ..+++.+||||++|+||+.
T Consensus         2 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           2 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEV--VKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEEE
T ss_pred             CchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCc--EeEcCcEEEECCeEEEEeC
Confidence            59999999999999999999999999999999999999999999876554  4789999999999999973

>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=99.91  E-value=1.1e-24  Score=128.64  Aligned_cols=68  Identities=25%  Similarity=0.349  Sum_probs=63.7

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      .|+.+|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..+..  ..+++.+||||++|.||+
T Consensus         3 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~~g~~~IRG~~I~~Is   70 (72)
T d1i4k1_           3 RPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEV--VRKVGSVVIRGDTVVFVS   70 (72)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSE--EEEEEEEEECGGGEEEEE
T ss_pred             ChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCe--EeEcceEEEeCCeEEEEE
Confidence            58999999999999999999999999999999999999999999976654  478999999999999997

>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=99.91  E-value=1e-24  Score=129.84  Aligned_cols=70  Identities=29%  Similarity=0.446  Sum_probs=64.1

Q ss_pred             CchhHHHhhcCCCEEEEEEcCC-cEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490            1 MLFFSYFKDLVGREVTVELKND-LAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL   72 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g-~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   72 (93)
                      ++|+.+|++++|++|+|+|++| ++|.|+|.+||+|||++|+||+++..+..  ..+++.+||||++|+||+.
T Consensus         4 ~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           4 VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEK--VRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEEE
T ss_pred             cccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCc--EeEcceEEEeCCEEEEEEC
Confidence            5799999999999999999976 79999999999999999999999876654  4789999999999999983

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=99.91  E-value=1.5e-24  Score=128.69  Aligned_cols=68  Identities=22%  Similarity=0.392  Sum_probs=63.6

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490            2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      .|+++|++++||+|.|+|+||++|+|+|.+||+|||++|+||+++..+..  ...++.+||||++|+||+
T Consensus         6 ~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~--~~~~~~~~IRG~~I~~I~   73 (74)
T d1mgqa_           6 RPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEV--TRRLGTVLIRGDNIVYIS   73 (74)
T ss_dssp             CTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEE
T ss_pred             CcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCe--EeEcceEEEeCCEEEEEe
Confidence            49999999999999999999999999999999999999999999877654  378899999999999996

>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=99.91  E-value=3.7e-24  Score=126.21  Aligned_cols=68  Identities=26%  Similarity=0.441  Sum_probs=62.3

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP   73 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~   73 (93)
                      +-++|++++||+|+|+|+||++|+|+|.+||+|||++|+||+++..++   .++++.+||||++|+||+.+
T Consensus         3 ~~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~~---~~~~g~v~iRG~~I~~I~~~   70 (71)
T d1i8fa_           3 LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN---VYKRGTMVVRGENVLFISPV   70 (71)
T ss_dssp             HHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETTE---EEEEEEEEECGGGEEEEEEC
T ss_pred             HhHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECCC---EEEcceEEEeCCeEEEEeCC
Confidence            458999999999999999999999999999999999999999987653   36789999999999999855

>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=99.90  E-value=7.7e-24  Score=136.97  Aligned_cols=80  Identities=28%  Similarity=0.415  Sum_probs=72.1

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchhhh
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDLL   82 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~~~   82 (93)
                      .+++|++++|++|.|+|+||++|+|+|.+||++||++|+||++...+      .++.++|||++|+||++|++.+|+.++
T Consensus         1 f~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~~~------k~~~v~IRG~~I~~I~~~e~~iD~re~   74 (127)
T d1m5q1_           1 FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGE------KFNRVFIMYRYIVHIDSTERRIDMREF   74 (127)
T ss_dssp             CHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETTCC------EEEEEEECGGGEEEEEECSCCCCHHHH
T ss_pred             ChhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECCCC------cccEEEEeCCeEEEEEcchhhcCHHHH
Confidence            36899999999999999999999999999999999999999987654      357899999999999999999999999


Q ss_pred             hHhhhh
Q 034490           83 HDATRR   88 (93)
Q Consensus        83 ~~~~~~   88 (93)
                      +..-.+
T Consensus        75 a~~~~k   80 (127)
T d1m5q1_          75 AKQAEK   80 (127)
T ss_dssp             HHHHHH
T ss_pred             HHHHhh
Confidence            765543

>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=99.90  E-value=1.2e-23  Score=125.28  Aligned_cols=68  Identities=25%  Similarity=0.335  Sum_probs=63.5

Q ss_pred             hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490            3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL   72 (93)
Q Consensus         3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   72 (93)
                      |..+|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..+..  ...++.+||||++|++|+.
T Consensus         8 ~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~~~~v~iRG~~I~~I~~   75 (76)
T d1th7a1           8 AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGS--GKKLGTIVIRGDNVILISP   75 (76)
T ss_dssp             HHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSC--EEEEEEEEECGGGEEEEEE
T ss_pred             HHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCc--ccCcceEEEECCEEEEEEe
Confidence            7899999999999999999999999999999999999999999887665  3789999999999999973

