Citrus Sinensis ID: 032889

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
Protein Sequence
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA
Secondary Structure (PSIPRED)
cccEEEEcEEEEEEEEEccccccHHHHHHHHHcccccccccHHHHHcccEEEEEEcccEEEEEEEEEEccccccccccEEEEEccccccccccccEEEEEEEEEEcccEEEEEEccccEEccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEEEEEEEcccEEEccccHHHHHccccccHHHHHHHHHHcccEEEEcHHHEEEEEEEEEEcccccEEEEEEEEHHcccccccccccccccEEEEEEEccEEEEEEcccccccccccccccccc
Coil and Loop (DISEMBL)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVqvkltggrqvtgtlKGYDQLLNLVLDEAVEFLrdaddplkttdqtrqLGLIVCRGTAVmlvsptdgtdeianpfmqpdga
Flexible Loop (DISEMBL)
MQAFVEINAVSFFIVCRSARVSFNLGflkslkmsgrKETVLDLAkfvdkgvqvkltggrqvtgtlkgYDQLLNLVLDEAVEFLRdaddplkttdqtrqlglivCRGTAVMLVsptdgtdeianpfmqpdga
Low Complexity Region (SEG)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA
Disordered region (IsUnstruct)
***FVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVS******************
Disordered Region (DISOPRED)
**AFVEINAVSFFIVCRSARVSF**********************FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD*********QTRQLGLIVCRGTAVMLVSPTDGTDEIAN*FM*****
Disordered Region (DISEMBL)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA
Disordered Region (DISPRO)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFM*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA
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	131	2.2.26 [Sep-21-2011]
Q9UK45	103	U6 snRNA-associated Sm-li	yes	no	0.763	0.970	0.55	4e-28
Q9CQQ8	103	U6 snRNA-associated Sm-li	yes	no	0.732	0.932	0.562	1e-27
Q54HF6	97	Probable U6 snRNA-associa	yes	no	0.687	0.927	0.6	1e-27
O74499	113	U6 snRNA-associated Sm-li	yes	no	0.694	0.805	0.543	1e-23
P53905	115	U6 snRNA-associated Sm-li	yes	no	0.641	0.730	0.482	3e-17
Q9N4G9	77	Probable small nuclear ri	no	no	0.511	0.870	0.373	5e-10
P62309	76	Small nuclear ribonucleop	no	no	0.488	0.842	0.388	7e-10
P62308	76	Small nuclear ribonucleop	no	no	0.488	0.842	0.388	7e-10
Q3ZBL0	76	Small nuclear ribonucleop	no	no	0.488	0.842	0.388	7e-10
A8MWD9	76	Small nuclear ribonucleop	no	no	0.488	0.842	0.375	4e-09

>sp|Q9UK45|LSM7_HUMAN U6 snRNA-associated Sm-like protein LSm7 OS=Homo sapiens GN=LSM7 PE=1 SV=1

 Score =  123 bits (308), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 55/100 (55%), Positives = 76/100 (76%)

Query: 32  KMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLK 91
           K   +KE++LDL+K++DK ++VK  GGR+ +G LKG+D LLNLVLD  +E++RD DD  K
Sbjct: 4   KEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDPDDQYK 63

Query: 92  TTDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA 131
            T+ TRQLGL+VCRGT+V+L+ P DG + I NPF+Q   A
Sbjct: 64  LTEDTRQLGLVVCRGTSVVLICPQDGMEAIPNPFIQQQDA 103

Binds specifically to the 3'-terminal U-tract of U6 snRNA.
Homo sapiens (taxid: 9606)

>sp|Q9CQQ8|LSM7_MOUSE U6 snRNA-associated Sm-like protein LSm7 OS=Mus musculus GN=Lsm7 PE=3 SV=1

 Score =  121 bits (304), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 54/96 (56%), Positives = 75/96 (78%)

Query: 32  KMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLK 91
           K   +KE++LDL+K++DK ++VK  GGR+ +G LKG+D LLNLVLD  +E++RD DD  K
Sbjct: 4   KEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTMEYMRDPDDQYK 63

Query: 92  TTDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQ 127
            T+ TRQLGL+VCRGT+V+L+ P DG + I NPF+Q
Sbjct: 64  LTEDTRQLGLVVCRGTSVVLICPQDGMEAIPNPFVQ 99

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

Mus musculus (taxid: 10090)

>sp|Q54HF6|LSM7_DICDI Probable U6 snRNA-associated Sm-like protein LSm7 OS=Dictyostelium discoideum GN=lsm7 PE=3 SV=1

 Score =  121 bits (304), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 54/90 (60%), Positives = 73/90 (81%)

Query: 36  RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
           +KE++LDL KF+ K + VK TGGR+V G LKGYDQL+N+ LD+  EF+RDA+DPL TTD+
Sbjct: 8   KKESILDLQKFLGKEICVKFTGGREVQGILKGYDQLVNITLDQTQEFIRDAEDPLITTDE 67

Query: 96  TRQLGLIVCRGTAVMLVSPTDGTDEIANPF 125
            R LGL+VCRG++VM+V PT+G + I NP+
Sbjct: 68  KRFLGLVVCRGSSVMMVCPTEGCEPIDNPY 97

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

Dictyostelium discoideum (taxid: 44689)

>sp|O74499|LSM7_SCHPO U6 snRNA-associated Sm-like protein LSm7 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm7 PE=1 SV=1

 Score =  107 bits (268), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/92 (54%), Positives = 72/92 (78%), Gaps = 1/92 (1%)

Query: 36  RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
           RKE++LDL+++ D+ +Q   TGGRQ+TG LKG+DQL+NLVLD+  E LR+ +D  K T  
Sbjct: 21  RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPED-GKLTGA 79

Query: 96  TRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQ 127
            R+LGL+V RGT ++L++P DG++EI NPF+Q
Sbjct: 80  IRKLGLVVVRGTTLVLIAPMDGSEEIPNPFVQ 111

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner.

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

>sp|P53905|LSM7_YEAST U6 snRNA-associated Sm-like protein LSm7 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM7 PE=1 SV=2

 Score = 87.0 bits (214), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 42/87 (48%), Positives = 61/87 (70%), Gaps = 3/87 (3%)

Query: 36  RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT--- 92
           ++E +LDLAK+ D  ++VKL GG+ V G LKGYDQL+NLVLD+ VE++ + DD   T   
Sbjct: 23  KREAILDLAKYKDSKIRVKLMGGKLVIGVLKGYDQLMNLVLDDTVEYMSNPDDENNTELI 82

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTDGTD 119
           +   R+LGL V RGT ++ +S  +G+D
Sbjct: 83  SKNARKLGLTVIRGTILVSLSSAEGSD 109

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. LSM7 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. LSM7, 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.

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

>sp|Q9N4G9|RUXG_CAEEL Probable small nuclear ribonucleoprotein G OS=Caenorhabditis elegans GN=snr-7 PE=3 SV=1

 Score = 62.8 bits (151), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 49/75 (65%), Gaps = 8/75 (10%)

Query: 42  DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
           +L K++DK + +KL G R+V+G L+G+D  +N+V+DEAVE+ +D          +  LG+
Sbjct: 8   ELKKYMDKEMDLKLNGNRRVSGILRGFDPFMNMVIDEAVEYQKDGG--------SVNLGM 59

Query: 102 IVCRGTAVMLVSPTD 116
            V RG +V+++ P +
Sbjct: 60  TVIRGNSVVIMEPKE 74

Associated with snRNP U1, U2, U4/U6 and U5.

Caenorhabditis elegans (taxid: 6239)

>sp|P62309|RUXG_MOUSE Small nuclear ribonucleoprotein G OS=Mus musculus GN=Snrpg PE=1 SV=1

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 46/72 (63%), Gaps = 8/72 (11%)

Query: 42  DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
           +L KF+DK + +KL GGR V G L+G+D  +NLV+DE VE        + T+ Q   +G+
Sbjct: 8   ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVE--------MATSGQQNNIGM 59

Query: 102 IVCRGTAVMLVS 113
           +V RG +++++ 
Sbjct: 60  VVIRGNSIIMLE 71

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5.

Mus musculus (taxid: 10090)

>sp|P62308|RUXG_HUMAN Small nuclear ribonucleoprotein G OS=Homo sapiens GN=SNRPG PE=1 SV=1

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 46/72 (63%), Gaps = 8/72 (11%)

Query: 42  DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
           +L KF+DK + +KL GGR V G L+G+D  +NLV+DE VE        + T+ Q   +G+
Sbjct: 8   ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVE--------MATSGQQNNIGM 59

Query: 102 IVCRGTAVMLVS 113
           +V RG +++++ 
Sbjct: 60  VVIRGNSIIMLE 71

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5.

Homo sapiens (taxid: 9606)

>sp|Q3ZBL0|RUXG_BOVIN Small nuclear ribonucleoprotein G OS=Bos taurus GN=SNRPG PE=3 SV=1

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 46/72 (63%), Gaps = 8/72 (11%)

Query: 42  DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
           +L KF+DK + +KL GGR V G L+G+D  +NLV+DE VE        + T+ Q   +G+
Sbjct: 8   ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVE--------MATSGQQNNIGM 59

Query: 102 IVCRGTAVMLVS 113
           +V RG +++++ 
Sbjct: 60  VVIRGNSIIMLE 71

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5.

Bos taurus (taxid: 9913)

>sp|A8MWD9|RUXGL_HUMAN Small nuclear ribonucleoprotein G-like protein OS=Homo sapiens PE=2 SV=2

 Score = 60.1 bits (144), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 8/72 (11%)

Query: 42  DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
           +L KF DK   +KL GGR V G L+G+D  +NLV+DE VE        + T+ Q + +G+
Sbjct: 8   ELKKFTDKKFSLKLNGGRHVQGILRGFDPFMNLVIDECVE--------MATSGQQKNIGM 59

Query: 102 IVCRGTAVMLVS 113
           +  RG +++++ 
Sbjct: 60  VEIRGNSIIMLE 71

Associated with snRNP U1, U2, U4/U6 and U5.

Homo sapiens (taxid: 9606)

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	131
224059650	99	predicted protein [Populus trichocarpa]	0.755	1.0	0.979	3e-48
351720779	99	uncharacterized protein LOC100306498 [Gl	0.755	1.0	0.969	8e-48
388507056	99	unknown [Medicago truncatula]	0.755	1.0	0.969	1e-47
356512406	99	PREDICTED: U6 snRNA-associated Sm-like p	0.755	1.0	0.959	3e-47
359487263	99	PREDICTED: U6 snRNA-associated Sm-like p	0.755	1.0	0.959	5e-47
449463763	99	PREDICTED: U6 snRNA-associated Sm-like p	0.755	1.0	0.959	7e-47
297736225	107	unnamed protein product [Vitis vinifera]	0.786	0.962	0.922	2e-46
255544228	99	conserved hypothetical protein [Ricinus	0.755	1.0	0.949	2e-46
388499482	99	unknown [Lotus japonicus]	0.755	1.0	0.949	3e-46
297814702	99	hypothetical protein ARALYDRAFT_484298 [	0.740	0.979	0.927	1e-44

>gi|224059650|ref|XP_002299952.1| predicted protein [Populus trichocarpa] gi|224104033|ref|XP_002313290.1| predicted protein [Populus trichocarpa] gi|118483640|gb|ABK93714.1| unknown [Populus trichocarpa] gi|222847210|gb|EEE84757.1| predicted protein [Populus trichocarpa] gi|222849698|gb|EEE87245.1| predicted protein [Populus trichocarpa]

 Score =  196 bits (497), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 97/99 (97%), Positives = 99/99 (100%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT
Sbjct: 1   MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 60

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA 131
           TDQTR+LGLIVCRGTAVMLVSPTDGTDEIANPF+QPDGA
Sbjct: 61  TDQTRRLGLIVCRGTAVMLVSPTDGTDEIANPFVQPDGA 99

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351720779|ref|NP_001235908.1| uncharacterized protein LOC100306498 [Glycine max] gi|255628715|gb|ACU14702.1| unknown [Glycine max]

 Score =  194 bits (494), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 96/99 (96%), Positives = 97/99 (97%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD DDPLKT
Sbjct: 1   MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDPDDPLKT 60

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA 131
           TDQTR LGLIVCRGTAVMLVSPTDGTDEIANPFMQPDG+
Sbjct: 61  TDQTRNLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGS 99

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388507056|gb|AFK41594.1| unknown [Medicago truncatula]

 Score =  194 bits (493), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 96/99 (96%), Positives = 97/99 (97%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD DDPLKT
Sbjct: 1   MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDPDDPLKT 60

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA 131
           TDQTR LGLIVCRGTAVMLVSPTDGTDEIANPF+QPDGA
Sbjct: 61  TDQTRSLGLIVCRGTAVMLVSPTDGTDEIANPFLQPDGA 99

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512406|ref|XP_003524910.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like [Glycine max]

 Score =  192 bits (489), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 95/99 (95%), Positives = 97/99 (97%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD DDPLKT
Sbjct: 1   MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDPDDPLKT 60

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA 131
           TDQTR LGLIVCRGTAVMLVSPTDGTDEIANPF+QPDG+
Sbjct: 61  TDQTRNLGLIVCRGTAVMLVSPTDGTDEIANPFIQPDGS 99

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487263|ref|XP_003633551.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 1 [Vitis vinifera] gi|359487265|ref|XP_003633552.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 2 [Vitis vinifera] gi|359487267|ref|XP_003633553.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 3 [Vitis vinifera] gi|359487269|ref|XP_003633554.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 4 [Vitis vinifera]

 Score =  192 bits (487), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 95/99 (95%), Positives = 97/99 (97%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD DDP KT
Sbjct: 1   MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDPDDPQKT 60

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA 131
           TDQTR+LGLIVCRGTAVMLVSPTDGTDEIANPF+QPDGA
Sbjct: 61  TDQTRRLGLIVCRGTAVMLVSPTDGTDEIANPFIQPDGA 99

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463763|ref|XP_004149601.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 1 [Cucumis sativus] gi|449463765|ref|XP_004149602.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 2 [Cucumis sativus] gi|449530742|ref|XP_004172352.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 1 [Cucumis sativus] gi|449530744|ref|XP_004172353.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 2 [Cucumis sativus]

 Score =  191 bits (486), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 95/99 (95%), Positives = 96/99 (96%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD DDPLKT
Sbjct: 1   MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDPDDPLKT 60

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA 131
           TDQTR LGLIVCRGTAVMLVSP DGTDEIANPF+QPDGA
Sbjct: 61  TDQTRPLGLIVCRGTAVMLVSPVDGTDEIANPFIQPDGA 99

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736225|emb|CBI24863.3| unnamed protein product [Vitis vinifera]

 Score =  190 bits (482), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 95/103 (92%), Positives = 99/103 (96%)

Query: 29  KSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADD 88
           ++L  SGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD DD
Sbjct: 5   ETLFQSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDPDD 64

Query: 89  PLKTTDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA 131
           P KTTDQTR+LGLIVCRGTAVMLVSPTDGTDEIANPF+QPDGA
Sbjct: 65  PQKTTDQTRRLGLIVCRGTAVMLVSPTDGTDEIANPFIQPDGA 107

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255544228|ref|XP_002513176.1| conserved hypothetical protein [Ricinus communis] gi|223547674|gb|EEF49167.1| conserved hypothetical protein [Ricinus communis]

 Score =  189 bits (481), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 94/99 (94%), Positives = 97/99 (97%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE+LRD DDPLKT
Sbjct: 1   MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEYLRDPDDPLKT 60

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA 131
           TDQTR+LGLIVCRGTAVMLVSPTDGTDEIANPF+Q DGA
Sbjct: 61  TDQTRRLGLIVCRGTAVMLVSPTDGTDEIANPFIQQDGA 99

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388499482|gb|AFK37807.1| unknown [Lotus japonicus]

 Score =  189 bits (480), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 94/99 (94%), Positives = 95/99 (95%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD DDPLKT
Sbjct: 1   MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDPDDPLKT 60

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA 131
           T QTR LGLIVCRGTAVMLVSPTDGTDEI NPF+QPDGA
Sbjct: 61  TAQTRSLGLIVCRGTAVMLVSPTDGTDEIENPFIQPDGA 99

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297814702|ref|XP_002875234.1| hypothetical protein ARALYDRAFT_484298 [Arabidopsis lyrata subsp. lyrata] gi|297321072|gb|EFH51493.1| hypothetical protein ARALYDRAFT_484298 [Arabidopsis lyrata subsp. lyrata]

 Score =  184 bits (466), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 90/97 (92%), Positives = 95/97 (97%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF+RD DDPLKT
Sbjct: 1   MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFVRDHDDPLKT 60

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPD 129
           TDQTR+LGLIVCRGTAVMLVSPTDGT+EIANPF+Q +
Sbjct: 61  TDQTRRLGLIVCRGTAVMLVSPTDGTEEIANPFVQAE 97

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	131
TAIR|locus:2056825	99	EMB2816 "AT2G03870" [Arabidops	0.717	0.949	0.946	7.3e-43
FB|FBgn0261068	110	LSm7 [Drosophila melanogaster	0.725	0.863	0.593	8.2e-28
UNIPROTKB|Q9UK45	103	LSM7 "U6 snRNA-associated Sm-l	0.763	0.970	0.55	2.2e-27
ZFIN|ZDB-GENE-030131-8284	103	lsm7 "LSM7 homolog, U6 small n	0.725	0.922	0.562	5.7e-27
DICTYBASE|DDB_G0289499	97	lsm7 "putative U6 small nuclea	0.687	0.927	0.6	1.9e-26
WB|WBGene00003081	104	lsm-7 [Caenorhabditis elegans	0.687	0.865	0.577	2.2e-25
UNIPROTKB|Q23543	104	lsm-7 "Protein LSM-7" [Caenorh	0.687	0.865	0.577	2.2e-25
ASPGD|ASPL0000056132	136	AN0767 [Emericella nidulans (t	0.687	0.661	0.574	5.3e-24
UNIPROTKB|G4NLE3	146	MGG_02938 "Uncharacterized pro	0.671	0.602	0.576	6.8e-24
POMBASE|SPCC285.12	113	lsm7 "U6 snRNP-associated prot	0.709	0.823	0.531	2.3e-23

TAIR|locus:2056825 EMB2816 "AT2G03870" [Arabidopsis thaliana (taxid:3702)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 89/94 (94%), Positives = 93/94 (98%)

Query:    33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
             MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF+RD DDPLKT
Sbjct:     1 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFVRDHDDPLKT 60

Query:    93 TDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFM 126
             TDQTR+LGLIVCRGTAVMLVSPTDGT+EIANPF+
Sbjct:    61 TDQTRRLGLIVCRGTAVMLVSPTDGTEEIANPFV 94

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

FB|FBgn0261068 LSm7 [Drosophila melanogaster (taxid:7227)]

 Score = 311 (114.5 bits), Expect = 8.2e-28, P = 8.2e-28
 Identities = 57/96 (59%), Positives = 77/96 (80%)

Query:    32 KMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLK 91
             K   RKE++LDL+K+++K ++VK  GGR+ +G LKGYD LLNLVLD  VE+LRD+D+P K
Sbjct:    13 KEKRRKESILDLSKYLEKQIRVKFAGGREASGILKGYDALLNLVLDNTVEYLRDSDEPYK 72

Query:    92 TTD-QTRQLGLIVCRGTAVMLVSPTDGTDEIANPFM 126
              T+ QTR LGL+VCRGTA++L+ P DG + IANPF+
Sbjct:    73 LTEEQTRSLGLVVCRGTALVLICPQDGVESIANPFI 108

GO:0005688 "U6 snRNP" evidence=ISS

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|Q9UK45 LSM7 "U6 snRNA-associated Sm-like protein LSm7" [Homo sapiens (taxid:9606)]

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 55/100 (55%), Positives = 76/100 (76%)

Query:    32 KMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLK 91
             K   +KE++LDL+K++DK ++VK  GGR+ +G LKG+D LLNLVLD  +E++RD DD  K
Sbjct:     4 KEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDPDDQYK 63

Query:    92 TTDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPDGA 131
              T+ TRQLGL+VCRGT+V+L+ P DG + I NPF+Q   A
Sbjct:    64 LTEDTRQLGLVVCRGTSVVLICPQDGMEAIPNPFIQQQDA 103

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=NAS

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

GO:0005634 "nucleus" evidence=NAS

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

GO:0005829 "cytosol" 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

ZFIN|ZDB-GENE-030131-8284 lsm7 "LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 54/96 (56%), Positives = 75/96 (78%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
             +KE++ DL+K++DK ++VK  GGR+ +G LKG+D LLNLVLD  +E++RD DD  K T+ 
Sbjct:     8 KKESIFDLSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYMRDPDDQYKLTED 67

Query:    96 TRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQP-DG 130
             TRQLGL+VCRGT+V+L+ P DG + I NPF+Q  DG
Sbjct:    68 TRQLGLVVCRGTSVVLICPQDGMEAIPNPFIQQQDG 103

GO:0003674 "molecular_function" evidence=ND

DICTYBASE|DDB_G0289499 lsm7 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 298 (110.0 bits), Expect = 1.9e-26, P = 1.9e-26
 Identities = 54/90 (60%), Positives = 73/90 (81%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
             +KE++LDL KF+ K + VK TGGR+V G LKGYDQL+N+ LD+  EF+RDA+DPL TTD+
Sbjct:     8 KKESILDLQKFLGKEICVKFTGGREVQGILKGYDQLVNITLDQTQEFIRDAEDPLITTDE 67

Query:    96 TRQLGLIVCRGTAVMLVSPTDGTDEIANPF 125
              R LGL+VCRG++VM+V PT+G + I NP+
Sbjct:    68 KRFLGLVVCRGSSVMMVCPTEGCEPIDNPY 97

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

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

GO:0006402 "mRNA catabolic process" evidence=ISS

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

GO:0005730 "nucleolus" evidence=ISS

GO:0005688 "U6 snRNP" evidence=ISS

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

WB|WBGene00003081 lsm-7 [Caenorhabditis elegans (taxid:6239)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 52/90 (57%), Positives = 72/90 (80%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
             +KE+V+DL +F+DK ++VK  GGR+ +G L+G+DQLLN+VLD+  E+LRD  +P    D+
Sbjct:     9 KKESVVDLTRFLDKEIRVKFQGGREASGVLRGFDQLLNMVLDDCREYLRDPQNPSVVGDE 68

Query:    96 TRQLGLIVCRGTAVMLVSPTDGTDEIANPF 125
             TRQLGLIV RGTA+ +VSP DG ++IANPF
Sbjct:    69 TRQLGLIVARGTAITVVSPADGLEQIANPF 98

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

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0008340 "determination of adult lifespan" evidence=IMP

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

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0008406 "gonad development" evidence=IMP

GO:0016477 "cell migration" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

UNIPROTKB|Q23543 lsm-7 "Protein LSM-7" [Caenorhabditis elegans (taxid:6239)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 52/90 (57%), Positives = 72/90 (80%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
             +KE+V+DL +F+DK ++VK  GGR+ +G L+G+DQLLN+VLD+  E+LRD  +P    D+
Sbjct:     9 KKESVVDLTRFLDKEIRVKFQGGREASGVLRGFDQLLNMVLDDCREYLRDPQNPSVVGDE 68

Query:    96 TRQLGLIVCRGTAVMLVSPTDGTDEIANPF 125
             TRQLGLIV RGTA+ +VSP DG ++IANPF
Sbjct:    69 TRQLGLIVARGTAITVVSPADGLEQIANPF 98

GO:0005515 "protein binding" evidence=IPI

ASPGD|ASPL0000056132 AN0767 [Emericella nidulans (taxid:162425)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 54/94 (57%), Positives = 74/94 (78%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
             +KE +LDL K++DK V+VK  GGR+V+G LKGYDQL+NLVLD+  E +RD D+  +TT  
Sbjct:    46 KKENILDLTKYMDKEVRVKFNGGREVSGILKGYDQLMNLVLDDVKESMRD-DEGNETT-- 102

Query:    96 TRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPD 129
              R LGLIV RGT ++L+SP DG+++IANPF+Q +
Sbjct:   103 -RALGLIVARGTLIVLISPADGSEQIANPFVQAE 135

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

GO:0030490 "maturation of SSU-rRNA" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

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

UNIPROTKB|G4NLE3 MGG_02938 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 274 (101.5 bits), Expect = 6.8e-24, P = 6.8e-24
 Identities = 53/92 (57%), Positives = 70/92 (76%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
             +KE +LDLAK++DK VQVK  GGR+V GTLKGYD L+NLVLDE  E +RD +      + 
Sbjct:    54 KKENILDLAKYMDKEVQVKFNGGREVIGTLKGYDALMNLVLDEVKETMRDEEG----NES 109

Query:    96 TRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQ 127
             +R LGL+V RGT ++ +SPTDG++ IANPF+Q
Sbjct:   110 SRPLGLVVVRGTLLVAISPTDGSESIANPFLQ 141

GO:0003674 "molecular_function" evidence=ND

POMBASE|SPCC285.12 lsm7 "U6 snRNP-associated protein Lsm7 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 269 (99.8 bits), Expect = 2.3e-23, P = 2.3e-23
 Identities = 50/94 (53%), Positives = 73/94 (77%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
             RKE++LDL+++ D+ +Q   TGGRQ+TG LKG+DQL+NLVLD+  E LR+ +D  K T  
Sbjct:    21 RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDG-KLTGA 79

Query:    96 TRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPD 129
              R+LGL+V RGT ++L++P DG++EI NPF+Q +
Sbjct:    80 IRKLGLVVVRGTTLVLIAPMDGSEEIPNPFVQAE 113

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=NAS

GO:0005688 "U6 snRNP" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006402 "mRNA catabolic process" evidence=ISS

GO:0008033 "tRNA processing" evidence=IEA

GO:0030490 "maturation of SSU-rRNA" evidence=ISO

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

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

---

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)
Q54HF6	LSM7_DICDI	No assigned EC number	0.6	0.6870	0.9278	yes	no
Q9UK45	LSM7_HUMAN	No assigned EC number	0.55	0.7633	0.9708	yes	no
Q9CQQ8	LSM7_MOUSE	No assigned EC number	0.5625	0.7328	0.9320	yes	no
O74499	LSM7_SCHPO	No assigned EC number	0.5434	0.6946	0.8053	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	131
cd01729	89	cd01729, LSm7, Like-Sm protein 7	1e-57
smart00651	67	smart00651, Sm, snRNP Sm proteins	4e-19
pfam01423	66	pfam01423, LSM, LSM domain	4e-18
cd01719	70	cd01719, Sm_G, Sm protein G	1e-17
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	8e-15
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	2e-13
cd01730	82	cd01730, LSm3, Like-Sm protein 3	8e-13
cd00600	63	cd00600, Sm_like, Sm and related proteins	2e-11
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	3e-11
cd01727	91	cd01727, LSm8, Like-Sm protein 8	2e-10
cd01717	80	cd01717, Sm_B, Sm protein B	9e-10
cd06168	73	cd06168, LSMD1, LSM domain containing 1	1e-08
cd01726	68	cd01726, LSm6, Like-Sm protein 6	3e-08
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	4e-07
cd01728	74	cd01728, LSm1, Like-Sm protein 1	6e-06
cd11679	65	cd11679, archaeal_Sm_like, archaeal Sm-related pro	2e-05
cd01718	79	cd01718, Sm_E, Sm protein E	2e-05
cd01722	69	cd01722, Sm_F, Sm protein F	3e-04
PTZ00138	89	PTZ00138, PTZ00138, small nuclear ribonucleoprotei	4e-04

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

 Score =  173 bits (440), Expect = 1e-57
 Identities = 62/89 (69%), Positives = 78/89 (87%)

Query: 37  KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQT 96
           KE++LDL+K+VDK ++VK  GGR+VTG LKGYDQLLNLVLD+ VE+LRD +DP K TD+T
Sbjct: 1   KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDET 60

Query: 97  RQLGLIVCRGTAVMLVSPTDGTDEIANPF 125
           R LGL+VCRGT+V+L+SP DGT+EI NPF
Sbjct: 61  RSLGLVVCRGTSVVLISPVDGTEEIENPF 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. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 89

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

 Score = 74.8 bits (185), Expect = 4e-19
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 7/74 (9%)

Query: 41  LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLG 100
             L K + K V V+L  GR+  GTLKG+DQ +NLVL++  E ++D        ++ R+LG
Sbjct: 1   KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD-------GEKKRKLG 53

Query: 101 LIVCRGTAVMLVSP 114
           L+  RG  ++ +  
Sbjct: 54  LVFIRGNNIVYIIL 67

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

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

 Score = 72.2 bits (178), Expect = 4e-18
 Identities = 30/73 (41%), Positives = 45/73 (61%), Gaps = 8/73 (10%)

Query: 42  DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
            L K + K V V+L  GR++ GTLKG+DQ +NLVLD+  E ++D            +LGL
Sbjct: 2   FLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKV--------NKLGL 53

Query: 102 IVCRGTAVMLVSP 114
           ++ RG  ++L+SP
Sbjct: 54  VLIRGNNIVLISP 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|212466 cd01719, Sm_G, Sm protein G

 Score = 71.4 bits (176), Expect = 1e-17
 Identities = 26/75 (34%), Positives = 46/75 (61%), Gaps = 8/75 (10%)

Query: 42  DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
           +L K++DK + +KL G R+V+G L+G+D  +NLVLD+AVE             +   +G+
Sbjct: 4   ELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVE--------EVGDGEKTPIGM 55

Query: 102 IVCRGTAVMLVSPTD 116
           +V RG +++++   D
Sbjct: 56  VVIRGNSIIMIEALD 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 G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Length = 70

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

 Score = 63.7 bits (156), Expect = 8e-15
 Identities = 30/72 (41%), Positives = 44/72 (61%), Gaps = 8/72 (11%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L + ++K V VKL GG++V G LKG+DQ LNLVL+ A E +          +  R+LG +
Sbjct: 6   LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEG--------ESVRKLGTV 57

Query: 103 VCRGTAVMLVSP 114
           + RG  V+ +SP
Sbjct: 58  LVRGDNVVFISP 69

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

 Score = 60.4 bits (147), Expect = 2e-13
 Identities = 29/72 (40%), Positives = 42/72 (58%), Gaps = 4/72 (5%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L K ++K V VKL  GR+  GTL G+DQ +NLVLD+  E +   D      +  R  G +
Sbjct: 12  LKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEE-IISHDGE---KNVRRLGGEV 67

Query: 103 VCRGTAVMLVSP 114
           + RG  ++L+SP
Sbjct: 68  LIRGDNIVLISP 79

Length = 79

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

 Score = 59.2 bits (144), Expect = 8e-13
 Identities = 31/82 (37%), Positives = 45/82 (54%), Gaps = 10/82 (12%)

Query: 41  LDLAKF-VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE--FLRDADDP-----LKT 92
           LDL +  +D+ V VKL G R++ G L  YDQ LN++L +  E     + D+       KT
Sbjct: 3   LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKT 62

Query: 93  TDQTRQLGLIVCRGTAVMLVSP 114
           T   R + ++  RG  V+LVSP
Sbjct: 63  T--KRNIPMLFVRGDGVILVSP 82

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

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

 Score = 54.9 bits (133), Expect = 2e-11
 Identities = 28/67 (41%), Positives = 40/67 (59%), Gaps = 8/67 (11%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L  F+ K V V+L  GR +TGTL  +D+ +NLVLD+ VE  RD         + R LGL+
Sbjct: 1   LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRD--------GKVRVLGLV 52

Query: 103 VCRGTAV 109
           + RG+ +
Sbjct: 53  LIRGSNI 59

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|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional

 Score = 55.0 bits (133), Expect = 3e-11
 Identities = 31/75 (41%), Positives = 43/75 (57%), Gaps = 9/75 (12%)

Query: 41  LD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQL 99
           LD L   ++  V V+L GGR+  G L+GYD  +NLVLD A E        ++  +  R+L
Sbjct: 6   LDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEE--------IQDGEVVRKL 57

Query: 100 GLIVCRGTAVMLVSP 114
           G +V RG  V+ VSP
Sbjct: 58  GKVVIRGDNVVYVSP 72

Length = 72

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

 Score = 53.3 bits (129), Expect = 2e-10
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L  +++K V V  T GR + GTLKG+DQ  NL+L    E +  +D+ ++       LGL 
Sbjct: 4   LEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEV----PLGLY 59

Query: 103 VCRGTAVMLVSPTD 116
           + RG  V ++   D
Sbjct: 60  LLRGDNVAVIGEVD 73

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

>gnl|CDD|212464 cd01717, Sm_B, Sm protein B

 Score = 51.0 bits (123), Expect = 9e-10
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTD---QTRQL 99
           + ++++  ++V L  GRQ  GT   +D+ +NLVL +  EF +      K  +   + R L
Sbjct: 5   MLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEEREEKRVL 64

Query: 100 GLIVCRGTAVMLVS 113
           GL++ RG  V+ ++
Sbjct: 65  GLVLLRGENVVSMT 78

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 80

>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1

 Score = 47.9 bits (115), Expect = 1e-08
 Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 3/64 (4%)

Query: 40  VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQL 99
            L L K + + ++V LT GR + GT    D+  N++L  A E+ + +D      ++ R L
Sbjct: 1   RLKLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLG---AEEPRSL 57

Query: 100 GLIV 103
           GL++
Sbjct: 58  GLVM 61

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

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

 Score = 46.7 bits (112), Expect = 3e-08
 Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 8/71 (11%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L K + K V VKL  G +  G L   D  +NLVL++  E++              + G  
Sbjct: 6   LKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYV--------DGQLVAKYGDA 57

Query: 103 VCRGTAVMLVS 113
             RG  V+ +S
Sbjct: 58  FIRGNNVLYIS 68

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|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein

 Score = 44.0 bits (104), Expect = 4e-07
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 9/71 (12%)

Query: 45  KFVDKGVQVKLTG-GRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIV 103
             V   ++V++ G   Q+ G L   D  +NL L + +E + +        ++ R LG +V
Sbjct: 7   SLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGE--------EKVRSLGTVV 58

Query: 104 CRGTAVMLVSP 114
            RG  ++L+ P
Sbjct: 59  LRGNNILLIQP 69

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

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

 Score = 41.0 bits (97), Expect = 6e-06
 Identities = 17/40 (42%), Positives = 26/40 (65%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
           L + +DK + V L  GR++ G L+ +DQ  NLVL++ VE
Sbjct: 6  SLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVE 45

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

>gnl|CDD|212490 cd11679, archaeal_Sm_like, archaeal Sm-related protein

 Score = 39.6 bits (93), Expect = 2e-05
 Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAV 80
          +L   +DK V V L+ G+  TG L G+D   LN+VL  A 
Sbjct: 4  ELNSLLDKEVIVTLSNGKTYTGQLVGFDPSSLNIVLTNAK 43

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|212465 cd01718, Sm_E, Sm protein E

 Score = 39.8 bits (94), Expect = 2e-05
 Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 7/52 (13%)

Query: 63  GTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP 114
           G + G+D+ +NLVLD+A E        LK T+  + LG I+ +G  + L+  
Sbjct: 35  GKIIGFDEYMNLVLDDAEEV------HLK-TNTRKPLGRILLKGDNITLIQN 79

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

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

 Score = 36.8 bits (86), Expect = 3e-04
 Identities = 15/40 (37%), Positives = 18/40 (45%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF 82
          L     K V VKL  G +  GTL   D  +NL L    E+
Sbjct: 6  LNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEY 45

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|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional

 Score = 36.6 bits (85), Expect = 4e-04
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 7/51 (13%)

Query: 63  GTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVS 113
           G + G+D+ +N+VLD+A E            +  + LG I+ +G  + L+ 
Sbjct: 43  GKILGFDEYMNMVLDDAEEVYT-------KKNTRKDLGRILLKGDNITLIM 86

Length = 89

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	131
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.91
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.91
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.85
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.84
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.83
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.83
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.83
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.81
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.8
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.8
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.78
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.77
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.77
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.77
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.76
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.74
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.73
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	99.7
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.69
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.69
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.69
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	99.58
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.53
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	99.52
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.5
KOG3168	177	consensus U1 snRNP component [Transcription]	99.48
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.46
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	99.31
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	99.11
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	99.06
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	98.95
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	98.84
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	98.69
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.57
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	97.83
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.22
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.69
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.26
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	96.15
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	95.44
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	95.35
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	94.67
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	94.66
PRK14638	150	hypothetical protein; Provisional	94.31
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	93.74
PRK14639	140	hypothetical protein; Provisional	93.32
PRK02001	152	hypothetical protein; Validated	93.29
PRK14644	136	hypothetical protein; Provisional	91.33
COG1923	77	Hfq Uncharacterized host factor I protein [General	91.28
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	91.02
PRK14640	152	hypothetical protein; Provisional	90.93
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	90.68
PRK14091	165	RNA-binding protein Hfq; Provisional	90.28
PRK14633	150	hypothetical protein; Provisional	89.64
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	89.16
PRK14091	165	RNA-binding protein Hfq; Provisional	88.61
PRK14642	197	hypothetical protein; Provisional	88.49
PRK14645	154	hypothetical protein; Provisional	88.26
PRK00092	154	ribosome maturation protein RimP; Reviewed	88.15
PRK14636	176	hypothetical protein; Provisional	87.47
PRK14632	172	hypothetical protein; Provisional	87.18
PRK14634	155	hypothetical protein; Provisional	87.12
PRK14643	164	hypothetical protein; Provisional	86.81
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	86.39
PRK14646	155	hypothetical protein; Provisional	86.38
KOG1073	361	consensus Uncharacterized mRNA-associated protein	86.33
PRK06955	300	biotin--protein ligase; Provisional	85.65
PRK14647	159	hypothetical protein; Provisional	85.44
PRK14631	174	hypothetical protein; Provisional	84.54
PRK14637	151	hypothetical protein; Provisional	83.21
PRK14641	173	hypothetical protein; Provisional	81.64
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	80.77
PF07073	80	ROF: Modulator of Rho-dependent transcription term	80.51
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	80.4

>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=99.91  E-value=7.3e-24  Score=143.37  Aligned_cols=79  Identities=71%  Similarity=1.192  Sum_probs=68.0

Q ss_pred             cCcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        38 ~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      +++++|.++++++|+|+|+|||+|.|+|.|||+||||+|++|+|+...+.+..+.....+.+|.++|||++|++|++.+
T Consensus         2 ~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           2 ESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             cchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            5788999999999999999999999999999999999999999998653322112235788999999999999999775

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.

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

Probab=99.91  E-value=1.2e-25  Score=155.58  Aligned_cols=101  Identities=61%  Similarity=1.070  Sum_probs=93.1

Q ss_pred             cccccccCccCcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCc
Q 032889           29 KSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTA  108 (131)
Q Consensus        29 ~~~~m~~~~~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~  108 (131)
                      +...+++++++.++|.+|++++|+|++.+||..+|+|+|||+.|||||+|++|+..+++++.+...+.|++|++++||..
T Consensus         8 ~~~~e~~kkEsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTa   87 (108)
T KOG1781|consen    8 RKKFEKPKKESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTA   87 (108)
T ss_pred             cccccccchhHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccE
Confidence            34456678999999999999999999999999999999999999999999999998888877766778999999999999


Q ss_pred             EEEEeeCCCCccccCCCCCCC
Q 032889          109 VMLVSPTDGTDEIANPFMQPD  129 (131)
Q Consensus       109 Iv~I~~~d~~~~~~~p~~~~~  129 (131)
                      +++|++.|+.++|.|||.+.+
T Consensus        88 lvlisp~dG~e~I~npf~~~e  108 (108)
T KOG1781|consen   88 LVLISPADGSEEIANPFVQQE  108 (108)
T ss_pred             EEEEcCCcchhhhccchhcCC
Confidence            999999999999999999864

>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=99.87  E-value=7.2e-22  Score=130.93  Aligned_cols=70  Identities=36%  Similarity=0.737  Sum_probs=63.3

Q ss_pred             cccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        40 ~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      +++|.++++|+|+|+|++||.++|+|.|||+||||+|+||+|+...        ...+.+|.++|||++|++|++.|+
T Consensus         2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~--------~~~~~lg~v~IRG~~I~~i~~~~~   71 (72)
T cd01719           2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG--------GEKNNIGMVVIRGNSIVMLEALER   71 (72)
T ss_pred             chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC--------CceeEeceEEECCCEEEEEEcccc
Confidence            4689999999999999999999999999999999999999998732        247889999999999999998763

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.

>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=99.86  E-value=2.7e-21  Score=129.85  Aligned_cols=73  Identities=26%  Similarity=0.530  Sum_probs=62.5

Q ss_pred             cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCC--CccCcceEEeceEEEeCCcEEEEee
Q 032889           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~--~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      .|.+|++++|+|+|+|||.+.|+|.|||+||||+|+||+|++......  .....+++.+|+++|||++|++|+.
T Consensus         4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            588999999999999999999999999999999999999987643211  1123467899999999999999974

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.

>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=99.86  E-value=2.9e-21  Score=128.32  Aligned_cols=72  Identities=36%  Similarity=0.587  Sum_probs=63.5

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      +.|.++++++|+|+++|||.+.|+|+|||+||||+|++|.|+....+.    ....+.+|.+++||++|++|++.|
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~----~~~~~~lG~~~iRG~~I~~i~~~d   73 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDE----GVEQVVLGLYIIRGDNIAVVGEID   73 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCC----CceeeEeceEEECCCEEEEEEccC
Confidence            478999999999999999999999999999999999999998754322    135778999999999999999876

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.

>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=99.86  E-value=3e-21  Score=128.72  Aligned_cols=71  Identities=34%  Similarity=0.500  Sum_probs=63.0

Q ss_pred             CcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        39 ~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      +.++|.++++++|.|+++|||+|.|+|.|||+||||+|+||.|+...++     ...++.+|.++|||++|++|+.
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 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD-----KYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC-----ccceeEeeEEEEECCEEEEEEc
Confidence            4567999999999999999999999999999999999999999876432     1346889999999999999975

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.

>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=2.8e-21  Score=130.74  Aligned_cols=75  Identities=36%  Similarity=0.569  Sum_probs=62.4

Q ss_pred             cccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCC-----ccCcceEEeceEEEeCCcEEEEe
Q 032889           40 VLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIVCRGTAVMLVS  113 (131)
Q Consensus        40 ~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~-----~~~~~~r~lg~v~IRG~~Iv~I~  113 (131)
                      |+++ ...++++|.|+|+|||.+.|+|.|||+||||+|+||+|++....++.     ......|.+|.++|||++|++|+
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            6676 56799999999999999999999999999999999999986532211     11235789999999999999987


Q ss_pred             e
Q 032889          114 P  114 (131)
Q Consensus       114 ~  114 (131)
                      +
T Consensus        82 ~   82 (82)
T cd01730          82 P   82 (82)
T ss_pred             C
Confidence            3

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

>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=99.85  E-value=3.4e-21  Score=125.88  Aligned_cols=64  Identities=45%  Similarity=0.742  Sum_probs=58.5

Q ss_pred             HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      |.++++++|+|+|+||+.|+|+|.|||+||||+|+||+|++..        ..++.+|.++|||++|++|++
T Consensus         5 L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           5 LKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG--------EPVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             HHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC--------CeEeEcCcEEEeCCEEEEEcC
Confidence            6789999999999999999999999999999999999998753        247789999999999999974

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=99.84  E-value=1.2e-20  Score=126.41  Aligned_cols=71  Identities=23%  Similarity=0.505  Sum_probs=61.5

Q ss_pred             cccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889           40 VLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT  115 (131)
Q Consensus        40 ~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~  115 (131)
                      |+++ .++++++|+|++++||++.|+|+|||+||||+|+||+|++..++.     ...+.+|.++|||++|++|++.
T Consensus         4 P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~-----~~~~~lg~v~iRG~nV~~i~p~   75 (76)
T cd01732           4 PLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEG-----RKITKLDQILLNGNNICMLVPG   75 (76)
T ss_pred             hHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCC-----ceeeEcCeEEEeCCeEEEEECC
Confidence            5564 688999999999999999999999999999999999999853221     2467899999999999999863

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

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.84  E-value=1.2e-20  Score=124.85  Aligned_cols=68  Identities=46%  Similarity=0.724  Sum_probs=59.8

Q ss_pred             Cccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           39 TVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        39 ~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      .|++ |.++++++|+|+|+||+.|+|+|.|||+|||++|+||.|...+        ...+.+|.++|||++|++|++
T Consensus         4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~~V~~i~~   72 (72)
T PRK00737          4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG--------EVVRKLGKVVIRGDNVVYVSP   72 (72)
T ss_pred             chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC--------CeEeEcCcEEEeCCEEEEEcC
Confidence            4555 5789999999999999999999999999999999999997532        246789999999999999963

>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=99.83  E-value=3e-20  Score=127.38  Aligned_cols=76  Identities=24%  Similarity=0.405  Sum_probs=62.4

Q ss_pred             CcccH-hhhc--CCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCC-----ccCcceEEeceEEEeCCcEE
Q 032889           39 TVLDL-AKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIVCRGTAVM  110 (131)
Q Consensus        39 ~~l~L-~~~l--~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~-----~~~~~~r~lg~v~IRG~~Iv  110 (131)
                      +|+++ .+.+  +++|+|+|++||.+.|+|.|||+||||+|+||+|.+....+..     ......+.+|.++|||++|+
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            57776 4565  8999999999999999999999999999999999986532110     11235778999999999999


Q ss_pred             EEee
Q 032889          111 LVSP  114 (131)
Q Consensus       111 ~I~~  114 (131)
                      +|+.
T Consensus        82 ~Is~   85 (87)
T cd01720          82 LVLR   85 (87)
T ss_pred             EEec
Confidence            9985

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.