>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=99.90  E-value=5.7e-24  Score=124.46  Aligned_cols=66  Identities=36%  Similarity=0.522  Sum_probs=58.7

Q ss_pred             HhhcCCCEEEEEEc-CCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE-cCC
Q 034490            7 FKDLVGREVTVELK-NDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ-LPP   74 (93)
Q Consensus         7 L~~~~gk~V~V~L~-~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~-~~~   74 (93)
                      |++++|++|.|+|+ +|++|+|+|.+||+|||++|+||+++..+..  ..+++.+||||++|+||+ +||
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~lg~~~IRG~nI~~I~~~pd   68 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVS--HGTLGEIFIRCNNVLYIRELPN   68 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEE--EEECCSEEECGGGEEEEEECCC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCc--ccCcCeEEEECCEEEEEEeCCC
Confidence            67899999999999 5678999999999999999999999876554  468999999999999997 554

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

Probab=99.86  E-value=2e-22  Score=123.65  Aligned_cols=71  Identities=18%  Similarity=0.351  Sum_probs=62.0

Q ss_pred             CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC-------------CCceEeeeeEEEecCeE
Q 034490            1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK-------------YPHMLSVRNCFIRGSVV   67 (93)
Q Consensus         1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~-------------~~~~~~~~~~~IRG~~I   67 (93)
                      |+|+.+|++++||+|+|.|+||++|.|+|.+||.|||++|+||.|+....             ....+.+|.+||||++|
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            68999999999999999999999999999999999999999999963210             11135689999999999


Q ss_pred             EEEE
Q 034490           68 RYVQ   71 (93)
Q Consensus        68 ~~I~   71 (93)
                      .+|+
T Consensus        84 v~I~   87 (92)
T d2fwka1          84 AMLV   87 (92)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9998

>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=99.80  E-value=9.4e-20  Score=112.04  Aligned_cols=73  Identities=22%  Similarity=0.279  Sum_probs=61.4

Q ss_pred             hhHHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC------------CCceEeeeeEEEecCeEE
Q 034490            3 FFSYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK------------YPHMLSVRNCFIRGSVVR   68 (93)
Q Consensus         3 p~~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~------------~~~~~~~~~~~IRG~~I~   68 (93)
                      |+.+|..++  +++|.|.|++|+.+.|+|.+||.|||++|+||+|+....            ....+.+|.+||||+||.
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            889999998  999999999999999999999999999999999963210            012367999999999999


Q ss_pred             EEEcCCC
Q 034490           69 YVQLPPD   75 (93)
Q Consensus        69 ~I~~~~~   75 (93)
                      +|..++.
T Consensus        83 ~I~~~p~   89 (93)
T d1b34b_          83 VVLRNPL   89 (93)
T ss_dssp             EEEECCC
T ss_pred             EEEcChh
Confidence            9987763

>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=99.80  E-value=1.3e-19  Score=108.65  Aligned_cols=67  Identities=13%  Similarity=0.192  Sum_probs=57.6

Q ss_pred             HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcC-----CC---CCceEeeeeEEEecCeEEEEEcC
Q 034490            7 FKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQ-----DK---YPHMLSVRNCFIRGSVVRYVQLP   73 (93)
Q Consensus         7 L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~-----~~---~~~~~~~~~~~IRG~~I~~I~~~   73 (93)
                      |.+++|++|+|.|+||+.+.|+|.+||.||||+|+||+|+..     ..   ....+.+|.++|||++|.+|++.
T Consensus         3 L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           3 MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEcc
Confidence            678999999999999999999999999999999999999631     11   11247899999999999999864

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

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

Probab=97.23  E-value=0.003  Score=36.36  Aligned_cols=65  Identities=17%  Similarity=0.324  Sum_probs=51.8

Q ss_pred             cCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCC-C------CceEeeeeEEEecCeEEEEEcCC
Q 034490           10 LVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDK-Y------PHMLSVRNCFIRGSVVRYVQLPP   74 (93)
Q Consensus        10 ~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~-~------~~~~~~~~~~IRG~~I~~I~~~~   74 (93)
                      ++|+++.+.-+.+.-|+|+|..+|. .--+.|+||...-.++ .      +...-++.+.-||+.|.-+.+.+
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e   74 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   74 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESS
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEecc
Confidence            6899999999999999999999996 4468999999873211 0      11235688999999999998765

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

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

Probab=96.71  E-value=0.0021  Score=35.12  Aligned_cols=33  Identities=24%  Similarity=0.372  Sum_probs=29.0