>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=99.83  E-value=4.8e-20  Score=123.19  Aligned_cols=71  Identities=23%  Similarity=0.438  Sum_probs=62.5

Q ss_pred             cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      .|.++++++|+|+|+|||.|.|+|.|||+||||+|+||.|++..+.+.  ...+.|.+|+++|||++|++|+.
T Consensus         4 ~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~--~~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           4 KLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSF--SPTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             HHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCcc--CCccEEEeeeEEEeCCeEEEEEE
Confidence            578999999999999999999999999999999999999998654321  12468999999999999999974

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.

>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=99.83  E-value=4e-20  Score=120.62  Aligned_cols=66  Identities=26%  Similarity=0.449  Sum_probs=57.9

Q ss_pred             ccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEe
Q 032889           40 VLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVS  113 (131)
Q Consensus        40 ~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~  113 (131)
                      |++ |.++++++|.|+|++|++|+|+|.|||+||||+|+||+|....        ...+.+|.++|||++|++|+
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~--------~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNG--------QLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCC--------ceeeEeCCEEEECCEEEEEC
Confidence            344 5789999999999999999999999999999999999986532        24778999999999999984

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.

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

Probab=99.81  E-value=2.5e-19  Score=115.81  Aligned_cols=66  Identities=38%  Similarity=0.660  Sum_probs=60.1

Q ss_pred             cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      .|.+++|++|+|.|+||+.++|+|.+||+|||++|+||.|....+       .+.+++|.++|||++|++|.+
T Consensus         2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~-------~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNG-------PEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTE-------SEEEEEEEEEEEGGGEEEEEE
T ss_pred             hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCC-------CcEeECcEEEEECCEEEEEEC
Confidence            478999999999999999999999999999999999999997542       158899999999999999974

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

>smart00651 Sm snRNP Sm proteins

Probab=99.80  E-value=3e-19  Score=115.30  Aligned_cols=66  Identities=41%  Similarity=0.731  Sum_probs=59.9

Q ss_pred             cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      .|.++++++|+|+|+||+.+.|+|.|||+||||+|+||.|+...+       .+.+.+|.++|||++|++|.+
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-------~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-------EKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC-------cEEeEeCCEEEcCCEEEEEeC
Confidence            478999999999999999999999999999999999999987542       358899999999999999863

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

>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=99.80  E-value=2.2e-19  Score=117.53  Aligned_cols=64  Identities=31%  Similarity=0.433  Sum_probs=56.8

Q ss_pred             cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEe
Q 032889           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVS  113 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~  113 (131)
                      .|.++++++|+|+|+||++|+|+|.|||+||||+|+||+|+...        ...+.+|.++|||++|.+|.
T Consensus         5 ~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~--------~~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           5 FLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG--------KSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             HHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC--------ccccCcCcEEEECCEEEEEC
Confidence            36789999999999999999999999999999999999987532        23667999999999999983

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.

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

Probab=99.78  E-value=4e-19  Score=117.47  Aligned_cols=68  Identities=43%  Similarity=0.820  Sum_probs=62.3

Q ss_pred             cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      +|.+|++|++.++|++||.+.|+|.|||.|||+||+++.|...+.        .+..+|.++|||++|+.+.+.+.
T Consensus         8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~--------~~~~ig~~vIrgnsiv~~eaL~~   75 (77)
T KOG1780|consen    8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDG--------DKNNIGMVVIRGNSIVMVEALER   75 (77)
T ss_pred             hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcC--------CcceeeeEEEeccEEEEEeeccc
Confidence            999999999999999999999999999999999999999986542        36789999999999999988763

>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=99.77  E-value=2.5e-18  Score=109.50  Aligned_cols=63  Identities=41%  Similarity=0.718  Sum_probs=57.7

Q ss_pred             HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEe
Q 032889           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVS  113 (131)
Q Consensus        43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~  113 (131)
                      |.+++|++|+|+|+||+.|.|+|.|||+|||++|+||.|....        ...+.+|.++|||++|.+|.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~--------~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE--------GKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC--------CcEEECCeEEEECCEEEEEC
Confidence            5688999999999999999999999999999999999998754        25889999999999999874

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.

>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=99.77  E-value=1.9e-18  Score=116.62  Aligned_cols=69  Identities=28%  Similarity=0.531  Sum_probs=57.6

Q ss_pred             Cccc-HhhhcCC--eEEEEEc--CCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEe
Q 032889           39 TVLD-LAKFVDK--GVQVKLT--GGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVS  113 (131)
Q Consensus        39 ~~l~-L~~~l~k--~V~V~L~--dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~  113 (131)
                      .|++ |.+|+++  +|.|+++  +||.+.|+|.|||+||||+|+||+|+...+       ...+.+|.++|||++|++|+
T Consensus         6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~-------~~~~~lG~iliRGnnV~~I~   78 (79)
T cd01718           6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKT-------KTRKPLGRILLKGDNITLIQ   78 (79)
T ss_pred             CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCC-------ceEeEcCcEEEeCCEEEEEc
Confidence            4555 4689998  5666665  999999999999999999999999997421       24678999999999999987


Q ss_pred             e
Q 032889          114 P  114 (131)
Q Consensus       114 ~  114 (131)
                      +
T Consensus        79 p   79 (79)
T cd01718          79 N   79 (79)
T ss_pred             C
Confidence            4

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.

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

Probab=99.77  E-value=3.5e-18  Score=114.58  Aligned_cols=71  Identities=42%  Similarity=0.703  Sum_probs=57.7

Q ss_pred             Cccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEee-cCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           39 TVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR-DADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        39 ~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~-~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      .|.+ |.++++++|.|+|++|++|.|+|.|||+||||+|+||.|+.. ++.     ....+..+.++|||++|++|.+
T Consensus         7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~-----~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958           7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGE-----KNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCc-----cccceeccEEEEECCcEEEEeC
Confidence            3444 578999999999999999999999999999999999999974 111     0023344599999999999863

>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=99.76  E-value=5e-18  Score=111.75  Aligned_cols=68  Identities=24%  Similarity=0.294  Sum_probs=59.3

Q ss_pred             cc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           41 LD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        41 l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      ++ |.+..|++|.|+|++|.+|+|+|.++|.|||++|+||++...++        +...+|.++|||++|.+|..||
T Consensus         2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g--------~~~~~~~v~IRG~nI~~v~lPd   70 (70)
T cd01721           2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDG--------RVSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCC--------cEeEcCcEEEeCCEEEEEEeCC
Confidence            44 46889999999999999999999999999999999998864332        2567899999999999999875

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

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

Probab=99.74  E-value=1.1e-17  Score=111.76  Aligned_cols=70  Identities=23%  Similarity=0.329  Sum_probs=60.2

Q ss_pred             cccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           40 VLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        40 ~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      |+++ .++.|++|.|+|++|+.++|+|.+||+|||++|+||+|...++       .....++.++|||++|.+|..++
T Consensus         2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g-------~~~~~~~~v~IRG~~I~~i~~p~   72 (76)
T cd01723           2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDG-------DKFWKMPECYIRGNTIKYLRVPD   72 (76)
T ss_pred             chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCC-------cEeeeCCcEEEeCCEEEEEEcCH
Confidence            5564 6889999999999999999999999999999999999874332       12456789999999999999876

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.

>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=99.73  E-value=3.9e-17  Score=112.54  Aligned_cols=68  Identities=25%  Similarity=0.364  Sum_probs=61.0

Q ss_pred             HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCC
Q 032889           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGT  118 (131)
Q Consensus        43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~  118 (131)
                      |.++.|++|.|+|++|..|+|+|.++|.|||++|+||++....        .....+|.++|||++|.+|..||..
T Consensus         6 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~--------~~~~~~~~v~IRG~nI~yi~lPd~l   73 (90)
T cd01724           6 LMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG--------RNPVPLDTLSIRGNNIRYFILPDSL   73 (90)
T ss_pred             HHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC--------CceeEcceEEEeCCEEEEEEcCCcC
Confidence            5788999999999999999999999999999999999988543        2366899999999999999999854

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.

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

Probab=99.70  E-value=3.7e-18  Score=115.22  Aligned_cols=80  Identities=34%  Similarity=0.507  Sum_probs=67.7

Q ss_pred             ccCcccHhh-hcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCC-----ccCcceEEeceEEEeCCcEE
Q 032889           37 KETVLDLAK-FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIVCRGTAVM  110 (131)
Q Consensus        37 ~~~~l~L~~-~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~-----~~~~~~r~lg~v~IRG~~Iv  110 (131)
                      ...|++|.+ +++.+|.|+++++|.++|+|.|||+|.|++|+|++|....-+..+     .....+|.+..+|+||++|+
T Consensus         3 v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vi   82 (91)
T KOG3460|consen    3 VEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVI   82 (91)
T ss_pred             ccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEE
Confidence            467899876 499999999999999999999999999999999999987533221     12356788999999999999


Q ss_pred             EEeeCC
Q 032889          111 LVSPTD  116 (131)
Q Consensus       111 ~I~~~d  116 (131)
                      .|+++-
T Consensus        83 lvspp~   88 (91)
T KOG3460|consen   83 LVSPPL   88 (91)
T ss_pred             EEcCcc
Confidence            999875

>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=99.69  E-value=1.6e-16  Score=106.78  Aligned_cols=65  Identities=25%  Similarity=0.323  Sum_probs=57.1

Q ss_pred             HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT  115 (131)
Q Consensus        43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~  115 (131)
                      |..+.|+.|.|+|++|..|+|+|.++|.|||++|+||++...+        .....+|.++|||++|.+|..|
T Consensus        14 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~--------~~~~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733          14 LQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN--------GKQVQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             HHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC--------CceeECCcEEEECCEEEEEEcC
Confidence            4678999999999999999999999999999999999877432        1355789999999999999865

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.

>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=99.69  E-value=1.5e-16  Score=107.52  Aligned_cols=70  Identities=24%  Similarity=0.265  Sum_probs=59.2

Q ss_pred             HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCC
Q 032889           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGT  118 (131)
Q Consensus        43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~  118 (131)
                      |.++.|++|.|+|++|..|+|+|.++|.|||++|+||++...+..      .....++.++|||++|.+|..||..
T Consensus         6 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~------~~~~~~~~v~IRG~~I~~I~lp~~~   75 (81)
T cd01725           6 FKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKY------PHMLSVKNCFIRGSVVRYVQLPADE   75 (81)
T ss_pred             HHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCc------ccccccCeEEEECCEEEEEEeChhH
Confidence            578899999999999999999999999999999999987643211      1234578999999999999999753

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.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.69  E-value=1.4e-16  Score=109.64  Aligned_cols=71  Identities=25%  Similarity=0.538  Sum_probs=57.0

Q ss_pred             cCccc-HhhhcCC--eEEEEEcC--CcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEE
Q 032889           38 ETVLD-LAKFVDK--GVQVKLTG--GRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLV  112 (131)
Q Consensus        38 ~~~l~-L~~~l~k--~V~V~L~d--Gr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I  112 (131)
                      ..|.. +.+++.+  +|.|.+.|  ++++.|+|.|||+||||+|+||+|++...       ...+.+|.++|||++|++|
T Consensus        13 ~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~-------~~~~~lG~ilIRGnnV~~I   85 (89)
T PTZ00138         13 TQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKK-------NTRKDLGRILLKGDNITLI   85 (89)
T ss_pred             cCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCC-------ceeeEcCeEEEcCCEEEEE
Confidence            34555 4578775  56677666  58999999999999999999999986432       2477899999999999999


Q ss_pred             eeC
Q 032889          113 SPT  115 (131)
Q Consensus       113 ~~~  115 (131)
                      ++.
T Consensus        86 ~~~   88 (89)
T PTZ00138         86 MAA   88 (89)
T ss_pred             EcC
Confidence            864

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

Probab=99.58  E-value=2.6e-16  Score=112.91  Aligned_cols=84  Identities=31%  Similarity=0.479  Sum_probs=72.3

Q ss_pred             cCcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        38 ~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      ..+.+|.+++++++.|.|+|||.+.|.|.+||||-|++|.+|+|++.-++     .......|..+|||+||++++..|.
T Consensus         9 ~~t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~-----~Y~di~~glfiIRGENVvllGeid~   83 (129)
T KOG1782|consen    9 PFTTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN-----KYCDIPRGLFIIRGENVVLLGEIDL   83 (129)
T ss_pred             CchhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc-----eecccCceEEEEecCcEEEEecCCc
Confidence            34556899999999999999999999999999999999999999987653     3567788999999999999999887


Q ss_pred             CccccCCCCC
Q 032889          118 TDEIANPFMQ  127 (131)
Q Consensus       118 ~~~~~~p~~~  127 (131)
                      ..+ +.|..+
T Consensus        84 dkE-~~~l~~   92 (129)
T KOG1782|consen   84 DKE-EEPLEQ   92 (129)
T ss_pred             chh-hcccee
Confidence            665 566544

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

Probab=99.53  E-value=1.9e-15  Score=99.79  Aligned_cols=72  Identities=25%  Similarity=0.401  Sum_probs=63.0

Q ss_pred             ccCccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889           37 KETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT  115 (131)
Q Consensus        37 ~~~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~  115 (131)
                      ...|.+ |.+.+|++|.|+|.+|-.|+|+|.|.|.||||.|+.++|+...        +.++++|.+||||++|.+|+..
T Consensus         4 ~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ng--------ql~n~ygdaFirGnnVlyIs~~   75 (77)
T KOG1783|consen    4 GSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNG--------QLKNKYGDAFIRGNNVLYISTQ   75 (77)
T ss_pred             ccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcC--------cccccccceeeccccEEEEEec
Confidence            344555 6789999999999999999999999999999999999998632        4688999999999999999875


Q ss_pred             C
Q 032889          116 D  116 (131)
Q Consensus       116 d  116 (131)
                      .
T Consensus        76 ~   76 (77)
T KOG1783|consen   76 K   76 (77)
T ss_pred             c
Confidence            3

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

Probab=99.52  E-value=1.2e-14  Score=99.65  Aligned_cols=73  Identities=32%  Similarity=0.532  Sum_probs=65.2

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      ..|..|++++|.|...|||.+.|.|+|||+..||+|+++.|+......    ..++..+|..+|||+||..|.++|+
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~----gv~q~~lGlyiirgeNva~ig~iDE   75 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETE----GVEQIVLGLYIIRGENVAVIGEIDE   75 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhc----chhheeeEEEEEecCccceeeecch
Confidence            468999999999999999999999999999999999999999765332    3467789999999999999999984

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

Probab=99.50  E-value=6.2e-14  Score=92.60  Aligned_cols=67  Identities=33%  Similarity=0.403  Sum_probs=60.0

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT  115 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~  115 (131)
                      +.|..+.+|+|.|+|+.|.+|+|+|++.|.||||.|.+|+|++..        ...-.+|.++||.+||.+|...
T Consensus        11 pFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG--------~~~g~lGEilIRCNNvlyi~gv   77 (79)
T KOG3482|consen   11 PFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG--------VSTGNLGEILIRCNNVLYIRGV   77 (79)
T ss_pred             HHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc--------cccccceeEEEEeccEEEEecC
Confidence            457889999999999999999999999999999999999998753        2466799999999999999754

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=99.48  E-value=5.9e-15  Score=111.08  Aligned_cols=77  Identities=25%  Similarity=0.506  Sum_probs=65.8

Q ss_pred             cccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCC-C-CccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADD-P-LKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        40 ~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~-~-~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      +..|.++++.+++|.++|||.+.|.+.+||+||||+|.||+|....... . .....++|-+|++++||++|++.+..+
T Consensus         6 sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg   84 (177)
T KOG3168|consen    6 SSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG   84 (177)
T ss_pred             hhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence            3457899999999999999999999999999999999999998764321 1 234568999999999999999998755

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

Probab=99.46  E-value=6.9e-14  Score=93.16  Aligned_cols=75  Identities=21%  Similarity=0.468  Sum_probs=64.8

Q ss_pred             ccCcccHh-hhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889           37 KETVLDLA-KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT  115 (131)
Q Consensus        37 ~~~~l~L~-~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~  115 (131)
                      ...|++|. +.+|.+++|.+++.|++.|+|+|||.|.|++|+|+.|+...++.     ....+++++++.|++|....+.
T Consensus         5 ~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~eg-----r~~tk~~~iLLnGNni~mLvPG   79 (84)
T KOG1775|consen    5 TLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEG-----RRMTKLDQILLNGNNITMLVPG   79 (84)
T ss_pred             hcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCc-----ceeeeeeeeeecCCcEEEEecC
Confidence            45678875 78999999999999999999999999999999999999765442     2456899999999999988765


Q ss_pred             C
Q 032889          116 D  116 (131)
Q Consensus       116 d  116 (131)
                      .
T Consensus        80 G   80 (84)
T KOG1775|consen   80 G   80 (84)
T ss_pred             C
Confidence            4

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

Probab=99.31  E-value=1.3e-12  Score=88.06  Aligned_cols=72  Identities=29%  Similarity=0.568  Sum_probs=56.8

Q ss_pred             cCcccH-hhhcCCe--EEEEEcC--CcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEE
Q 032889           38 ETVLDL-AKFVDKG--VQVKLTG--GRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLV  112 (131)
Q Consensus        38 ~~~l~L-~~~l~k~--V~V~L~d--Gr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I  112 (131)
                      -.|..| .+|+..+  |.|.|.+  |-.++|.++|||+|||+||++|+|.....+       ..+.+|.++++||+|..|
T Consensus        11 v~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~-------~rk~lGRilLKGDnItli   83 (88)
T KOG1774|consen   11 VQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTK-------SRKELGRILLKGDNITLI   83 (88)
T ss_pred             cCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccccc-------CCCccccEEEcCCcEEEE
Confidence            446666 5887764  5566644  889999999999999999999999865432       344899999999999999


Q ss_pred             eeCC
Q 032889          113 SPTD  116 (131)
Q Consensus       113 ~~~d  116 (131)
                      ...+
T Consensus        84 ~~~~   87 (88)
T KOG1774|consen   84 QSAG   87 (88)
T ss_pred             eecC
Confidence            7653

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

Probab=99.11  E-value=1.6e-10  Score=83.27  Aligned_cols=72  Identities=25%  Similarity=0.299  Sum_probs=63.4

Q ss_pred             CcccHh-hhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           39 TVLDLA-KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        39 ~~l~L~-~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      .|+.|. ..-+.++.|+|++|.+|.|.|+.+|.+|||.|.+++++..+++       +...+..+.|||++|.++..+|.
T Consensus         2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgd-------kf~r~pEcYirGttIkylri~d~   74 (134)
T KOG3293|consen    2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGD-------KFFRMPECYIRGTTIKYLRIPDE   74 (134)
T ss_pred             cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCC-------ceeecceeEEecceeEEEeccHH
Confidence            367775 4688999999999999999999999999999999999876543       46778899999999999999874

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

Probab=99.06  E-value=6.4e-10  Score=76.10  Aligned_cols=68  Identities=28%  Similarity=0.287  Sum_probs=56.9

Q ss_pred             hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           44 AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        44 ~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      ..++|++|.|.|+++-.+.|+|.|.|+|.|+.|.|..-...+.      -..--.+..++|||+.|.+|..+..
T Consensus         8 kslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~k------yPhm~Sv~ncfIRGSvvrYv~l~kd   75 (96)
T KOG3448|consen    8 KSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDK------YPHMLSVKNCFIRGSVVRYVQLPKD   75 (96)
T ss_pred             HHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCccc------CCCeeeeeeEEEeccEEEEEEeChh
Confidence            5679999999999999999999999999999999986553221      1245567889999999999998763

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

Probab=98.95  E-value=3.8e-09  Score=74.65  Aligned_cols=79  Identities=20%  Similarity=0.262  Sum_probs=67.5

Q ss_pred             cccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCC
Q 032889           40 VLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGT  118 (131)
Q Consensus        40 ~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~  118 (131)
                      |..| .+.-+.-|.+++..|..|+|+|.-.|.+||+.|+|+.-...++        ....+.+++|||+.|.++..||..
T Consensus         6 piKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg--------~vs~le~V~IRGS~IRFlvlPdmL   77 (119)
T KOG3172|consen    6 PIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDG--------RVSQLEQVFIRGSKIRFLVLPDML   77 (119)
T ss_pred             ceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCC--------cceeeeeEEEecCeEEEEECchHh
Confidence            4454 4678899999999999999999999999999999998776543        355788999999999999999977


Q ss_pred             ccccCCCCCC
Q 032889          119 DEIANPFMQP  128 (131)
Q Consensus       119 ~~~~~p~~~~  128 (131)
                      +  ++|+|+-
T Consensus        78 K--nAPmFkk   85 (119)
T KOG3172|consen   78 K--NAPMFKK   85 (119)
T ss_pred             h--cCccccc
Confidence            6  8999863

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

Probab=98.84  E-value=7.2e-10  Score=78.47  Aligned_cols=76  Identities=21%  Similarity=0.340  Sum_probs=60.6

Q ss_pred             cCcccHh-hh--cCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCC---CC--ccCcceEEeceEEEeCCcE
Q 032889           38 ETVLDLA-KF--VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADD---PL--KTTDQTRQLGLIVCRGTAV  109 (131)
Q Consensus        38 ~~~l~L~-~~--l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~---~~--~~~~~~r~lg~v~IRG~~I  109 (131)
                      .+|+++. ..  -..+|.|.++|++.+.|++.|||.|+|++|+++.|.|.....   +.  +.....|.+|.++||||+|
T Consensus        23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv  102 (114)
T KOG3459|consen   23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV  102 (114)
T ss_pred             cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence            4566653 22  456899999999999999999999999999999999876321   11  1234588999999999999


Q ss_pred             EEEe
Q 032889          110 MLVS  113 (131)
Q Consensus       110 v~I~  113 (131)
                      +.+.
T Consensus       103 I~v~  106 (114)
T KOG3459|consen  103 ILVL  106 (114)
T ss_pred             EEEE
Confidence            9886

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

Probab=98.69  E-value=1.3e-07  Score=66.90  Aligned_cols=67  Identities=22%  Similarity=0.331  Sum_probs=58.3

Q ss_pred             cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      -|.++.+.+|.|.|++|+...|++.+.|.+||..|.++.-....         ++.++..+.|||++|.++..+|.
T Consensus         6 ~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~---------~pv~l~~lsirgnniRy~~lpD~   72 (109)
T KOG3428|consen    6 FLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG---------EPVRLDTLSIRGNNIRYYILPDS   72 (109)
T ss_pred             HHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC---------CceeEEEEEeecceEEEEEccCC
Confidence            36788999999999999999999999999999999998765431         35678899999999999999874

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

Probab=98.57  E-value=4.7e-08  Score=63.54  Aligned_cols=38  Identities=24%  Similarity=0.344  Sum_probs=32.5

Q ss_pred             CCeEEEEEcC----CcEEEEEEEEEcCccceEecceEEEeec
Q 032889           48 DKGVQVKLTG----GRQVTGTLKGYDQLLNLVLDEAVEFLRD   85 (131)
Q Consensus        48 ~k~V~V~L~d----Gr~i~G~L~~fD~~mNLVL~da~E~~~~   85 (131)
                      +.+|+|.++.    +..++|.|+|||+||||+|.|+.|.+..
T Consensus         8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~   49 (66)
T cd01739           8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK   49 (66)
T ss_pred             CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence            3678888865    4578899999999999999999999864

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

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

Probab=97.83  E-value=4.2e-05  Score=50.56  Aligned_cols=67  Identities=15%  Similarity=0.236  Sum_probs=40.0

Q ss_pred             HhhhcCCeEEEEEcCCcEEEEEEEEEcC---ccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEE
Q 032889           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQ---LLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVM  110 (131)
Q Consensus        43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~---~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv  110 (131)
                      +..++|++|.|+++||..|+|.|.+++.   -+-++|.-+........+. ...........++|+++.|+
T Consensus         7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~-~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN-SDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-------EEEEEEE-GGGEEE-----
T ss_pred             HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc-CCccCCCCCceEEEeccccC
Confidence            3578999999999999999999999998   8999998887654321110 11123345567777777665

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

Probab=97.22  E-value=0.0026  Score=44.32  Aligned_cols=76  Identities=12%  Similarity=0.166  Sum_probs=55.9

Q ss_pred             hhhcCCeEEEEEcCCcEEEEEEEEEcC-ccceEecceEEEeecCCCC-CccCcceEEeceEEEeCCcEEEEeeCCCCc
Q 032889           44 AKFVDKGVQVKLTGGRQVTGTLKGYDQ-LLNLVLDEAVEFLRDADDP-LKTTDQTRQLGLIVCRGTAVMLVSPTDGTD  119 (131)
Q Consensus        44 ~~~l~k~V~V~L~dGr~i~G~L~~fD~-~mNLVL~da~E~~~~~~~~-~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~~  119 (131)
                      ..|+|++|.+..+++-.|+|+|..+|. ...|.|.+|.-+-.++... ............+..||+.|.-+...+...
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~   81 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP   81 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence            468999999999999999999999995 8999999988664432111 111122345788999999999998876433

>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=96.69  E-value=0.01  Score=35.83  Aligned_cols=35  Identities=20%  Similarity=0.300  Sum_probs=30.5

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEE
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE   81 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E   81 (131)
                      ++|++|+|.+ ++..++|+..++|....|++.....
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g   35 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG   35 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence            4789999999 6777899999999999999987544

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

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

Probab=96.26  E-value=0.039  Score=36.83  Aligned_cols=67  Identities=12%  Similarity=0.179  Sum_probs=49.5

Q ss_pred             hhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCCCC--CccCcceEEeceEEEeCCcEEE
Q 032889           45 KFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIVCRGTAVML  111 (131)
Q Consensus        45 ~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~~~--~~~~~~~r~lg~v~IRG~~Iv~  111 (131)
                      .|+|+++.+..+.+-.|+|+|.++| +-.-+.|.|+..+-.++...  .+......-+..++.||+.|.-
T Consensus         3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD   72 (74)
T cd01736           3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD   72 (74)
T ss_pred             cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence            5899999999999999999999999 55667799987665443211  1112234567889999998754

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.

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

Probab=96.15  E-value=0.011  Score=45.11  Aligned_cols=65  Identities=26%  Similarity=0.280  Sum_probs=46.2

Q ss_pred             cCcccHhhhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        38 ~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      .+|+.+.+|++|.|+|.+.| +++.|.|..+| -.-||||-+-.|-            .++  ..-+|-|-+|..|...+
T Consensus         7 ~~p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e~------------~~~--sv~~I~ghaVk~vevl~   71 (166)
T PF06372_consen    7 KSPLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQED------------GKR--SVKVIMGHAVKSVEVLS   71 (166)
T ss_dssp             S-HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-TT------------S-E--EEEEE-GGGEEEEEEEE
T ss_pred             CCHHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcccC------------Cce--eEEEEEccceEEEEEcc
Confidence            56788899999999999999 99999999999 5778998864321            122  24788999999999765


Q ss_pred             C
Q 032889          117 G  117 (131)
Q Consensus       117 ~  117 (131)
                      +
T Consensus        72 ~   72 (166)
T PF06372_consen   72 E   72 (166)
T ss_dssp             -
T ss_pred             C
Confidence            4

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.

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

Probab=95.44  E-value=0.032  Score=35.89  Aligned_cols=33  Identities=21%  Similarity=0.363  Sum_probs=28.1

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d   78 (131)
                      --+.+|.|.|.+|-.++|.+.|||+|+=++-.+
T Consensus         9 ~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716           9 KEKIPVTIYLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             HcCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence            345789999999999999999999998766544

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

>TIGR02383 Hfq RNA chaperone Hfq

Probab=95.35  E-value=0.035  Score=35.74  Aligned_cols=33  Identities=24%  Similarity=0.336  Sum_probs=28.2

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d   78 (131)
                      --+.+|.|.|.+|-.+.|.+.|||+|+=|+-.+
T Consensus        13 ~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383        13 KERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             HcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            345789999999999999999999998776544

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.

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

Probab=94.67  E-value=0.097  Score=33.66  Aligned_cols=36  Identities=11%  Similarity=0.170  Sum_probs=30.2

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEE
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE   81 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E   81 (131)
                      .+|..|++++..|.+++|.+.+||.-.++++-.+.+
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            478999999999999999999999777776555433

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.

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=94.66  E-value=0.072  Score=35.98  Aligned_cols=35  Identities=17%  Similarity=0.377  Sum_probs=29.6

Q ss_pred             hhcCCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889           45 KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (131)
Q Consensus        45 ~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da   79 (131)
                      +--+.+|.|.|.+|-.+.|.+.|||+|+=|+-.+.
T Consensus        16 r~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g   50 (79)
T PRK00395         16 RKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG   50 (79)
T ss_pred             HHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence            34567899999999999999999999987776553

>PRK14638 hypothetical protein; Provisional

Probab=94.31  E-value=0.078  Score=39.53  Aligned_cols=36  Identities=14%  Similarity=0.354  Sum_probs=30.0

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEec
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~   77 (131)
                      .+..+++|++|+|++++++.++|+|.++|.- ++.|.
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            4467889999999999999999999999963 45553

>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=93.74  E-value=0.56  Score=31.73  Aligned_cols=59  Identities=19%  Similarity=0.175  Sum_probs=43.8

Q ss_pred             HhhhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           43 LAKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        43 L~~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      |....|++|.+.|-++.++.|++.|+| ...|+..++-. .   +         -...+..++|.+.|++++.
T Consensus        19 l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-T---P---------lGv~~eAlLR~~DVi~~~f   78 (80)
T PF11095_consen   19 LLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-T---P---------LGVQPEALLRCSDVISISF   78 (80)
T ss_dssp             HHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-T---T---------TTEEEEEEEEGGGEEEEEE
T ss_pred             HHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-C---C---------cccChhheeecCCEEEEEe
Confidence            456789999999999999999999999 56677666632 1   1         1125789999999999875

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.

>PRK14639 hypothetical protein; Provisional

Probab=93.32  E-value=0.15  Score=37.52  Aligned_cols=36  Identities=19%  Similarity=0.306  Sum_probs=30.3

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEec
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~   77 (131)
                      -+..+++|++|+|++.+++.+.|+|.++|. .++.|.
T Consensus        81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~-~~i~l~  116 (140)
T PRK14639         81 EHFAKSIGELVKITTNEKEKFEGKIVSVDD-ENITLE  116 (140)
T ss_pred             HHHHHhCCCEEEEEECCCcEEEEEEEEEeC-CEEEEE
Confidence            346788999999999999999999999997 455553

>PRK02001 hypothetical protein; Validated

Probab=93.29  E-value=0.15  Score=38.16  Aligned_cols=36  Identities=22%  Similarity=0.448  Sum_probs=30.3

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEec
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~   77 (131)
                      -+..+++|+.|+|++.+++.++|+|.++|.- ++.|.
T Consensus        83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~  118 (152)
T PRK02001         83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE  118 (152)
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence            4467889999999999999999999999964 45553

>PRK14644 hypothetical protein; Provisional

Probab=91.33  E-value=0.51  Score=34.66  Aligned_cols=35  Identities=20%  Similarity=0.319  Sum_probs=29.4

Q ss_pred             cHhhhcCCeEEEEEcCC----cEEEEEEEEEcCccceEec
Q 032889           42 DLAKFVDKGVQVKLTGG----RQVTGTLKGYDQLLNLVLD   77 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dG----r~i~G~L~~fD~~mNLVL~   77 (131)
                      ++.+++|+.|.|++++.    +.++|+|.++|. -++.|.
T Consensus        79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~-~~i~l~  117 (136)
T PRK14644         79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNP-ETITLK  117 (136)
T ss_pred             HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeC-CEEEEE
Confidence            56788999999999876    899999999997 356564

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

Probab=91.28  E-value=0.39  Score=32.25  Aligned_cols=31  Identities=19%  Similarity=0.394  Sum_probs=26.2

Q ss_pred             hhcCCeEEEEEcCCcEEEEEEEEEcCccceE
Q 032889           45 KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (131)
Q Consensus        45 ~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLV   75 (131)
                      +.-+.+|.|.|.||-.+.|.+.|||+|.=|+
T Consensus        16 Rk~~i~VtIfLvNG~~L~G~V~sfD~f~VlL   46 (77)
T COG1923          16 RKEKIPVTIFLVNGFKLQGQVESFDNFVVLL   46 (77)
T ss_pred             HhcCCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence            3456789999999999999999999997443

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

Probab=91.02  E-value=1.5  Score=28.58  Aligned_cols=52  Identities=25%  Similarity=0.314  Sum_probs=38.3

Q ss_pred             cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      .|++++|++|.|.+..|+. +|+|.+... -.++|+..                   -...+||=..|++|.+
T Consensus        15 ~lq~liG~~vvV~T~~g~v-~G~L~~V~p-DhIvl~~~-------------------~~~~~IR~~~IV~v~p   66 (66)
T PF10842_consen   15 TLQSLIGQRVVVQTTRGSV-RGILVDVKP-DHIVLEEN-------------------GTPFFIRIAQIVWVMP   66 (66)
T ss_pred             HHHHhcCCEEEEEEcCCcE-EEEEEeecC-CEEEEEeC-------------------CcEEEEEeeeEEEEcC
Confidence            4789999999999976665 999999873 23455432                   1247889889988753

>PRK14640 hypothetical protein; Provisional

Probab=90.93  E-value=0.56  Score=34.91  Aligned_cols=36  Identities=22%  Similarity=0.375  Sum_probs=29.1

Q ss_pred             ccHhhhcCCeEEEEE----cCCcEEEEEEEEEcCccceEec
Q 032889           41 LDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVLD   77 (131)
Q Consensus        41 l~L~~~l~k~V~V~L----~dGr~i~G~L~~fD~~mNLVL~   77 (131)
                      .+..+++|++|.|++    .+++.++|+|.++|. -++.|.
T Consensus        90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~-~~v~l~  129 (152)
T PRK14640         90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQG-DMITLT  129 (152)
T ss_pred             HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeC-CEEEEE
Confidence            446788999999999    567999999999996 355554

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

Probab=90.68  E-value=0.54  Score=31.28  Aligned_cols=36  Identities=39%  Similarity=0.515  Sum_probs=28.4

Q ss_pred             cccHhhhcCCeEEEEEc---CC-cEEEEEEEEEcCccceEe
Q 032889           40 VLDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        40 ~l~L~~~l~k~V~V~L~---dG-r~i~G~L~~fD~~mNLVL   76 (131)
                      +.+..+++|+.|.|+++   +| +.+.|+|.++|.- +++|
T Consensus        17 ~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l   56 (83)
T cd01734          17 EADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL   56 (83)
T ss_pred             HHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence            34567889999999997   55 5899999999973 4444

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.

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=90.28  E-value=0.69  Score=35.27  Aligned_cols=33  Identities=18%  Similarity=0.310  Sum_probs=27.7

Q ss_pred             cCCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (131)
Q Consensus        47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da   79 (131)
                      -..+|.|.|.+|-.++|++.+||+|.=|.-.+.
T Consensus        23 ~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g   55 (165)
T PRK14091         23 TKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG   55 (165)
T ss_pred             cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            446789999999999999999999986665553

>PRK14633 hypothetical protein; Provisional

Probab=89.64  E-value=0.63  Score=34.59  Aligned_cols=36  Identities=17%  Similarity=0.276  Sum_probs=28.9

Q ss_pred             ccHhhhcCCeEEEEE----cCCcEEEEEEEEEcCccceEec
Q 032889           41 LDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVLD   77 (131)
Q Consensus        41 l~L~~~l~k~V~V~L----~dGr~i~G~L~~fD~~mNLVL~   77 (131)
                      .+..+++|++|.|++    .+++.++|+|.++|.. ++.|.
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            446788999999999    4678999999999873 55553

>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=89.16  E-value=0.73  Score=33.48  Aligned_cols=35  Identities=31%  Similarity=0.589  Sum_probs=25.9

Q ss_pred             ccHhhhcCCeEEEEE----cCCcEEEEEEEEEcCccceEe
Q 032889           41 LDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        41 l~L~~~l~k~V~V~L----~dGr~i~G~L~~fD~~mNLVL   76 (131)
                      .++.+++|++|.|++    .+.+.++|+|.++|. -.++|
T Consensus        80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            356789999999999    456789999999998 45555

; PDB: 1IB8_A.

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=88.61  E-value=1.4  Score=33.56  Aligned_cols=33  Identities=18%  Similarity=0.325  Sum_probs=28.3

Q ss_pred             cCCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (131)
Q Consensus        47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da   79 (131)
                      -..+|.|.|.+|-.+.|.+.|||+|.=|.-.+.
T Consensus       103 ~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g  135 (165)
T PRK14091        103 SGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG  135 (165)
T ss_pred             cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            456899999999999999999999987766554

>PRK14642 hypothetical protein; Provisional

Probab=88.49  E-value=0.96  Score=35.38  Aligned_cols=35  Identities=17%  Similarity=0.366  Sum_probs=28.7

Q ss_pred             ccHhhhcCCeEEEEEc-------------CCcEEEEEEEEEcCccceEe
Q 032889           41 LDLAKFVDKGVQVKLT-------------GGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~-------------dGr~i~G~L~~fD~~mNLVL   76 (131)
                      .+..+++|+.|.|+|+             +.+.++|+|.++|.. ++.|
T Consensus        93 ~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         93 QDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             HHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            4466789999999998             679999999999973 4444

>PRK14645 hypothetical protein; Provisional

Probab=88.26  E-value=0.8  Score=34.31  Aligned_cols=34  Identities=18%  Similarity=0.302  Sum_probs=27.5

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEe
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL   76 (131)
                      -+..+++|++|.|++ +++.++|+|.++|.- .+.|
T Consensus        95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l  128 (154)
T PRK14645         95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF  128 (154)
T ss_pred             HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence            345678999999986 899999999999963 4544

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=88.15  E-value=0.94  Score=33.57  Aligned_cols=31  Identities=32%  Similarity=0.594  Sum_probs=26.6

Q ss_pred             cccHhhhcCCeEEEEE----cCCcEEEEEEEEEcC
Q 032889           40 VLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQ   70 (131)
Q Consensus        40 ~l~L~~~l~k~V~V~L----~dGr~i~G~L~~fD~   70 (131)
                      +-++.+++|+.|+|++    .+++.++|+|.++|.
T Consensus        90 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         90 ARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             HHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence            3456788999999997    578899999999997

>PRK14636 hypothetical protein; Provisional

Probab=87.47  E-value=0.97  Score=34.59  Aligned_cols=35  Identities=29%  Similarity=0.546  Sum_probs=28.0

Q ss_pred             ccHhhhcCCeEEEEEc---CC-cEEEEEEEEEcCccceEe
Q 032889           41 LDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~---dG-r~i~G~L~~fD~~mNLVL   76 (131)
                      -+..+++|++|.|+++   +| +.++|+|.++|. .++.|
T Consensus        91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~-~~v~l  129 (176)
T PRK14636         91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDG-DTVTI  129 (176)
T ss_pred             HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeC-CEEEE
Confidence            4467889999999997   45 699999999986 34555

>PRK14632 hypothetical protein; Provisional

Probab=87.18  E-value=1.1  Score=34.15  Aligned_cols=36  Identities=19%  Similarity=0.389  Sum_probs=28.6

Q ss_pred             ccHhhhcCCeEEEEEcC-------CcEEEEEEEEEcCccceEec
Q 032889           41 LDLAKFVDKGVQVKLTG-------GRQVTGTLKGYDQLLNLVLD   77 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~d-------Gr~i~G~L~~fD~~mNLVL~   77 (131)
                      -+..+++|+.|.|++.+       .+.++|+|.++|. -++.|.
T Consensus        91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~-~~i~l~  133 (172)
T PRK14632         91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEG-DTVVLR  133 (172)
T ss_pred             HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeC-CEEEEE
Confidence            34678899999999975       6799999999985 355553

>PRK14634 hypothetical protein; Provisional

Probab=87.12  E-value=1.1  Score=33.48  Aligned_cols=36  Identities=19%  Similarity=0.264  Sum_probs=28.3

Q ss_pred             ccHhhhcCCeEEEEEcC----CcEEEEEEEEEcCccceEec
Q 032889           41 LDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQLLNLVLD   77 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~d----Gr~i~G~L~~fD~~mNLVL~   77 (131)
                      .+..+++|++|+|++.+    .+.++|+|.++|. .++.|.
T Consensus        93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~-~~v~l~  132 (155)
T PRK14634         93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNE-DHLQIN  132 (155)
T ss_pred             HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeC-CEEEEE
Confidence            45678899999999963    3789999999996 445553

>PRK14643 hypothetical protein; Provisional

Probab=86.81  E-value=1.2  Score=33.80  Aligned_cols=31  Identities=23%  Similarity=0.324  Sum_probs=26.4

Q ss_pred             ccHhhhcCCeEEEEEcC----CcEEEEEEEEEcCc
Q 032889           41 LDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQL   71 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~d----Gr~i~G~L~~fD~~   71 (131)
                      .+..+++|++|.|++++    .+.++|+|.++|.-
T Consensus        97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            45678899999999965    68999999999964

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=86.39  E-value=1.9  Score=32.47  Aligned_cols=34  Identities=29%  Similarity=0.546  Sum_probs=29.0

Q ss_pred             cHhhhcCCeEEEEE----cCCcEEEEEEEEEcCccceEe
Q 032889           42 DLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        42 ~L~~~l~k~V~V~L----~dGr~i~G~L~~fD~~mNLVL   76 (131)
                      +..+++|+.|.|+|    .+++.+.|+|.++|.-. +++
T Consensus        93 ~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~  130 (153)
T COG0779          93 HFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL  130 (153)
T ss_pred             HHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence            35678999999999    78999999999999776 444

>PRK14646 hypothetical protein; Provisional

Probab=86.38  E-value=1.3  Score=33.14  Aligned_cols=36  Identities=22%  Similarity=0.231  Sum_probs=28.3