Q ss_pred             CCEEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q 034490           12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENTR   44 (93)
Q Consensus        12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~   44 (93)
                      ..+|+|-|.||-.++|.+.+||.|.=+...+..
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            789999999999999999999999877765543

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

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

Probab=96.39  E-value=0.0022  Score=35.66  Aligned_cols=28  Identities=25%  Similarity=0.465  Sum_probs=25.5

Q ss_pred             CCEEEEEEcCCcEEEEEEEEeccccceE
Q 034490           12 GREVTVELKNDLAIRGTLHSVDQYLNIK   39 (93)
Q Consensus        12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~   39 (93)
                      ..+|+|-|.||-.++|.+.+||.|.=+.
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvLL   41 (66)
T d1u1sa1          14 RVPVSIYLVNGIKLQGQIESFDQFVILL   41 (66)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             CCcEEEEEEcCcEEEEEEEEEcceEEEE
Confidence            7899999999999999999999997643

>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=96.12  E-value=0.011  Score=30.36  Aligned_cols=47  Identities=19%  Similarity=0.254  Sum_probs=34.2

Q ss_pred             cCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEe
Q 034490           10 LVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIR   63 (93)
Q Consensus        10 ~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IR   63 (93)
                      ++||+|+|..- +.+++|+-.++|+.-.|.|+......      ...-|++.+|
T Consensus         1 f~gk~V~v~~g-~~~i~G~a~gId~~G~Lll~t~~g~~------~~~sGEVSlR   47 (47)
T d1biaa2           1 FINRPVKLIIG-DKEIFGISRGIDKQGALLLEQDGIIK------PWMGGEISLR   47 (47)
T ss_dssp             TTTSEEEEEET-TEEEEEEEEEECTTSCEEEEETTEEE------EESSCEEEEC
T ss_pred             CCCCEEEEEEC-CeEEEEEEeeECCCCcEEEEECCCEE------EEEEEEEEeC
Confidence            57999999765 47899999999999999997432211      2334666665

>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=95.07  E-value=0.051  Score=29.37  Aligned_cols=60  Identities=22%  Similarity=0.338  Sum_probs=42.2

Q ss_pred             HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490            5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ   71 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~   71 (93)
                      ..|..-.|++|-|.......++|+|..||.-. +.|+|++....++      -..++++=+.|.+|.
T Consensus         5 ktL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~GNk------~k~llv~idD~nWim   64 (66)
T d1ycya1           5 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGNR------GKQMLIGLEDINWIM   64 (66)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEEE------EEEEEEEGGGEEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHhccc------cceeEEEeccceeEE
Confidence            35677889999999999999999999999864 7789999875432      234566666666654

>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=93.11  E-value=0.05  Score=29.97  Aligned_cols=32  Identities=22%  Similarity=0.272  Sum_probs=26.5

Q ss_pred             HHHhhcCCCEEEEEEcC---C-cEEEEEEEEecccc
Q 034490            5 SYFKDLVGREVTVELKN---D-LAIRGTLHSVDQYL   36 (93)
Q Consensus         5 ~~L~~~~gk~V~V~L~~---g-~~~~G~L~~~D~~m   36 (93)
                      .-++.++|+.|.|+|+.   | +.++|+|.++|+..
T Consensus         7 ~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~   42 (74)
T d1ib8a1           7 DAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE   42 (74)
T ss_dssp             HHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE
T ss_pred             HHHHHhCCCEEEEEEecccCCceEEEEEEEeecCCe
Confidence            34678899999999973   4 89999999999753

>d2grea1 b.49.3.1 (A:74-186) Deblocking aminopeptidase YhfE {Bacillus cereus [TaxId: 1396]}

class: All beta proteins
fold: Domain of alpha and beta subunits of F1 ATP synthase-like
superfamily: Aminopeptidase/glucanase lid domain
family: Aminopeptidase/glucanase lid domain
domain: Deblocking aminopeptidase YhfE
species: Bacillus cereus [TaxId: 1396]

Probab=80.27  E-value=0.91  Score=26.63  Aligned_cols=24  Identities=17%  Similarity=0.253  Sum_probs=20.8

Q ss_pred             hhcCCCEEEEEEcCCcEEEEEEEE
Q 034490            8 KDLVGREVTVELKNDLAIRGTLHS   31 (93)
Q Consensus         8 ~~~~gk~V~V~L~~g~~~~G~L~~   31 (93)
                      +.+.|++|+|..++|..|.|++-.
T Consensus        24 ~~l~gq~V~I~t~~G~~i~Gvig~   47 (113)
T d2grea1          24 NSVEGEYCEIETSSGKTYTGTILM   47 (113)
T ss_dssp             GGTTTCEEEEECTTSCEEEEEEEC
T ss_pred             hhcccCEEEEEcCCCCEEEEEEec
Confidence            457899999999999999999743