Q ss_pred             ccHhhhcCCeEEEEEcC----CcEEEEEEEEEcCccceEec
Q 032889           41 LDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQLLNLVLD   77 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~d----Gr~i~G~L~~fD~~mNLVL~   77 (131)
                      -+..+++|++|+|+|++    -+.++|+|.++|.- ++.|.
T Consensus        93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~  132 (155)
T PRK14646         93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN  132 (155)
T ss_pred             HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            45678899999999954    36789999999973 56553

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

Probab=86.33  E-value=3  Score=35.50  Aligned_cols=72  Identities=15%  Similarity=0.180  Sum_probs=53.7

Q ss_pred             hhhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCC--CCC-ccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           44 AKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDAD--DPL-KTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        44 ~~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~--~~~-~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      ..|||++|.++-+..-.|+|+|.-+| +-.=|-|.+|.-+-.++.  ++. .....+ ....++.||+.|.-+...+
T Consensus         5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~k-Vy~YIlFRGSDIKDL~V~~   80 (361)
T KOG1073|consen    5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDK-VYDYILFRGSDIKDLIVQE   80 (361)
T ss_pred             cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCcc-ceeeEEecCcccceeeecc
Confidence            46899999999999999999999999 888899999754433221  111 112222 6789999999999777654

>PRK06955 biotin--protein ligase; Provisional

Probab=85.65  E-value=3.6  Score=33.56  Aligned_cols=33  Identities=24%  Similarity=0.400  Sum_probs=28.8

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d   78 (131)
                      ++|++|+|...+++.++|++.|+|....|++..
T Consensus       247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~  279 (300)
T PRK06955        247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT  279 (300)
T ss_pred             cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence            488999997667788999999999999999964

>PRK14647 hypothetical protein; Provisional

Probab=85.44  E-value=1.5  Score=32.79  Aligned_cols=35  Identities=17%  Similarity=0.321  Sum_probs=27.5

Q ss_pred             ccHhhhcCCeEEEEEc---------CCcEEEEEEEEEcCccceEe
Q 032889           41 LDLAKFVDKGVQVKLT---------GGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~---------dGr~i~G~L~~fD~~mNLVL   76 (131)
                      .++.+++|++|.|+++         +.+.++|+|.++|. ..+.|
T Consensus        92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~-~~v~l  135 (159)
T PRK14647         92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD-GVVTI  135 (159)
T ss_pred             HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC-CEEEE
Confidence            4567889999999995         35899999999995 34444

>PRK14631 hypothetical protein; Provisional

Probab=84.54  E-value=1.7  Score=33.21  Aligned_cols=35  Identities=17%  Similarity=0.334  Sum_probs=28.0

Q ss_pred             ccHhhhcCCeEEEEEc----CCcEEEEEEEEEc--CccceEe
Q 032889           41 LDLAKFVDKGVQVKLT----GGRQVTGTLKGYD--QLLNLVL   76 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~----dGr~i~G~L~~fD--~~mNLVL   76 (131)
                      .+..+++|+.|.|++.    +.+.++|+|.++|  . .++.|
T Consensus       110 ~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~-~~v~l  150 (174)
T PRK14631        110 EQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLEN-EEIQV  150 (174)
T ss_pred             HHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCC-CEEEE
Confidence            4567889999999995    5699999999998  4 34444

>PRK14637 hypothetical protein; Provisional

Probab=83.21  E-value=2.1  Score=31.92  Aligned_cols=36  Identities=31%  Similarity=0.363  Sum_probs=27.2

Q ss_pred             ccHhhhcCCeEEEEEcCCcEE-EEEEEEEcCccceEec
Q 032889           41 LDLAKFVDKGVQVKLTGGRQV-TGTLKGYDQLLNLVLD   77 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i-~G~L~~fD~~mNLVL~   77 (131)
                      .+..+++|++|.|++.+.+.+ +|+|.++|.- ++.|.
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            446678999999999544556 7999999964 55554

>PRK14641 hypothetical protein; Provisional

Probab=81.64  E-value=2.3  Score=32.50  Aligned_cols=29  Identities=21%  Similarity=0.324  Sum_probs=24.4

Q ss_pred             ccHhhhcCCeEEEEEcC----CcEEEEEEEEEc
Q 032889           41 LDLAKFVDKGVQVKLTG----GRQVTGTLKGYD   69 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~d----Gr~i~G~L~~fD   69 (131)
                      -+..+++|+.|.|++.+    .+.++|+|.++|
T Consensus        97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            34567899999999965    568999999995

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

Probab=80.77  E-value=8  Score=31.47  Aligned_cols=31  Identities=26%  Similarity=0.644  Sum_probs=27.2

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEcCccceEec
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~   77 (131)
                      ++|++|.+.. ++..++|++.++|....|++.
T Consensus       270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~  300 (319)
T PRK11886        270 FLGREVKLII-GDKEISGIARGIDEQGALLLE  300 (319)
T ss_pred             ccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence            5889999987 456799999999999999996

>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins

Probab=80.51  E-value=1.5  Score=29.55  Aligned_cols=62  Identities=23%  Similarity=0.230  Sum_probs=29.5

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCCccccCCC
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPF  125 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~~~~~~p~  125 (131)
                      .-+.+|+++|+||..+.|+  +.|-..|-   +-.|+..-          ...-+...||=++|.++++..     +||-
T Consensus        15 ~~~~~v~L~l~dG~~~~g~--A~dt~~~~---~k~E~L~l----------~~~~~~~~i~Ld~I~~~~al~-----~nPh   74 (80)
T PF07073_consen   15 MYRYPVKLTLKDGEQIEGK--ALDTRTNA---KKEECLVL----------EQDGGEQEIRLDQIASMSALT-----DNPH   74 (80)
T ss_dssp             TTTT-EEEE-TTT--EEES--S-EEE------SSS-EEEE----------EETTEEEEESTT--SEEE---------ETT
T ss_pred             hcCCeEEEEEeCCCEEEEE--EEEEEEec---CceEEEEE----------ecCCcEEEEEhhheeeeeecC-----CCCe
Confidence            4567999999999999997  44433331   22233221          111245678999999999765     5665


Q ss_pred             CC
Q 032889          126 MQ  127 (131)
Q Consensus       126 ~~  127 (131)
                      |+
T Consensus        75 F~   76 (80)
T PF07073_consen   75 FG   76 (80)
T ss_dssp             TE
T ss_pred             ee
Confidence            43

ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.

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

Probab=80.40  E-value=3.1  Score=31.52  Aligned_cols=36  Identities=22%  Similarity=0.242  Sum_probs=32.0

Q ss_pred             hhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceE
Q 032889           45 KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV   80 (131)
Q Consensus        45 ~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~   80 (131)
                      ++-+-+|+|.+.||..+.|.+.+|++--|.+|..+.
T Consensus        26 r~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~   61 (165)
T PF03614_consen   26 RFNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP   61 (165)
T ss_pred             HhcCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence            445678999999999999999999999999998754

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	131
3swn_C	117	Structure Of The Lsm657 Complex: An Assembly Interm		1e-24
4emk_C	113	Crystal Structure Of Splsm567 Length = 113		3e-24
3cw1_G	76	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		6e-11
1th7_A	81	Crystal Structure Of An Archaeal Sm Protein From Su		2e-07
3bw1_A	96	Crystal Structure Of Homomeric Yeast Lsm3 Exhibitin		9e-07
1i5l_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm1) Fr		9e-07
4emg_A	93	Crystal Structure Of Splsm3 Length = 93		9e-06
1i81_A	83	Crystal Structure Of A Heptameric Lsm Protein From		1e-05
1jbm_A	86	Heptameric Crystal Structure Of Mth649, An Sm-Like		2e-04
1loj_A	87	Crystal Structure Of A Methanobacterial Sm-Like Arc		2e-04
1jri_A	85	The Crystal Structure Of An Sm-Like Archaeal Protei		2e-04
1h64_1	75	Crystal Structure Of The Sm-Related Protein Of P. A		4e-04
1m8v_A	77	Structure Of Pyrococcus Abyssii Sm Protein In Compl		5e-04
1ljo_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm2) Fr		7e-04

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

Iteration: 1
 Score =  107 bits (268), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 50/92 (54%), Positives = 72/92 (78%), Gaps = 1/92 (1%)
Query: 36  RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
           RKE++LDL+++ D+ +Q   TGGRQ+TG LKG+DQL+NLVLD+  E LR+ +D  K T  
Sbjct: 25  RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPED-GKLTGA 83
Query: 96  TRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQ 127
            R+LGL+V RGT ++L++P DG++EI NPF+Q
Sbjct: 84  IRKLGLVVVRGTTLVLIAPMDGSEEIPNPFVQ 115

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

Iteration: 1
 Score =  107 bits (266), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 50/92 (54%), Positives = 71/92 (77%), Gaps = 1/92 (1%)
Query: 36  RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
           RKE++LDL+++ D+ +Q   TGGRQ+TG LKG+DQL NLVLD+  E LR+ +D  K T  
Sbjct: 21  RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLXNLVLDDVEEQLRNPED-GKLTGA 79
Query: 96  TRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQ 127
            R+LGL+V RGT ++L++P DG++EI NPF+Q
Sbjct: 80  IRKLGLVVVRGTTLVLIAPXDGSEEIPNPFVQ 111

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 46/72 (63%), Gaps = 8/72 (11%)
Query: 42  DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
           +L KF+DK + +KL GGR V G L+G+D  +NLV+DE VE        + T+ Q   +G+
Sbjct: 8   ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVE--------MATSGQQNNIGM 59
Query: 102 IVCRGTAVMLVS 113
           +V RG +++++ 
Sbjct: 60  VVIRGNSIIMLE 71

>pdb|1TH7|A Chain A, Crystal Structure Of An Archaeal Sm Protein From Sulfolobus Solfataricus Length = 81

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 42/72 (58%), Gaps = 8/72 (11%)
Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           LA+ ++  V VKL G ++V G L+ YDQ +NLVL ++ E   D           ++LG I
Sbjct: 14  LAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSG--------KKLGTI 65
Query: 103 VCRGTAVMLVSP 114
           V RG  V+L+SP
Sbjct: 66  VIRGDNVILISP 77

>pdb|3BW1|A Chain A, Crystal Structure Of Homomeric Yeast Lsm3 Exhibiting Novel Octameric Ring Organisation Length = 96

Iteration: 1
 Score = 48.9 bits (115), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 50/84 (59%), Gaps = 3/84 (3%)
Query: 38  ETVLDLAKF-VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQT 96
           ET LDL K  +D+ V +KL G R + GTL+ +D   N+VL +AVE +   ++  + ++  
Sbjct: 9   ETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNE-ELSESE 67
Query: 97  RQLGLIVCRGTAVMLVS-PTDGTD 119
           R+  ++  RG  V L+S P++  D
Sbjct: 68  RRCEMVFIRGDTVTLISTPSEDDD 91

>pdb|1I5L|A Chain A, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From Archaeoglobus Fulgidus Complexed With Short Poly-U Rna Length = 77

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 8/77 (10%)
Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L + +   V V+L GGR+  GTL GYD  +NLVL +A E        ++  +  R++G +
Sbjct: 9   LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEE--------IQNGEVVRKVGSV 60
Query: 103 VCRGTAVMLVSPTDGTD 119
           V RG  V+ VSP  G +
Sbjct: 61  VIRGDTVVFVSPAPGGE 77

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 44/82 (53%), Gaps = 10/82 (12%)
Query: 41  LDLAKF-VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL-------RDADDPLKT 92
           LDL +  +D+ V VKL G R++ G L  YD+ LN VL +A E +        D D  LKT
Sbjct: 11  LDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNXVLGDAEEIVTIFDDEETDKDKALKT 70
Query: 93  TDQTRQLGLIVCRGTAVMLVSP 114
               +    +  RG +V+L++P
Sbjct: 71  I--RKHYEXLFVRGDSVILIAP 90

>pdb|1I81|A Chain A, Crystal Structure Of A Heptameric Lsm Protein From Methanobacterium Thermoautotrophicum Length = 83

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 8/72 (11%)
Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L   ++  V +KL G R+  G LK +D  +NLVL++A E        L+  + TR+LG +
Sbjct: 20  LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE--------LEDGEVTRRLGTV 71
Query: 103 VCRGTAVMLVSP 114
           + RG  ++ +SP
Sbjct: 72  LIRGDNIVYISP 83

>pdb|1JBM|A Chain A, Heptameric Crystal Structure Of Mth649, An Sm-Like Archaeal Protein From Methanobacterium Thermautotrophicum Length = 86

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 8/71 (11%)
Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L   ++  V +KL G R+  G LK +D  +NLVL++A E        L+  + TR+LG +
Sbjct: 18  LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE--------LEDGEVTRRLGTV 69
Query: 103 VCRGTAVMLVS 113
           + RG  ++ +S
Sbjct: 70  LIRGDNIVYIS 80

>pdb|1LOJ|A Chain A, Crystal Structure Of A Methanobacterial Sm-Like Archaeal Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump) Length = 87

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 8/71 (11%)
Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L   ++  V +KL G R+  G LK +D  +NLVL++A E        L+  + TR+LG +
Sbjct: 18  LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE--------LEDGEVTRRLGTV 69
Query: 103 VCRGTAVMLVS 113
           + RG  ++ +S
Sbjct: 70  LIRGDNIVYIS 80

>pdb|1JRI|A Chain A, The Crystal Structure Of An Sm-Like Archaeal Protein With Two Heptamers In The Asymmetric Unit. Length = 85

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 8/71 (11%)
Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L   ++  V +KL G R+  G LK +D  +NLVL++A E        L+  + TR+LG +
Sbjct: 18  LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE--------LEDGEVTRRLGTV 69
Query: 103 VCRGTAVMLVS 113
           + RG  ++ +S
Sbjct: 70  LIRGDNIVYIS 80

>pdb|1H64|1 Chain 1, Crystal Structure Of The Sm-Related Protein Of P. Abyssi The Biological Unit Is A Heptamer Length = 75

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 8/74 (10%)
Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           + + +DK V V L  G +  G L GYD  LN+VL +A E ++D        +  ++ G I
Sbjct: 9   IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADA-EMIQDG-------EVVKRYGKI 60
Query: 103 VCRGTAVMLVSPTD 116
           V RG  V+ +SPT+
Sbjct: 61  VIRGDNVLAISPTE 74

>pdb|1M8V|A Chain A, Structure Of Pyrococcus Abyssii Sm Protein In Complex With A Uridine Heptamer Length = 77

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 8/74 (10%)
Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           + + +DK V V L  G +  G L GYD  LN+VL +A E ++D        +  ++ G I
Sbjct: 11  IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADA-EMIQDG-------EVVKRYGKI 62
Query: 103 VCRGTAVMLVSPTD 116
           V RG  V+ +SPT+
Sbjct: 63  VIRGDNVLAISPTE 76

>pdb|1LJO|A Chain A, Crystal Structure Of An Sm-Like Protein (Af-Sm2) From Archaeoglobus Fulgidus At 1.95a Resolution Length = 77

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 9/72 (12%)
Query: 46  FVDKGVQVKLTGGR-QVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVC 104
            V K ++V++ G   Q+ G L+G D  +NL L  A+E         K  ++ R LG IV 
Sbjct: 13  MVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAME--------CKGEEKVRSLGEIVL 64
Query: 105 RGTAVMLVSPTD 116
           RG  V+L+ P +
Sbjct: 65  RGNNVVLIQPQE 76

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	131
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	5e-36
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	3e-27
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	9e-27
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	2e-26
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	4e-25
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	1e-23
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	3e-22
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	2e-21
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	8e-21
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	1e-20
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	4e-20
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	3e-19
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	2e-17
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	4e-17
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	2e-15
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	3e-12
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	2e-11
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-10
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	3e-09
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	9e-09
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	5e-06
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	1e-05
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	2e-05
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	3e-05

>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 =  118 bits (298), Expect = 5e-36
 Identities = 50/94 (53%), Positives = 73/94 (77%), Gaps = 1/94 (1%)

Query: 36  RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ 95
           RKE++LDL+++ D+ +Q   TGGRQ+TG LKG+DQL+NLVLD+  E LR+ +D  K T  
Sbjct: 21  RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDG-KLTGA 79

Query: 96  TRQLGLIVCRGTAVMLVSPTDGTDEIANPFMQPD 129
            R+LGL+V RGT ++L++P DG++EI NPF+Q +
Sbjct: 80  IRKLGLVVVRGTTLVLIAPMDGSEEIPNPFVQAE 113

>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 = 95.1 bits (237), Expect = 3e-27
 Identities = 32/87 (36%), Positives = 47/87 (54%), Gaps = 9/87 (10%)

Query: 33  MSGRKETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLK 91
           M+   ET    LA+ ++  V VKL G ++V G L+ YDQ +NLVL ++ E   D      
Sbjct: 3   MNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD------ 56

Query: 92  TTDQTRQLGLIVCRGTAVMLVSPTDGT 118
                ++LG IV RG  V+L+SP   +
Sbjct: 57  --GSGKKLGTIVIRGDNVILISPLQTS 81

>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 = 93.9 bits (234), Expect = 9e-27
 Identities = 30/84 (35%), Positives = 47/84 (55%), Gaps = 10/84 (11%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MS  K    +L KF+DK + +KL GGR V G L+G+D  +NLV+DE VE           
Sbjct: 1   MS--KAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATS------- 51

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTD 116
             Q   +G++V RG +++++   +
Sbjct: 52  -GQQNNIGMVVIRGNSIIMLEALE 74

>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 = 93.6 bits (233), Expect = 2e-26
 Identities = 28/86 (32%), Positives = 47/86 (54%), Gaps = 2/86 (2%)

Query: 36  RKETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTD 94
             ET LD L   +D+ V +KL G R + GTL+ +D   N+VL +AVE +   ++  + ++
Sbjct: 7   HMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNE-ELSE 65

Query: 95  QTRQLGLIVCRGTAVMLVSPTDGTDE 120
             R+  ++  RG  V L+S     D+
Sbjct: 66  SERRCEMVFIRGDTVTLISTPSEDDD 91

>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 = 89.6 bits (223), Expect = 4e-25
 Identities = 32/86 (37%), Positives = 44/86 (51%), Gaps = 10/86 (11%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           M  R   VL+  + +   V V+L GGR+  GTL GYD  +NLVL +A E           
Sbjct: 1   MPPRPLDVLN--RSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG------- 51

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTDGT 118
            +  R++G +V RG  V+ VSP  G 
Sbjct: 52  -EVVRKVGSVVIRGDTVVFVSPAPGG 76

>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 = 86.3 bits (214), Expect = 1e-23
 Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 10/89 (11%)

Query: 30  SLKMSGRKETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADD 88
           +  +S    T+   L   + K V VKL    ++ G L+ +DQ +NL+L++A E +     
Sbjct: 2   ASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII----- 56

Query: 89  PLKTTDQTRQLGLIVCRGTAVMLVSPTDG 117
                    + G +V RG  V+ +SP  G
Sbjct: 57  ----DGNVYKRGTMVVRGENVLFISPVPG 81

>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 = 83.0 bits (205), Expect = 3e-22
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 5/77 (6%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQT-----R 97
           +   +D+ V VKL G R++ G L  YD+ LN+VL +A E +   DD     D+      +
Sbjct: 14  VRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRK 73

Query: 98  QLGLIVCRGTAVMLVSP 114
              ++  RG +V+L++P
Sbjct: 74  HYEMLFVRGDSVILIAP 90

>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 = 80.8 bits (200), Expect = 2e-21
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 8/72 (11%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L   ++  V +KL G R+  G LK +D  +NLVL++A E            + TR+LG +
Sbjct: 20  LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG--------EVTRRLGTV 71

Query: 103 VCRGTAVMLVSP 114
           + RG  ++ +SP
Sbjct: 72  LIRGDNIVYISP 83

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

 Score = 79.5 bits (196), Expect = 8e-21
 Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 4/83 (4%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           M+  K +   + + +D  ++  L  GR   GT K +D+ +NL+L +  EF +      K 
Sbjct: 1   MTVGKSS--KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQ 58

Query: 93  TD--QTRQLGLIVCRGTAVMLVS 113
            +  + R LGL++ RG  ++ ++
Sbjct: 59  AEREEKRVLGLVLLRGENLVSMT 81

>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 = 78.1 bits (193), Expect = 1e-20
 Identities = 28/84 (33%), Positives = 41/84 (48%), Gaps = 10/84 (11%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           M+ R   V+   + +DK V V L  G +  G L GYD  LN+VL +A             
Sbjct: 1   MAERPLDVIH--RSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG------- 51

Query: 93  TDQTRQLGLIVCRGTAVMLVSPTD 116
            +  ++ G IV RG  V+ +SPT+
Sbjct: 52  -EVVKRYGKIVIRGDNVLAISPTE 74

>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 = 78.5 bits (193), Expect = 4e-20
 Identities = 19/79 (24%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQ------- 95
           + K +   + V + G ++ +G L+G+D+ +N+VLD+  E+   AD+   +          
Sbjct: 33  IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVM 92

Query: 96  TRQLGLIVCRGTAVMLVSP 114
             +L  I+  G  V ++ P
Sbjct: 93  VNRLETILLSGNNVAMLVP 111

>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 = 75.1 bits (185), Expect = 3e-19
 Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 8/74 (10%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L K + K V ++L+ G    G L   D  +NL L+   E++           +T   G  
Sbjct: 9   LNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNG--------KKTNVYGDA 60

Query: 103 VCRGTAVMLVSPTD 116
             RG  V+ VS  D
Sbjct: 61  FIRGNNVLYVSALD 74

>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 = 70.0 bits (172), Expect = 2e-17
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 9/75 (12%)

Query: 43  LAKFVDKGVQVKLTGGR-QVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
           +   V K ++V++ G   Q+ G L+G D  +NL L  A+E         K  ++ R LG 
Sbjct: 10  VKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMEC--------KGEEKVRSLGE 61

Query: 102 IVCRGTAVMLVSPTD 116
           IV RG  V+L+ P +
Sbjct: 62  IVLRGNNVVLIQPQE 76

>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 = 69.8 bits (171), Expect = 4e-17
 Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 8/78 (10%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L     K V VKL  G +  G L   D  +N+ L    E++            +  LG +
Sbjct: 11  LNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDG--------ALSGHLGEV 62

Query: 103 VCRGTAVMLVSPTDGTDE 120
           + R   V+ +   +  +E
Sbjct: 63  LIRCNNVLYIRGVEEEEE 80

>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 = 65.6 bits (160), Expect = 2e-15
 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           + K +   + V +   R+  GTL G+D  +N+VL +  E+          T  T +   +
Sbjct: 25  IDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEY-------DTVTGVTEKHSEM 77

Query: 103 VCRGTAVMLVSPTDGTD 119
           +  G  + ++ P    +
Sbjct: 78  LLNGNGMCMLIPGGKPE 94

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

 Score = 57.5 bits (139), Expect = 3e-12
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 7/66 (10%)

Query: 51  VQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVM 110
           V +      ++ G + G+D+ +NLVLD+A E           T   +QLG I+ +G  + 
Sbjct: 33  VWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEI-------HSKTKSRKQLGRIMLKGDNIT 85

Query: 111 LVSPTD 116
           L+    
Sbjct: 86  LLQSVS 91

>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 = 55.6 bits (134), Expect = 2e-11
 Identities = 22/73 (30%), Positives = 28/73 (38%), Gaps = 9/73 (12%)

Query: 43  LAKFVDKGVQVKL-TGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
           L   V+  V VKL     +  GTL   D   NL L+EA EF+               LG 
Sbjct: 26  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG--------VSHGTLGE 77

Query: 102 IVCRGTAVMLVSP 114
           I  R   V+ +  
Sbjct: 78  IFIRCNNVLYIRE 90

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 54.7 bits (131), Expect = 4e-10
 Identities = 20/88 (22%), Positives = 42/88 (47%), Gaps = 2/88 (2%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF--LRDADDPLKTTDQTRQLG 100
           + + +D  ++  L  GR   GT K +D+ +NL+L +  EF  ++  +      ++ R LG
Sbjct: 9   MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 68

Query: 101 LIVCRGTAVMLVSPTDGTDEIANPFMQP 128
           L++ RG  ++ ++      +       P
Sbjct: 69  LVLLRGENLVSMTVEGPPPKDTGIARVP 96

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

 Score = 50.3 bits (120), Expect = 3e-09
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 6/81 (7%)

Query: 40  VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDAD------DPLKTT 93
           VL  +   +  V +     +++ G +K +D+  N+VL+   E   +           K  
Sbjct: 31  VLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPV 90

Query: 94  DQTRQLGLIVCRGTAVMLVSP 114
           ++ R +  +  RG +V++V  
Sbjct: 91  NKDRYISKMFLRGDSVIVVLR 111

>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 = 49.0 bits (117), Expect = 9e-09
 Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 7/74 (9%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L     + + V+L  G    G L+  D  +NL L E +  + D        D+  +L   
Sbjct: 21  LNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPD-------GDKFFRLPEC 73

Query: 103 VCRGTAVMLVSPTD 116
             RG  +  +   D
Sbjct: 74  YIRGNNIKYLRIQD 87

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

 Score = 41.9 bits (98), Expect = 5e-06
 Identities = 19/74 (25%), Positives = 29/74 (39%), Gaps = 8/74 (10%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L K   + V ++L  G QV GT+ G D  +N  L      L++ +          QL  +
Sbjct: 7   LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE--------PVQLETL 58

Query: 103 VCRGTAVMLVSPTD 116
             RG  +      D
Sbjct: 59  SIRGNNIRYFILPD 72

>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 = 41.2 bits (96), Expect = 1e-05
 Identities = 13/74 (17%), Positives = 23/74 (31%), Gaps = 8/74 (10%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L +     V  +   G    G L   +  +N  +       RD         +  QL  +
Sbjct: 10  LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG--------RVAQLEQV 61

Query: 103 VCRGTAVMLVSPTD 116
             RG+ +  +   D
Sbjct: 62  YIRGSKIRFLILPD 75

>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 = 40.5 bits (94), Expect = 2e-05
 Identities = 15/42 (35%), Positives = 20/42 (47%)

Query: 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          V +L   + + VQV L+ G    G L   D  LN+VL  A  
Sbjct: 2  VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASN 43

>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 = 38.5 bits (90), Expect = 3e-05
 Identities = 13/74 (17%), Positives = 22/74 (29%), Gaps = 8/74 (10%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L +     V  +   G    G L   +  +N  +       RD         +  QL  +
Sbjct: 10  LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG--------RVAQLEQV 61

Query: 103 VCRGTAVMLVSPTD 116
             RG  +  +   D
Sbjct: 62  YIRGCKIRFLILPD 75

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	131
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.95
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.88
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.87
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.87
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.87
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.87
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.87
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.87
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.86
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.86
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.86
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.86
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.86
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.85
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.84
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.84
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.84
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.83
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.83
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.83
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.82
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.8
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.76
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.75
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.01
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.61
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	96.53
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	95.95
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	95.78
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	95.69
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	95.6
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	95.45
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	95.2
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	95.19
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	94.78
1ycy_A	71	Conserved hypothetical protein; structural genomic	94.43
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	93.8
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	93.21
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	90.83
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	90.29
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	89.81
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	89.04
2xk0_A	69	Polycomb protein PCL; transcription, aromatic CAGE	87.55
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	84.21
1bia_A	321	BIRA bifunctional protein; transcription regulatio	82.53
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	80.42

>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=99.95  E-value=5.7e-28  Score=171.61  Aligned_cols=98  Identities=51%  Similarity=0.894  Sum_probs=58.5

Q ss_pred             cccccCccCcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEE
Q 032889           31 LKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVM  110 (131)
Q Consensus        31 ~~m~~~~~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv  110 (131)
                      ....++++..++|.+|++++|+|+|+|||+|+|+|+|||+||||||+||+|++..++.. +.....+.+|+++|||++|+
T Consensus        16 ~~~~~kke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~-~~~~~~r~lG~v~IRG~nIv   94 (113)
T 4emk_C           16 PTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDG-KLTGAIRKLGLVVVRGTTLV   94 (113)
T ss_dssp             ----------------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC----------CCEEEEEEEEECTTTEE
T ss_pred             CccCCccchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCc-ccccceeEccEEEECCCeEE
Confidence            34556788889999999999999999999999999999999999999999998643211 12246899999999999999


Q ss_pred             EEeeCCCCccccCCCCCCC
Q 032889          111 LVSPTDGTDEIANPFMQPD  129 (131)
Q Consensus       111 ~I~~~d~~~~~~~p~~~~~  129 (131)
                      +|+++|+.++++|||.+++
T Consensus        95 ~I~~~d~~ee~~~p~~~~~  113 (113)
T 4emk_C           95 LIAPMDGSEEIPNPFVQAE  113 (113)
T ss_dssp             EEEECC-------------
T ss_pred             EEEecCccccccCccccCC
Confidence            9999999999999998864

>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=99.88  E-value=2e-22  Score=138.97  Aligned_cols=78  Identities=31%  Similarity=0.474  Sum_probs=65.0

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCCc
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGTD  119 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~~  119 (131)
                      ..|.++++++|+|+|+|||.|+|+|+|||+||||+|+||+|++..++++. .....+.+|.++|||++|++|.+++..+
T Consensus        13 ~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~-~~~~~r~lG~v~IRG~nVv~I~~~d~~~   90 (96)
T 3bw1_A           13 DLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEE-LSESERRCEMVFIRGDTVTLISTPSEDD   90 (96)
T ss_dssp             HHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTC-CCEEEEEEEEEEECGGGEEEEECCC---
T ss_pred             HHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccc-cCcceeEcCEEEECCCEEEEEEecCccc
Confidence            35689999999999999999999999999999999999999987543211 1245789999999999999999988544

>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=99.87  E-value=2.7e-22  Score=134.07  Aligned_cols=77  Identities=42%  Similarity=0.607  Sum_probs=65.7

Q ss_pred             cccCccCccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEE
Q 032889           33 MSGRKETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVML  111 (131)
Q Consensus        33 m~~~~~~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~  111 (131)
                      |+.-+..|.. |.++++++|+|+|+|||+|+|+|.|||+|||++|+||+|++.+        ...+.+|.++|||++|++
T Consensus         3 m~~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~~I~~   74 (81)
T 1th7_A            3 MNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD--------GSGKKLGTIVIRGDNVIL   74 (81)
T ss_dssp             CCTTCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSS--------SCEEEEEEEEECGGGEEE
T ss_pred             ccccccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecC--------CceeECCEEEECCCEEEE
Confidence            4444445655 5799999999999999999999999999999999999999753        357899999999999999


Q ss_pred             EeeCCC
Q 032889          112 VSPTDG  117 (131)
Q Consensus       112 I~~~d~  117 (131)
                      |.++++
T Consensus        75 i~~~~~   80 (81)
T 1th7_A           75 ISPLQT   80 (81)
T ss_dssp             EEEC--
T ss_pred             EEecCC
Confidence            998863

>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=99.87  E-value=1.7e-22  Score=133.81  Aligned_cols=70  Identities=39%  Similarity=0.786  Sum_probs=53.0

Q ss_pred             CcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        39 ~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      .+..|.+++|++|+|+|+|||+|+|+|.|||+||||+|+||+|++..        ...+.+|.++|||++|++|++.|
T Consensus         5 ~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~lg~v~iRG~~I~~i~~~d   74 (76)
T 3s6n_G            5 HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATS--------GQQNNIGMVVIRGNSIIMLEALE   74 (76)
T ss_dssp             ---------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC------------CBSSEEECSSSEEEEEC--
T ss_pred             chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccC--------CcEeEcCEEEECCCeEEEEEecc
Confidence            55689999999999999999999999999999999999999998753        24688999999999999999876

>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=99.87  E-value=2.6e-22  Score=140.79  Aligned_cols=85  Identities=22%  Similarity=0.304  Sum_probs=55.5

Q ss_pred             ccCcccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889           37 KETVLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT  115 (131)
Q Consensus        37 ~~~~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~  115 (131)
                      +..|+.+ .+++|++|+|+|++|++|+|+|.|||+||||+|+||+|...++       ...+.+|.++|||++|++|..+
T Consensus        14 ~~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg-------~~~~~lg~v~IRG~nI~~I~~p   86 (105)
T 4emh_A           14 PMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDG-------DKFFRLPECYIRGNNIKYLRIQ   86 (105)
T ss_dssp             ------------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTS-------CEEEEEEEEEECGGGEEEEEC-
T ss_pred             CCcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCC-------ceeeEcCeEEEeCCeEEEEecC
Confidence            4556664 6899999999999999999999999999999999999986432       2478899999999999999999


Q ss_pred             CCCccccCCCCCCCC
Q 032889          116 DGTDEIANPFMQPDG  130 (131)
Q Consensus       116 d~~~~~~~p~~~~~~  130 (131)
                      |  +.+++|+++...
T Consensus        87 d--~l~d~p~~~~~~   99 (105)
T 4emh_A           87 D--EVLSQVAKQQAQ   99 (105)
T ss_dssp             ---------------
T ss_pred             H--HHhhhhhhhhhc
Confidence            8  566899988653

>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=5e-22  Score=136.41  Aligned_cols=80  Identities=34%  Similarity=0.561  Sum_probs=63.2

Q ss_pred             CccCcccHhhh-cCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCC-----ccCcceEEeceEEEeCCcE
Q 032889           36 RKETVLDLAKF-VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIVCRGTAV  109 (131)
Q Consensus        36 ~~~~~l~L~~~-l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~-----~~~~~~r~lg~v~IRG~~I  109 (131)
                      ....|++|.+. ++++|+|+|+|||.|+|+|.|||+||||+|+||+|++....+..     ......+.+|+++|||++|
T Consensus         6 ~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nV   85 (93)
T 4emg_A            6 AVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSV   85 (93)
T ss_dssp             ---CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGE
T ss_pred             ccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeE
Confidence            45678898654 99999999999999999999999999999999999986422111     1123578999999999999


Q ss_pred             EEEeeC
Q 032889          110 MLVSPT  115 (131)
Q Consensus       110 v~I~~~  115 (131)
                      ++|+++
T Consensus        86 v~I~p~   91 (93)
T 4emg_A           86 ILIAPP   91 (93)
T ss_dssp             EEEECC
T ss_pred             EEEEec
Confidence            999975

>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=99.87  E-value=7.6e-22  Score=135.99  Aligned_cols=73  Identities=23%  Similarity=0.413  Sum_probs=63.9

Q ss_pred             ccCcccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889           37 KETVLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT  115 (131)
Q Consensus        37 ~~~~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~  115 (131)
                      ...|++| .++++++|+|+|++||+|+|+|+|||+||||+|+||+|++...       ...+.+|.++|||++|++|.+.
T Consensus        18 ~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~-------~~~~~lg~v~IRG~nI~~i~p~   90 (94)
T 4emk_A           18 TILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVT-------GVTEKHSEMLLNGNGMCMLIPG   90 (94)
T ss_dssp             --CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTT-------CCEEEEEEEEECSTTEEEEEEC
T ss_pred             cccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCC-------CcEeEcCEEEEcCCEEEEEEeC
Confidence            5667775 6899999999999999999999999999999999999998321       2488999999999999999987


Q ss_pred             C
Q 032889          116 D  116 (131)
Q Consensus       116 d  116 (131)
                      .
T Consensus        91 ~   91 (94)
T 4emk_A           91 G   91 (94)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.87  E-value=6.8e-22  Score=130.67  Aligned_cols=71  Identities=44%  Similarity=0.698  Sum_probs=63.0

Q ss_pred             ccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCC
Q 032889           40 VLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGT  118 (131)
Q Consensus        40 ~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~  118 (131)
                      |.. |.++++++|+|+|+|||.|+|+|.|||+|||++|+||+|++.+        ...+.+|.++|||++|++|.++|+.
T Consensus         5 P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~~I~~i~~~d~~   76 (77)
T 1i4k_A            5 PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG--------EVVRKVGSVVIRGDTVVFVSPAPGG   76 (77)
T ss_dssp             HHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEEEEECC--
T ss_pred             HHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecC--------CcEeECCEEEECCCEEEEEEeCCCC
Confidence            444 6789999999999999999999999999999999999999753        3588999999999999999998854

>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=99.86  E-value=8.4e-22  Score=131.74  Aligned_cols=71  Identities=35%  Similarity=0.581  Sum_probs=62.7

Q ss_pred             cCccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           38 ETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        38 ~~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      ..|.. |.++++++|+|+|+|||+|+|+|.|||+||||+|+||+|+ ..        ...+.+|.++|||++|++|.++|
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-ID--------GNVYKRGTMVVRGENVLFISPVP   80 (81)
T ss_dssp             CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ET--------TEEEEEEEEEECGGGEEEEEECC
T ss_pred             cchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cC--------CcccCCCEEEECCCEEEEEEeCC
Confidence            44555 5789999999999999999999999999999999999999 31        35889999999999999999886


Q ss_pred             C
Q 032889          117 G  117 (131)
Q Consensus       117 ~  117 (131)
                      +
T Consensus        81 g   81 (81)
T 1i8f_A           81 G   81 (81)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=99.86  E-value=7.4e-22  Score=133.74  Aligned_cols=76  Identities=22%  Similarity=0.309  Sum_probs=64.8

Q ss_pred             CccCccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           36 RKETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        36 ~~~~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      ++..|+. |.++++++|+|+|+||+.|+|+|.|||+||||+|+||+|+...        ...+.+|.++|||++|++|.+
T Consensus         3 ~~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g--------~~~~~lg~v~IRG~nI~~i~~   74 (86)
T 3s6n_F            3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDG--------ALSGHLGEVLIRCNNVLYIRG   74 (86)
T ss_dssp             CCCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEESSEEECGGGEEEEEE
T ss_pred             cCcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCC--------ceeeEccEEEEeCCeEEEEEe
Confidence            3556766 4689999999999999999999999999999999999998631        247899999999999999999


Q ss_pred             CCCCc
Q 032889          115 TDGTD  119 (131)
Q Consensus       115 ~d~~~  119 (131)
                      +|+.+
T Consensus        75 ~d~~~   79 (86)
T 3s6n_F           75 VEEEE   79 (86)
T ss_dssp             CC---
T ss_pred             CCccc
Confidence            98644

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

Probab=99.86  E-value=1.1e-21  Score=129.21  Aligned_cols=69  Identities=39%  Similarity=0.584  Sum_probs=62.0

Q ss_pred             ccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           40 VLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        40 ~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      |.. |.++++++|+|+|+|||.|+|+|.|||+|||++|+||+|++.+        ...+.+|.++|||++|++|.+++
T Consensus         5 P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 1h64_1            5 PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG--------EVVKRYGKIVIRGDNVLAISPTE   74 (75)
T ss_dssp             HHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEEEEEC-
T ss_pred             HHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeC--------CceeECCEEEECCCEEEEEEeCC
Confidence            444 6789999999999999999999999999999999999999753        35889999999999999999876

>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=99.86  E-value=1.1e-21  Score=133.50  Aligned_cols=78  Identities=24%  Similarity=0.426  Sum_probs=64.7

Q ss_pred             cccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCC--CCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADD--PLKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        40 ~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~--~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      ...|.++++++|+|+|+|||+|+|+|+|||+||||+|+||+|++.....  ..+.....+.+|+++|||++|++|..++.
T Consensus         6 ~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~~~~~   85 (91)
T 1d3b_B            6 SSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGP   85 (91)
T ss_dssp             -CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEEEC
T ss_pred             hHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEEcCCC
Confidence            3578999999999999999999999999999999999999998643111  01123468899999999999999998763

>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=99.86  E-value=2.5e-21  Score=128.12  Aligned_cols=70  Identities=34%  Similarity=0.589  Sum_probs=62.3

Q ss_pred             Cccc-HhhhcCCeEEEEEcCC-cEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           39 TVLD-LAKFVDKGVQVKLTGG-RQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        39 ~~l~-L~~~l~k~V~V~L~dG-r~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      .|.. |.++++++|+|+|+|| ++|+|+|.|||+|||++|+||+|++..        ...+.+|.++|||++|++|.++|
T Consensus         5 ~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~nI~~i~~~d   76 (77)
T 1ljo_A            5 LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE--------EKVRSLGEIVLRGNNVVLIQPQE   76 (77)
T ss_dssp             CHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEEEEEC-
T ss_pred             chHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecC--------CcEeECCeEEEeCCeEEEEEeCC
Confidence            3444 6799999999999999 999999999999999999999999742        35889999999999999999886

>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=99.85  E-value=6.6e-21  Score=127.99  Aligned_cols=70  Identities=37%  Similarity=0.642  Sum_probs=62.0

Q ss_pred             ccCccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           37 KETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        37 ~~~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      ...|.. |.++++++|+|+|+|||+|+|+|.|||+|||++|+||+|++.+        ...+.+|.++|||++|++|.+
T Consensus        13 ~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           13 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG--------EVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             TTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEEEEC
T ss_pred             CcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecC--------CcccCCCEEEECCCEEEEEEC
Confidence            344555 5789999999999999999999999999999999999999743        358899999999999999974

>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=99.84  E-value=3.5e-21  Score=127.02  Aligned_cols=69  Identities=30%  Similarity=0.477  Sum_probs=61.3

Q ss_pred             ccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           40 VLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        40 ~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      |+. |.+++|++|+|+|+||++|+|+|.|||+|||++|+||+|+...        ...+.+|.++|||++|++|++.|
T Consensus         5 P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 4emk_B            5 PNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNG--------KKTNVYGDAFIRGNNVLYVSALD   74 (75)
T ss_dssp             HHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETT--------EEEEEEEEEEEEGGGSSEEEEC-
T ss_pred             hHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecC--------CcccEecEEEEcCCeEEEEEecC
Confidence            444 5789999999999999999999999999999999999998632        35789999999999999999875

>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=99.84  E-value=2.2e-21  Score=138.87  Aligned_cols=83  Identities=28%  Similarity=0.476  Sum_probs=64.6

Q ss_pred             ccCcccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCC--CCCccCcc-----eEEeceEEEeCCc
Q 032889           37 KETVLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDAD--DPLKTTDQ-----TRQLGLIVCRGTA  108 (131)
Q Consensus        37 ~~~~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~--~~~~~~~~-----~r~lg~v~IRG~~  108 (131)
                      ...|++| .++++++|+|+|+|||.|+|+|+|||+||||+|+||+|++...+  +.......     .+.+|+++|||++
T Consensus        26 ~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~n  105 (121)
T 2fwk_A           26 IILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNN  105 (121)
T ss_dssp             CCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGG
T ss_pred             ccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCE
Confidence            3456775 68999999999999999999999999999999999999985411  10000112     7889999999999


Q ss_pred             EEEEeeCCCCc
Q 032889          109 VMLVSPTDGTD  119 (131)
Q Consensus       109 Iv~I~~~d~~~  119 (131)
                      |++|.+.+...
T Consensus       106 Vv~I~~~~~~~  116 (121)
T 2fwk_A          106 VAMLVPGGDPD  116 (121)
T ss_dssp             EEEEESSSCC-
T ss_pred             EEEEEecCCCC
Confidence            99999887544

>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=99.84  E-value=4.1e-21  Score=131.78  Aligned_cols=78  Identities=23%  Similarity=0.479  Sum_probs=64.6

Q ss_pred             ccccCccCcccH-hhhcCCeEEEEE----cCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeC
Q 032889           32 KMSGRKETVLDL-AKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRG  106 (131)
Q Consensus        32 ~m~~~~~~~l~L-~~~l~k~V~V~L----~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG  106 (131)
                      +|......|++| .++++++++|++    ++||+|+|+|.|||+||||+|+||+|+..++       ...+.+|.++|||
T Consensus         9 ~~~~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~-------~~~~~lg~v~iRG   81 (92)
T 3s6n_E            9 KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT-------KSRKQLGRIMLKG   81 (92)
T ss_dssp             -----CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSS-------CCEEEEEEEEECG
T ss_pred             ccceeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCC-------CceeEcCeEEEeC
Confidence            333345668886 589999999999    9999999999999999999999999997532       2578999999999


Q ss_pred             CcEEEEeeCC
Q 032889          107 TAVMLVSPTD  116 (131)
Q Consensus       107 ~~Iv~I~~~d  116 (131)
                      ++|++|++.+
T Consensus        82 ~nV~~i~~~~   91 (92)
T 3s6n_E           82 DNITLLQSVS   91 (92)
T ss_dssp             GGEEEEEEC-
T ss_pred             CEEEEEEeCC
Confidence            9999999875

>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=99.83  E-value=2.4e-20  Score=123.22  Aligned_cols=70  Identities=17%  Similarity=0.209  Sum_probs=62.5

Q ss_pred             CcccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           39 TVLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        39 ~~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      .|.++ .+++|++|.|+|++|++|+|+|.|||+|||++|+||+|+..+        ...+.+|.++|||++|.+|..||
T Consensus         5 ~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~--------~~~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            5 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD--------GRVAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTT--------SCEEEEEEEEECGGGEEEEEECC
T ss_pred             CHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCC--------CcEEEcCeEEEeCCEEEEEEcCC
Confidence            46664 689999999999999999999999999999999999998632        24789999999999999999875

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

Probab=99.83  E-value=1.3e-20  Score=129.46  Aligned_cols=72  Identities=31%  Similarity=0.343  Sum_probs=60.5

Q ss_pred             ccCccc-HhhhcCCeEEEEEcCC-cEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           37 KETVLD-LAKFVDKGVQVKLTGG-RQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        37 ~~~~l~-L~~~l~k~V~V~L~dG-r~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      +..|.. |.+++|++|+|+|+|| ++|+|+|.|||+||||+|+||+|++..        ...+.+|.++|||++|++|.+
T Consensus        19 ~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~--------~~~~~lg~v~IRG~nI~~I~~   90 (93)
T 1n9r_A           19 PVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG--------VSHGTLGEIFIRCNNVLYIRE   90 (93)
T ss_dssp             -------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETT--------EEEEECCSEEECGGGEEEEEE
T ss_pred             cCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCC--------CeEeEcCEEEEcCCeEEEEEe
Confidence            344544 5789999999999999 999999999999999999999999632        357899999999999999998


Q ss_pred             CC
Q 032889          115 TD  116 (131)
Q Consensus       115 ~d  116 (131)
                      ++
T Consensus        91 ~~   92 (93)
T 1n9r_A           91 LP   92 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.83  E-value=1.8e-20  Score=146.73  Aligned_cols=76  Identities=25%  Similarity=0.466  Sum_probs=65.0

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecC-CCC-CccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDA-DDP-LKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~-~~~-~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      .+|.+|++|+|+|+|+|||+|+|+|+|||+||||||+||+|++... ++. .....+++++|+++|||+||++|+..+
T Consensus         7 ~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isve~   84 (231)
T 3pgw_B            7 SKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEG   84 (231)
T ss_pred             HHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEecC
Confidence            4789999999999999999999999999999999999999997521 111 122457899999999999999999765

>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=99.82  E-value=3.9e-20  Score=131.77  Aligned_cols=80  Identities=20%  Similarity=0.371  Sum_probs=60.7

Q ss_pred             ccCcccH-hhhc--CCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCC------ccCcceEEeceEEEeCC
Q 032889           37 KETVLDL-AKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL------KTTDQTRQLGLIVCRGT  107 (131)
Q Consensus        37 ~~~~l~L-~~~l--~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~------~~~~~~r~lg~v~IRG~  107 (131)
                      ...|+++ .+++  +++|+|+|+|||.|.|+|+|||+||||+|+||+|++....+..      +.....|.+|.++|||+
T Consensus        25 ~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~  104 (118)
T 1b34_B           25 NTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGD  104 (118)
T ss_dssp             -CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGG
T ss_pred             ccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCC
Confidence            4567775 5778  5999999999999999999999999999999999975421110      11234678999999999


Q ss_pred             cEEEEeeCC
Q 032889          108 AVMLVSPTD  116 (131)
Q Consensus       108 ~Iv~I~~~d  116 (131)
                      +|++|.+.+
T Consensus       105 nVv~I~~~~  113 (118)
T 1b34_B          105 SVIVVLRNP  113 (118)
T ss_dssp             GEEEEEECC
T ss_pred             EEEEEEeCc
Confidence            999999876

>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=99.80  E-value=2.6e-19  Score=127.73  Aligned_cols=68  Identities=28%  Similarity=0.375  Sum_probs=61.6

Q ss_pred             cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      .|.++++++|.|+|+||++|+|+|.+||+||||+|+||+|+..+        ...+.+|.++|||++|++|.++|.
T Consensus         6 ~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~--------~~~~~lg~v~IRG~nI~~I~~pd~   73 (119)
T 1b34_A            6 FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKN--------REPVQLETLSIRGNNIRYFILPDS   73 (119)
T ss_dssp             HHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTT--------SCCEEEEEEEECGGGEEEEECCTT
T ss_pred             HHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCC--------CceeEcceEEEcCCeEEEEEeccc
Confidence            36789999999999999999999999999999999999998632        236789999999999999999985

>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=99.76  E-value=1.1e-18  Score=125.81  Aligned_cols=78  Identities=18%  Similarity=0.238  Sum_probs=65.8

Q ss_pred             Cccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           39 TVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        39 ~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      .|++ |.++++++|.|+|++|++|+|+|.+||+||||+|+||+|+..++        +...++.++|||++|.+|..+|.
T Consensus         5 ~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g--------~~~~l~~v~IRGnnI~~I~lpd~   76 (126)
T 2y9a_D            5 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG--------RVAQLEQVYIRGSKIRFLILPDM   76 (126)
T ss_dssp             CSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTS--------CCEEEEEEEECGGGEEEEECCSS
T ss_pred             cHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCC--------cEeecccEEEeCCEEEEEEcccc
Confidence            4555 46899999999999999999999999999999999999986331        36789999999999999998874


Q ss_pred             CccccCCCC
Q 032889          118 TDEIANPFM  126 (131)
Q Consensus       118 ~~~~~~p~~  126 (131)
                      ..  ..|++
T Consensus        77 l~--~~~~l   83 (126)
T 2y9a_D           77 LK--NAPML   83 (126)
T ss_dssp             CS--SSSHH
T ss_pred             cc--chHHh
Confidence            33  44443

>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=99.75  E-value=2.7e-18  Score=124.45  Aligned_cols=65  Identities=23%  Similarity=0.349  Sum_probs=59.6

Q ss_pred             cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCC
Q 032889           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGT  118 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~  118 (131)
                      .|.+++|++|+|+|+||+.|+|+|.|||+||||+|+||+|+.            .+.+|.++|||++|++|.+++..
T Consensus         4 ~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~------------~~~lg~v~IRG~nI~~I~~~d~~   68 (130)
T 1m5q_A            4 ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA------------GEKFNRVFIMYRYIVHIDSTERR   68 (130)
T ss_dssp             HHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT------------CCEEEEEEECGGGEEEEEECCCC
T ss_pred             HHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc------------CCEeceEEEeCCeEEEEEcCCcc
Confidence            578999999999999999999999999999999999999862            35789999999999999998854

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

Probab=99.01  E-value=8.3e-10  Score=74.64  Aligned_cols=68  Identities=21%  Similarity=0.244  Sum_probs=58.3

Q ss_pred             cCcccHhhhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        38 ~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      ..|++|..++||+|+|+|.||++|+|.|.+|| ...|++|.|+.    +          ......++|.|..|..|...+
T Consensus         7 ~~p~el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~----~----------~~~~~~~iI~G~aI~eI~v~~   72 (86)
T 1y96_A            7 KGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFL----E----------DGSMSVTGIMGHAVQTVETMN   72 (86)
T ss_dssp             SCHHHHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEEC----T----------TSCEEEEEECGGGEEEEEEEE
T ss_pred             CCHHHHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeecc----c----------CCeEEEEEEecceEEEEEEec
Confidence            56889999999999999999999999999999 99999999981    1          123478999999999999876


Q ss_pred             CCc
Q 032889          117 GTD  119 (131)
Q Consensus       117 ~~~  119 (131)
                      ..+
T Consensus        73 ~~~   75 (86)
T 1y96_A           73 EGD   75 (86)
T ss_dssp             CCC
T ss_pred             chh
Confidence            433

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

Probab=97.61  E-value=0.00086  Score=45.15  Aligned_cols=73  Identities=15%  Similarity=0.206  Sum_probs=57.0

Q ss_pred             hhhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCCCC-CccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           44 AKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDP-LKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        44 ~~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~~~-~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      ..|+|+++.+..+.+-.|+|+|...| +..-+.|.+|.-+-.++... ........-+..++.||+.|.-+...+
T Consensus         9 ~~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~~   83 (88)
T 2vxe_A            9 LPELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVN   83 (88)
T ss_dssp             SCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEECC
T ss_pred             CcccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEEec
Confidence            46899999999999999999999999 67789999987765443221 112223445689999999999998876

>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=96.53  E-value=0.012  Score=39.95  Aligned_cols=73  Identities=11%  Similarity=0.196  Sum_probs=55.6

Q ss_pred             hhhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCCCC-CccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           44 AKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDP-LKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        44 ~~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~~~-~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      ..|+|+++.+..+.+-.|+|+|..+| +-.-|.|.+|.-+-.++... ........-+..++.||+.|.-+...+
T Consensus        15 ~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e   89 (95)
T 2fb7_A           15 TPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   89 (95)
T ss_dssp             -CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESC
T ss_pred             CcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEec
Confidence            57999999999999999999999999 67778999987654332211 112233445689999999999998765

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

Probab=95.95  E-value=0.019  Score=37.14  Aligned_cols=34  Identities=18%  Similarity=0.244  Sum_probs=28.9

Q ss_pred             hhcCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889           45 KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (131)
Q Consensus        45 ~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d   78 (131)
                      +--+.+|.|.|.+|-.++|.+.|||+|+=++-.+
T Consensus        22 r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   55 (71)
T 2qtx_A           22 RLNGKKVKIFLRNGEVLDAEVTGVSNYEIMVKVG   55 (71)
T ss_dssp             GGTTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             HHcCCcEEEEEeCCeEEEEEEEEEcceEEEEEeC
Confidence            4466789999999999999999999998666544

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

Probab=95.78  E-value=0.011  Score=39.26  Aligned_cols=30  Identities=23%  Similarity=0.437  Sum_probs=26.7

Q ss_pred             cCCeEEEEEcCCcEEEEEEEEEcCccceEe
Q 032889           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL   76 (131)
                      -+.+|.|.|.+|-.++|.+.+||+|+=|+-
T Consensus        18 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~   47 (82)
T 1u1s_A           18 ERVPVSIYLVNGIKLQGQIESFDQFVILLK   47 (82)
T ss_dssp             TTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEcceEEEEe
Confidence            467899999999999999999999986654

>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=95.69  E-value=0.013  Score=38.14  Aligned_cols=29  Identities=24%  Similarity=0.473  Sum_probs=25.8

Q ss_pred             CCeEEEEEcCCcEEEEEEEEEcCccceEe
Q 032889           48 DKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        48 ~k~V~V~L~dGr~i~G~L~~fD~~mNLVL   76 (131)
                      +.+|.|.|.+|-.++|++.+||+|+=++-
T Consensus        21 k~~Vti~L~nG~~l~G~I~~fD~f~vlL~   49 (74)
T 2ylb_A           21 RVPVSIYLVNGIKLQGQIESFDQFVILLK   49 (74)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             CCcEEEEEeCCCEEEEEEEEECCcEEEEE
Confidence            67899999999999999999999985553

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

Probab=95.60  E-value=0.02  Score=37.66  Aligned_cols=32  Identities=34%  Similarity=0.470  Sum_probs=27.6

Q ss_pred             cCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (131)
Q Consensus        47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d   78 (131)
                      -+.+|.|.|.+|-.++|.+.+||+|+=++-.+
T Consensus        22 ~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~~~   53 (78)
T 3ahu_A           22 ENTYVTVFLLNGFQLRGQVKGFDNFTVLLESE   53 (78)
T ss_dssp             HTCCEEEEETTSCEEEEEEEEECSSEEEEESS
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceEEEEEEC
Confidence            46789999999999999999999998666433

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

Probab=95.45  E-value=0.017  Score=38.03  Aligned_cols=29  Identities=24%  Similarity=0.453  Sum_probs=25.7

Q ss_pred             cCCeEEEEEcCCcEEEEEEEEEcCccceE
Q 032889           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (131)
Q Consensus        47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLV   75 (131)
                      -..+|.|.|.+|-.++|++.+||+|+=++
T Consensus        19 ~k~~VtI~LvnG~~L~G~I~~fD~f~VlL   47 (79)
T 3sb2_A           19 EHVPVSIYLVNGIKLQGHVESFDQYVVLL   47 (79)
T ss_dssp             TTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             cCCeEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            44679999999999999999999998665

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

Probab=95.20  E-value=0.03  Score=39.79  Aligned_cols=39  Identities=26%  Similarity=0.416  Sum_probs=33.9

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEe--cceE
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL--DEAV   80 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL--~da~   80 (131)
                      +++..|+|..|.|+|+||..++|++..+| --+|+|  .+|.
T Consensus         5 ~~~sqFlGy~V~v~LkDgs~~qG~I~~vd-~k~LtL~~~~a~   45 (125)
T 4a53_A            5 MSVADFYGSNVEVLLNNDSKARGVITNFD-SSNSILQLRLAN   45 (125)
T ss_dssp             CCHHHHTTCEEEEEETTSCEEEEEEEEEE-TTTTEEEEEETT
T ss_pred             ccHHHhcCceEEEEECCCCEeeEEEEeec-CCeeEEeccccc
Confidence            35689999999999999999999999999 456777  8873

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

Probab=95.19  E-value=0.036  Score=36.25  Aligned_cols=32  Identities=22%  Similarity=0.342  Sum_probs=27.4

Q ss_pred             cCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (131)
Q Consensus        47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d   78 (131)
                      -..+|.|.|.+|-.++|++.+||+|+=++-.+
T Consensus        18 ~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~~~   49 (77)
T 1kq1_A           18 NQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQ   49 (77)
T ss_dssp             HTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             cCCeEEEEEeCCCEEEEEEEEECCcEEEEEEC
Confidence            36789999999999999999999998665433

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

Probab=94.78  E-value=0.033  Score=38.48  Aligned_cols=30  Identities=23%  Similarity=0.437  Sum_probs=26.2

Q ss_pred             cCCeEEEEEcCCcEEEEEEEEEcCccceEe
Q 032889           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL   76 (131)
                      -..+|.|.|.+|-.++|++.+||+|+=++-
T Consensus        20 ~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~   49 (104)
T 2y90_A           20 ERVPVSIYLVNGIKLQGQIESFDQFVILLK   49 (104)
T ss_dssp             TTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             cCCcEEEEEeCCCEEEEEEEEECCcEEEEE
Confidence            445899999999999999999999986655

>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=94.43  E-value=0.26  Score=31.22  Aligned_cols=59  Identities=19%  Similarity=0.320  Sum_probs=42.0

Q ss_pred             HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      |.++.|+||-|...+...|+|+|.-||.- -|.|.|+..+..            .+-..++++=+.|-.|..
T Consensus        11 L~~WKg~rvAv~vg~ehSFtGiledFDeE-viLL~dV~D~~G------------Nk~k~liv~idDinWimL   69 (71)
T 1ycy_A           11 LKEWKGHKVAVSVGGDHSFTGTLEDFDEE-VILLKDVVDVIG------------NRGKQMLIGLEDINWIML   69 (71)
T ss_dssp             HHHHTTSEEEEEEC----CEEEEEEECSS-EEEEEEEEETTE------------EEEEEEEEEGGGEEEEEE
T ss_pred             HHHhCCcEEEEEecCcceeeeehhhcCcc-eeehhhHHHHhc------------cccceeEEEeccceEEEe
Confidence            67899999999999999999999999965 477899887642            222356677676666544

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

Probab=93.80  E-value=0.14  Score=33.91  Aligned_cols=62  Identities=10%  Similarity=0.148  Sum_probs=48.6

Q ss_pred             hhhcCCeEEEEEcCCc-EEEEEEEEEcCc-cceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           44 AKFVDKGVQVKLTGGR-QVTGTLKGYDQL-LNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        44 ~~~l~k~V~V~L~dGr-~i~G~L~~fD~~-mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      .+|+|+.|.+..+++- .|.|.|..+|.. .||.|.++.   ..+        -+.....+.+|+.-|..+..++
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f---~NG--------~~~~s~eVtls~~DI~~L~ii~   68 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF---HNG--------VKCLVPEVTFRAGDITELKILE   68 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE---ETT--------EECSSSEEEEEGGGCSEEEEEE
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh---hCC--------CCCCCcEEEEEecChhheEEEe
Confidence            4799999999999999 999999999965 589999995   221        1223345889999888777654

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

Probab=93.21  E-value=0.43  Score=31.68  Aligned_cols=59  Identities=15%  Similarity=0.174  Sum_probs=46.7

Q ss_pred             HhhhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           43 LAKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        43 L~~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      |....|++|.+.+.++-.+.|++.++| ...|+..++-. .   +         --.++..++|+..|++++.
T Consensus        24 l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-T---P---------iGv~~eAlLR~~Dii~~sF   83 (85)
T 1y96_B           24 LLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQ-T---P---------IGVQAEALLRCSDIISYTF   83 (85)
T ss_dssp             HHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEC-C---T---------TCCEEEEEEEGGGEEEEEE
T ss_pred             HHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcC-C---C---------cccchhhhhhcCCEEEEEe
Confidence            456689999999999999999999999 66777776632 1   1         1136789999999999875

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

Probab=90.83  E-value=0.29  Score=31.37  Aligned_cols=40  Identities=20%  Similarity=0.211  Sum_probs=31.1

Q ss_pred             ccCcccHhhhcC--CeEEEEEcCCcEEEEEEEEEcCccceEe
Q 032889           37 KETVLDLAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        37 ~~~~l~L~~~l~--k~V~V~L~dGr~i~G~L~~fD~~mNLVL   76 (131)
                      -.+.-.|+.|+.  ..|.|+|.+|..++|++.-+|+++=.+-
T Consensus         8 lPsvR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L~   49 (70)
T 3hfo_A            8 LPSVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLV   49 (70)
T ss_dssp             CHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             CCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEEE
Confidence            334445677744  5799999999999999999999875554

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

Probab=90.29  E-value=0.25  Score=31.83  Aligned_cols=39  Identities=21%  Similarity=0.320  Sum_probs=30.6

Q ss_pred             cCcccHhhhcC--CeEEEEEcCCcEEEEEEEEEcCccceEe
Q 032889           38 ETVLDLAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        38 ~~~l~L~~~l~--k~V~V~L~dGr~i~G~L~~fD~~mNLVL   76 (131)
                      .+.-.|+.|+.  ..|.|+|.+|..++|++.-+|.++=.+-
T Consensus        11 PsvR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L~   51 (72)
T 3hfn_A           11 PSIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIA   51 (72)
T ss_dssp             HHHHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             CcHHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEEE
Confidence            33445678865  4689999999999999999999875444

>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=89.81  E-value=0.43  Score=37.26  Aligned_cols=34  Identities=32%  Similarity=0.499  Sum_probs=30.6

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da   79 (131)
                      ++|++|+|.+.+|..++|+..|+|....|+|...
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            3789999998889999999999999999999754

>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=89.04  E-value=0.35  Score=35.31  Aligned_cols=34  Identities=26%  Similarity=0.370  Sum_probs=27.1

Q ss_pred             cHhhhcCCeEEEEE----cCCcEEEEEEEEEcCccceEe
Q 032889           42 DLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        42 ~L~~~l~k~V~V~L----~dGr~i~G~L~~fD~~mNLVL   76 (131)
                      +..+++|+.|.|++    .+.+.++|+|.++|.- .++|
T Consensus        98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~-~v~l  135 (164)
T 1ib8_A           98 AVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED-ELTM  135 (164)
T ss_dssp             HHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT-EEEE
T ss_pred             HHHHhCCcEEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence            35678999999999    4558999999999964 3444

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

Probab=87.55  E-value=1.6  Score=27.77  Aligned_cols=42  Identities=21%  Similarity=0.313  Sum_probs=30.9

Q ss_pred             hhh-cCCeEEEEEcCCcEEEEEEEEEcCccceE-ecceEEEeec
Q 032889           44 AKF-VDKGVQVKLTGGRQVTGTLKGYDQLLNLV-LDEAVEFLRD   85 (131)
Q Consensus        44 ~~~-l~k~V~V~L~dGr~i~G~L~~fD~~mNLV-L~da~E~~~~   85 (131)
                      .+| +|..|.++-+||+.|-|+++...+..=+| .+|-.|.|..
T Consensus        14 ~~~~~geDVL~rw~DG~fYLGtIVd~~~~~ClV~FeD~S~~Wv~   57 (69)
T 2xk0_A           14 VTYALQEDVFIKCNDGRFYLGTIIDQTSDQYLIRFDDQSEQWCE   57 (69)
T ss_dssp             CCCCTTCEEEEECTTSCEEEEEEEEECSSCEEEEETTCCEEEEC
T ss_pred             cccccCCeEEEEecCCCEEEEEEEecCCceEEEEecCCcceeee
Confidence            455 89999999999999999997766444333 3666666653

>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=84.21  E-value=0.74  Score=34.97  Aligned_cols=31  Identities=19%  Similarity=0.265  Sum_probs=26.7

Q ss_pred             cCCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (131)
Q Consensus        47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da   79 (131)
                      +|++|+|...++  ++|+..|+|....|+|.+.
T Consensus       187 ~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~  217 (233)
T 2eay_A          187 LGEEVKLLGEGK--ITGKLVGLSEKGGALILTE  217 (233)
T ss_dssp             TTSEEEETTEEE--EEEEEEEECTTSCEEEEET
T ss_pred             cCCEEEEEECCe--EEEEEEEECCCCeEEEEEC
Confidence            789999876554  9999999999999999753

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

Probab=82.53  E-value=2.7  Score=33.19  Aligned_cols=33  Identities=21%  Similarity=0.520  Sum_probs=28.4

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da   79 (131)
                      ++|++|+|... +..++|+..|+|....|+|.+.
T Consensus       271 ~~g~~V~v~~~-~~~~~G~~~gid~~G~L~v~~~  303 (321)
T 1bia_A          271 FINRPVKLIIG-DKEIFGISRGIDKQGALLLEQD  303 (321)
T ss_dssp             TTTSEEEEEET-TEEEEEEEEEECTTSCEEEEET
T ss_pred             hcCCEEEEEEC-CcEEEEEEEEECCCCeEEEEEC
Confidence            37899999875 5589999999999999999753

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

Probab=80.42  E-value=3.4  Score=31.35  Aligned_cols=32  Identities=19%  Similarity=0.208  Sum_probs=28.5

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d   78 (131)
                      ++|++|+|...++..++|+..|+|....|+ .+
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            389999999888777999999999999999 64

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	131
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	3e-21
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	8e-20
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	2e-18
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	4e-18
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	8e-18
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	8e-18
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	5e-17
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-16
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	5e-16
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	1e-15
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	3e-11
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	3e-10
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	3e-09

>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 = 79.1 bits (195), Expect = 3e-21
 Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF--LRDADDPLKTTDQTRQLG 100
           + + +D  ++  L  GR   GT K +D+ +NL+L +  EF  ++  +      ++ R LG
Sbjct: 3   MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 62

Query: 101 LIVCRGTAVMLVSP 114
           L++ RG  ++ ++ 
Sbjct: 63  LVLLRGENLVSMTV 76

>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 = 75.7 bits (186), Expect = 8e-20
 Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDAD-------DPLKTTDQ 95
           + K +   + V + G ++ +G L+G+D+ +N+VLD+  E+   AD       +       
Sbjct: 10  IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVM 69

Query: 96  TRQLGLIVCRGTAVMLVSP 114
             +L  I+  G  V ++ P
Sbjct: 70  VNRLETILLSGNNVAMLVP 88

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

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

 Score = 71.7 bits (176), Expect = 2e-18
 Identities = 32/83 (38%), Positives = 46/83 (55%), Gaps = 9/83 (10%)

Query: 33  MSGRKETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLK 91
           M+   ET    LA+ ++  V VKL G ++V G L+ YDQ +NLVL ++ E   D      
Sbjct: 1   MNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD------ 54

Query: 92  TTDQTRQLGLIVCRGTAVMLVSP 114
                ++LG IV RG  V+L+SP
Sbjct: 55  --GSGKKLGTIVIRGDNVILISP 75

>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 = 70.9 bits (174), Expect = 4e-18
 Identities = 28/72 (38%), Positives = 39/72 (54%), Gaps = 8/72 (11%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L + +   V V+L GGR+  GTL GYD  +NLVL +A E            +  R++G +
Sbjct: 8   LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG--------EVVRKVGSV 59

Query: 103 VCRGTAVMLVSP 114
           V RG  V+ VSP
Sbjct: 60  VIRGDTVVFVSP 71

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

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

 Score = 70.1 bits (172), Expect = 8e-18
 Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 8/73 (10%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           + + +DK V V L  G +  G L GYD  LN+VL +A              +  ++ G I
Sbjct: 7   IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG--------EVVKRYGKI 58

Query: 103 VCRGTAVMLVSPT 115
           V RG  V+ +SPT
Sbjct: 59  VIRGDNVLAISPT 71

>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 = 70.1 bits (172), Expect = 8e-18
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 8/72 (11%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L   ++  V +KL G R+  G LK +D  +NLVL++A E            + TR+LG +
Sbjct: 11  LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG--------EVTRRLGTV 62

Query: 103 VCRGTAVMLVSP 114
           + RG  ++ +SP
Sbjct: 63  LIRGDNIVYISP 74

>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 = 68.8 bits (168), Expect = 5e-17
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 6/81 (7%)

Query: 40  VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADD------PLKTT 93
           VL  +   +  V +     +++ G +K +D+  N+VL+   E   +           K  
Sbjct: 6   VLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPV 65

Query: 94  DQTRQLGLIVCRGTAVMLVSP 114
           ++ R +  +  RG +V++V  
Sbjct: 66  NKDRYISKMFLRGDSVIVVLR 86

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

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

 Score = 66.7 bits (163), Expect = 2e-16
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 9/72 (12%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L   + K V VKL    ++ G L+ +DQ +NL+L++A E                + G +
Sbjct: 7   LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI---------IDGNVYKRGTM 57

Query: 103 VCRGTAVMLVSP 114
           V RG  V+ +SP
Sbjct: 58  VVRGENVLFISP 69

>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 = 65.5 bits (160), Expect = 5e-16
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 9/73 (12%)

Query: 43  LAKFVDKGVQVKLT-GGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
           +   V K ++V++     Q+ G L+G D  +NL L  A+E   +        ++ R LG 
Sbjct: 10  VKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE--------EKVRSLGE 61

Query: 102 IVCRGTAVMLVSP 114
           IV RG  V+L+ P
Sbjct: 62  IVLRGNNVVLIQP 74

>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 = 64.3 bits (157), Expect = 1e-15
 Identities = 22/73 (30%), Positives = 28/73 (38%), Gaps = 9/73 (12%)

Query: 43  LAKFVDKGVQVKL-TGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGL 101
           L   V+  V VKL     +  GTL   D   NL L+EA EF+               LG 
Sbjct: 1   LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG--------VSHGTLGE 52

Query: 102 IVCRGTAVMLVSP 114
           I  R   V+ +  
Sbjct: 53  IFIRCNNVLYIRE 65

>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 = 53.2 bits (128), Expect = 3e-11
 Identities = 13/74 (17%), Positives = 22/74 (29%), Gaps = 8/74 (10%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L +     V  +   G    G L   +  +N  +       RD         +  QL  +
Sbjct: 7   LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG--------RVAQLEQV 58

Query: 103 VCRGTAVMLVSPTD 116
             RG  +  +   D
Sbjct: 59  YIRGCKIRFLILPD 72

>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 52.0 bits (125), Expect = 3e-10
 Identities = 14/40 (35%), Positives = 19/40 (47%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          +L   + + VQV L+ G    G L   D  LN+VL  A  
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASN 43

>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 = 48.2 bits (115), Expect = 3e-09
 Identities = 19/74 (25%), Positives = 29/74 (39%), Gaps = 8/74 (10%)

Query: 43  LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           L K   + V ++L  G QV GT+ G D  +N  L      L++         +  QL  +
Sbjct: 6   LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNR--------EPVQLETL 57

Query: 103 VCRGTAVMLVSPTD 116
             RG  +      D
Sbjct: 58  SIRGNNIRYFILPD 71

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	131
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.89
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.86
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.86
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.86
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.85
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.85
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.85
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.84
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.83
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.82
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.79
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.74
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.65
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	97.37
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	96.65
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	94.74
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	94.31
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	93.65
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	93.47

>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=99.89  E-value=2e-23  Score=138.36  Aligned_cols=74  Identities=26%  Similarity=0.469  Sum_probs=63.4

Q ss_pred             cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCC--CccCcceEEeceEEEeCCcEEEEeeC
Q 032889           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIVCRGTAVMLVSPT  115 (131)
Q Consensus        42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~--~~~~~~~r~lg~v~IRG~~Iv~I~~~  115 (131)
                      +|.+|++++|+|+|+|||.|.|+|.|||+||||+|+||.|++......  .......|.+|+++|||++|++|+..
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEcc
Confidence            578999999999999999999999999999999999999987543221  22334678999999999999999864

>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=99.86  E-value=4.5e-22  Score=128.93  Aligned_cols=66  Identities=33%  Similarity=0.592  Sum_probs=60.5

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT  115 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~  115 (131)
                      ..|.++++++|+|+|+||+.|+|+|.|||+||||+|+||+|+..         .+.+++|.++|||++|++|+++
T Consensus         5 ~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~---------~~~~~~g~v~iRG~~I~~I~~~   70 (71)
T d1i8fa_           5 ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID---------GNVYKRGTMVVRGENVLFISPV   70 (71)
T ss_dssp             HHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEET---------TEEEEEEEEEECGGGEEEEEEC
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEEC---------CCEEEcceEEEeCCeEEEEeCC
Confidence            46889999999999999999999999999999999999999864         2478899999999999999864

>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=99.86  E-value=6.1e-22  Score=127.89  Aligned_cols=68  Identities=38%  Similarity=0.566  Sum_probs=61.2

Q ss_pred             Cccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           39 TVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        39 ~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      .|++ |.+++|++|+|+|+||+.|+|+|.|||+||||+|+||.|+...        ...+++|.++|||++|++|++
T Consensus         2 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           2 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG--------EVVKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEEEEE
T ss_pred             CchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecC--------CcEeEcCcEEEECCeEEEEeC
Confidence            4666 4689999999999999999999999999999999999998642        357889999999999999986

>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=99.86  E-value=5.8e-22  Score=128.48  Aligned_cols=68  Identities=44%  Similarity=0.701  Sum_probs=60.6

Q ss_pred             Cccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           39 TVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        39 ~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      .|++ |.++++++|+|+|+||+.|+|+|.|||+||||+|+||+|+...        ...+++|.++|||++|++|++
T Consensus         3 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~~g~~~IRG~~I~~Isp   71 (72)
T d1i4k1_           3 RPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG--------EVVRKVGSVVIRGDTVVFVSP   71 (72)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSS--------SEEEEEEEEEECGGGEEEEEC
T ss_pred             ChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecC--------CeEeEcceEEEeCCeEEEEEc
Confidence            3556 4689999999999999999999999999999999999998643        357889999999999999974

>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=99.85  E-value=1.1e-21  Score=128.43  Aligned_cols=69  Identities=43%  Similarity=0.673  Sum_probs=61.3

Q ss_pred             Cccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889           39 TVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT  115 (131)
Q Consensus        39 ~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~  115 (131)
                      .|.. |.+++|++|+|+|+||+.|+|+|.|||+||||+|+||+|+..+        .+++.+|.++|||++|++|++.
T Consensus         7 ~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~~~~v~iRG~~I~~I~~~   76 (76)
T d1th7a1           7 TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD--------GSGKKLGTIVIRGDNVILISPL   76 (76)
T ss_dssp             HHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSS--------SCEEEEEEEEECGGGEEEEEEC
T ss_pred             cHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecC--------CcccCcceEEEECCEEEEEEeC
Confidence            3444 5789999999999999999999999999999999999998653        3478999999999999999874

>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=99.85  E-value=1.1e-21  Score=133.12  Aligned_cols=78  Identities=21%  Similarity=0.378  Sum_probs=59.0

Q ss_pred             CcccH-hhhc--CCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCC------ccCcceEEeceEEEeCCcE
Q 032889           39 TVLDL-AKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL------KTTDQTRQLGLIVCRGTAV  109 (131)
Q Consensus        39 ~~l~L-~~~l--~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~------~~~~~~r~lg~v~IRG~~I  109 (131)
                      +|+++ .+++  +++|+|.|+|||.+.|+|.|||+||||||+||+|++.......      +.....|.+|+++|||+||
T Consensus         2 GPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnV   81 (93)
T d1b34b_           2 GPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSV   81 (93)
T ss_dssp             CHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGE
T ss_pred             CcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEE
Confidence            46665 4666  8999999999999999999999999999999999987533221      1234578999999999999


Q ss_pred             EEEeeCC
Q 032889          110 MLVSPTD  116 (131)
Q Consensus       110 v~I~~~d  116 (131)
                      ++|..+.
T Consensus        82 v~I~~~p   88 (93)
T d1b34b_          82 IVVLRNP   88 (93)
T ss_dssp             EEEEECC
T ss_pred             EEEEcCh
Confidence            9998654

>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=99.85  E-value=2.9e-21  Score=125.74  Aligned_cols=69  Identities=38%  Similarity=0.659  Sum_probs=61.5

Q ss_pred             cCccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           38 ETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        38 ~~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      ..|++ |.++++++|.|.|+||+.|.|+|.|||+||||+|+||.|+..+        ...+.+|.++|||++|.+|+|
T Consensus         5 ~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~--------~~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           5 QRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG--------EVTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             TCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEEEEC
T ss_pred             cCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCC--------CeEeEcceEEEeCCEEEEEeC
Confidence            44666 4689999999999999999999999999999999999998643        357889999999999999975

>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=99.84  E-value=1.4e-21  Score=131.97  Aligned_cols=77  Identities=26%  Similarity=0.479  Sum_probs=62.1

Q ss_pred             Cccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCC-------CccCcceEEeceEEEeCCcEE
Q 032889           39 TVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP-------LKTTDQTRQLGLIVCRGTAVM  110 (131)
Q Consensus        39 ~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~-------~~~~~~~r~lg~v~IRG~~Iv  110 (131)
                      .|++ |.++++++|+|.|+|||.|.|+|.|||+||||+|+||.|++......       .......|++|+++|||++|+
T Consensus         5 ~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~Vv   84 (92)
T d2fwka1           5 LPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVA   84 (92)
T ss_dssp             CHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEE
T ss_pred             ChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEEE
Confidence            4566 46899999999999999999999999999999999999997643211       112345678999999999999


Q ss_pred             EEeeC
Q 032889          111 LVSPT  115 (131)
Q Consensus       111 ~I~~~  115 (131)
                      +|++.
T Consensus        85 ~I~p~   89 (92)
T d2fwka1          85 MLVPG   89 (92)
T ss_dssp             EEESS
T ss_pred             EEEeC
Confidence            99863

>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=99.83  E-value=1.2e-20  Score=121.30  Aligned_cols=65  Identities=34%  Similarity=0.445  Sum_probs=57.7

Q ss_pred             HhhhcCCeEEEEEc-CCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889           43 LAKFVDKGVQVKLT-GGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT  115 (131)
Q Consensus        43 L~~~l~k~V~V~L~-dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~  115 (131)
                      |.++++++|.|+|+ +|++|+|+|.+||+|||++|+||+|+..+        ...+++|.++|||++|.+|...
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~lg~~~IRG~nI~~I~~~   66 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG--------VSHGTLGEIFIRCNNVLYIREL   66 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETT--------EEEEECCSEEECGGGEEEEEEC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecC--------CcccCcCeEEEECCEEEEEEeC
Confidence            56899999999999 56889999999999999999999998642        3577899999999999999854

>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=99.82  E-value=2.4e-20  Score=121.86  Aligned_cols=68  Identities=35%  Similarity=0.593  Sum_probs=59.9

Q ss_pred             Cccc-HhhhcCCeEEEEEcCC-cEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889           39 TVLD-LAKFVDKGVQVKLTGG-RQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP  114 (131)
Q Consensus        39 ~~l~-L~~~l~k~V~V~L~dG-r~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~  114 (131)
                      .|+. |.++++++|+|+|++| |.|.|+|.|||+|||++|+||+|+..+        ...+.+|.++|||++|.+|.+
T Consensus         5 ~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           5 LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE--------EKVRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             CHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEEEEE
T ss_pred             ccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCC--------CcEeEcceEEEeCCEEEEEEC
Confidence            4555 5689999999999865 899999999999999999999998643        358899999999999999986

>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=99.79  E-value=2.2e-19  Score=116.22  Aligned_cols=69  Identities=17%  Similarity=0.212  Sum_probs=61.5

Q ss_pred             cccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889           40 VLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD  116 (131)
Q Consensus        40 ~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d  116 (131)
                      |+.+ .++.|++|+|+|+||++|+|+|.++|.|||++|+||.++..+        .+.++++.++|||++|.+|..||
T Consensus         3 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~--------~~~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           3 PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD--------GRVAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             HHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTT--------SCEEEEEEEEECGGGEEEEEECC
T ss_pred             chHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCC--------CcEeEcCeEEEECCEEEEEEcCC
Confidence            5564 688999999999999999999999999999999999987643        24678999999999999999886

>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=99.74  E-value=6.4e-18  Score=111.43  Aligned_cols=69  Identities=28%  Similarity=0.381  Sum_probs=61.4

Q ss_pred             HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCCc
Q 032889           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGTD  119 (131)
Q Consensus        43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~~  119 (131)
                      |.++.|++|.|+|++|..|+|+|.++|.|||++|+||.+...++        +..+++.++|||++|.+|..||..+
T Consensus         6 L~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~--------~~~~~~~v~IRG~~Ir~i~lPd~l~   74 (80)
T d1b34a_           6 LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNR--------EPVQLETLSIRGNNIRYFILPDSLP   74 (80)
T ss_dssp             HHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTS--------CCEEEEEEEECGGGEEEEECCTTCC
T ss_pred             HHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCC--------CEEEcccEEEcCCEEEEEECCCCcc
Confidence            57889999999999999999999999999999999999875432        3678999999999999999987543

>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=99.65  E-value=1.4e-16  Score=113.31  Aligned_cols=65  Identities=23%  Similarity=0.344  Sum_probs=58.0

Q ss_pred             ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      ..|.+++|++|.|.|+||+.|.|+|.+||+|||++|+||++..            ...++.++|||++|.+|..++.
T Consensus         3 ~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~------------~~k~~~v~IRG~~I~~I~~~e~   67 (127)
T d1m5q1_           3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA------------GEKFNRVFIMYRYIVHIDSTER   67 (127)
T ss_dssp             HHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETT------------CCEEEEEEECGGGEEEEEECSC
T ss_pred             hHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECC------------CCcccEEEEeCCeEEEEEcchh
Confidence            4688999999999999999999999999999999999998742            2247889999999999998874

>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=97.37  E-value=0.0014  Score=41.84  Aligned_cols=72  Identities=11%  Similarity=0.192  Sum_probs=55.9

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCCCC-CccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDP-LKTTDQTRQLGLIVCRGTAVMLVSPTDG  117 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~~~-~~~~~~~r~lg~v~IRG~~Iv~I~~~d~  117 (131)
                      |+|+++.+..+.+-.|+|+|..+| +-.-+.|.|+.-+-.++... .+......-++.++.||+.|.-+...+.
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e~   75 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEP   75 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESSC
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEeccC
Confidence            799999999999999999999999 55568899988765443211 1222345567899999999999998764

>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=96.65  E-value=0.0035  Score=35.72  Aligned_cols=33  Identities=24%  Similarity=0.597  Sum_probs=29.1

Q ss_pred             hcCCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (131)
Q Consensus        46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da   79 (131)
                      |++++|+|.. ++++++|+..++|....|+|...
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t~   33 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQD   33 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEET
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEEC
Confidence            6899999976 56889999999999999999754

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

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

Probab=94.74  E-value=0.03  Score=33.55  Aligned_cols=34  Identities=21%  Similarity=0.310  Sum_probs=29.3

Q ss_pred             cCCeEEEEEcCCcEEEEEEEEEcCccceEecceE
Q 032889           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV   80 (131)
Q Consensus        47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~   80 (131)
                      -..+|.|.|.+|-.+.|.+.|||+|.=+.-.+..
T Consensus        13 ~~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~~~   46 (60)
T d1kq1a_          13 NQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGK   46 (60)
T ss_dssp             HTCEEEEEETTSCEEEEEEEEECSSEEEEEETTE
T ss_pred             cCCcEEEEEECCcEEEEEEEEEcceEEEEEeCCc
Confidence            4578999999999999999999999877766544

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

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

Probab=94.31  E-value=0.027  Score=34.38  Aligned_cols=29  Identities=24%  Similarity=0.476  Sum_probs=25.5

Q ss_pred             cCCeEEEEEcCCcEEEEEEEEEcCccceE
Q 032889           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (131)
Q Consensus        47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLV   75 (131)
                      -..+|.|.|.+|-.+.|.+.|||+|.=|.
T Consensus        13 ~~~~VtifL~nGvkl~G~I~~fD~ftvLL   41 (66)
T d1u1sa1          13 ERVPVSIYLVNGIKLQGQIESFDQFVILL   41 (66)
T ss_dssp             TTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             cCCcEEEEEEcCcEEEEEEEEEcceEEEE
Confidence            45789999999999999999999997543

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

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

Probab=93.65  E-value=0.22  Score=29.62  Aligned_cols=58  Identities=19%  Similarity=0.338  Sum_probs=40.5

Q ss_pred             HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEe
Q 032889           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVS  113 (131)
Q Consensus        43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~  113 (131)
                      |.++.|+||-|.......++|+|.-||.- -|.|.|+..+..            .+-..++++=+.|-.|.
T Consensus         7 L~~WKg~kvAv~vgsehSFtGiledFDeE-viLL~dV~D~~G------------Nk~k~llv~idD~nWim   64 (66)
T d1ycya1           7 LKEWKGHKVAVSVGGDHSFTGTLEDFDEE-VILLKDVVDVIG------------NRGKQMLIGLEDINWIM   64 (66)
T ss_dssp             HHHHTTSEEEEEEC----CEEEEEEECSS-EEEEEEEEETTE------------EEEEEEEEEGGGEEEEE
T ss_pred             HHHhCCcEEEEEecCcceeEEEhhhcCcc-eEeehhhHHHhc------------cccceeEEEeccceeEE
Confidence            67899999999999999999999999965 477899887643            22234666666655543

>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=93.47  E-value=0.04  Score=33.53  Aligned_cols=36  Identities=25%  Similarity=0.245  Sum_probs=28.9

Q ss_pred             cccHhhhcCCeEEEEEc----CCcEEEEEEEEEcCccceEe
Q 032889           40 VLDLAKFVDKGVQVKLT----GGRQVTGTLKGYDQLLNLVL   76 (131)
Q Consensus        40 ~l~L~~~l~k~V~V~L~----dGr~i~G~L~~fD~~mNLVL   76 (131)
                      +.+..+|+|+.|.|+|+    +-+.++|+|.++|.-. +.|
T Consensus         6 ~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~-i~l   45 (74)
T d1ib8a1           6 KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE-LTM   45 (74)
T ss_dssp             HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE-EEE
T ss_pred             HHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCCe-EEE
Confidence            45678999999999984    4579999999999753 444