Citrus Sinensis ID: 033737

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110--
Protein Sequence
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVTN
Secondary Structure (PSIPRED)
ccccEEEcEEEEEEEEEcccEEccccccccccccccccccccHHHHcccEEEEEEcccEEEEEEEEEEcccccEEEccEEEEEEcccccccccccEEEEEEEEEEccEEEEc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEEEEEEEccccccccHHHHHHHccccccHHHHHHHHHHcccEEEEEccccEEEEEEEEEcccccEEEEEEEEHHccccccccccHccccccEEEEcccHcccc
Coil and Loop (DISEMBL)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVqvkltggrqvtgtlKGYDQLLNLVLDEAVEFLrdaddplkttdqtrqlglignccdacvtn
Flexible Loop (DISEMBL)
MQAFVEINAVSFFIVCRSARVSFNLGflkslkmsgrKETVLDLAkfvdkgvqvkltggrqvtgtlkgYDQLLNLVLDEAVEFLrdaddplkttdqtrqlglignCCDACVTN
Low Complexity Region (SEG)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVTN
Disordered region (IsUnstruct)
***FVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV**
Disordered Region (DISOPRED)
*******NAVSFFIVCRSAR*************************FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL************TRQLGLIGNCCDACV**
Disordered Region (DISEMBL)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVTN
Disordered Region (DISPRO)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVTN
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	112	2.2.26 [Sep-21-2011]
Q54HF6	97	Probable U6 snRNA-associa	yes	no	0.598	0.690	0.611	1e-17
Q9UK45	103	U6 snRNA-associated Sm-li	yes	no	0.633	0.689	0.549	2e-17
Q9CQQ8	103	U6 snRNA-associated Sm-li	yes	no	0.633	0.689	0.549	3e-17
O74499	113	U6 snRNA-associated Sm-li	yes	no	0.589	0.584	0.537	2e-13
P53905	115	U6 snRNA-associated Sm-li	yes	no	0.589	0.573	0.507	7e-13
Q9N4G9	77	Probable small nuclear ri	no	no	0.401	0.584	0.466	2e-07
O82221	80	Probable small nuclear ri	no	no	0.357	0.5	0.575	3e-07
P62309	76	Small nuclear ribonucleop	no	no	0.473	0.697	0.409	4e-07
P62308	76	Small nuclear ribonucleop	no	no	0.473	0.697	0.409	4e-07
Q3ZBL0	76	Small nuclear ribonucleop	no	no	0.473	0.697	0.409	4e-07

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

 Score = 88.6 bits (218), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 41/67 (61%), Positives = 54/67 (80%)

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  TRQLGLI 102
            R LGL+
Sbjct: 68  KRFLGLV 74

Binds specifically to the 3'-terminal U-tract of U6 snRNA.
Dictyostelium discoideum (taxid: 44689)

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

 Score = 87.8 bits (216), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 39/71 (54%), Positives = 55/71 (77%)

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  TTDQTRQLGLI 102
            T+ TRQLGL+
Sbjct: 64  LTEDTRQLGLV 74

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 = 87.0 bits (214), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 39/71 (54%), Positives = 55/71 (77%)

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  TTDQTRQLGLI 102
            T+ TRQLGL+
Sbjct: 64  LTEDTRQLGLV 74

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

Mus musculus (taxid: 10090)

>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 = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/67 (53%), Positives = 51/67 (76%), Gaps = 1/67 (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  TRQLGLI 102
            R+LGL+
Sbjct: 80  IRKLGLV 86

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 = 72.4 bits (176), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 35/69 (50%), Positives = 49/69 (71%), Gaps = 3/69 (4%)

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

Query: 93  TDQTRQLGL 101
           +   R+LGL
Sbjct: 83  SKNARKLGL 91

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 = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/45 (46%), Positives = 35/45 (77%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDA 86
          +L K++DK + +KL G R+V+G L+G+D  +N+V+DEAVE+ +D 
Sbjct: 8  ELKKYMDKEMDLKLNGNRRVSGILRGFDPFMNMVIDEAVEYQKDG 52

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

Caenorhabditis elegans (taxid: 6239)

>sp|O82221|RUXG_ARATH Probable small nuclear ribonucleoprotein G OS=Arabidopsis thaliana GN=At2g23930 PE=2 SV=1

 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/40 (57%), Positives = 31/40 (77%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          DL K++DK +Q+KL   R VTGTL+G+DQ +NLV+D  VE
Sbjct: 9  DLKKYMDKKLQIKLNANRMVTGTLRGFDQFMNLVVDNTVE 48

Probable common Sm protein, is found in U1 and U2 snRNPs.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 8/61 (13%)

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 I 102
           +
Sbjct: 60  V 60

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 = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 8/61 (13%)

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 I 102
           +
Sbjct: 60  V 60

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 = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 8/61 (13%)

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 I 102
           +
Sbjct: 60  V 60

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)

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	112
294464784	80	unknown [Picea sitchensis]	0.714	1.0	0.887	4e-33
224059650	99	predicted protein [Populus trichocarpa]	0.625	0.707	0.985	8e-31
351720779	99	uncharacterized protein LOC100306498 [Gl	0.625	0.707	0.971	2e-30
449463763	99	PREDICTED: U6 snRNA-associated Sm-like p	0.625	0.707	0.971	2e-30
388507056	99	unknown [Medicago truncatula]	0.625	0.707	0.971	2e-30
356512406	99	PREDICTED: U6 snRNA-associated Sm-like p	0.625	0.707	0.971	2e-30
15227722	99	U6 snRNA-associated Sm-like protein LSm7	0.625	0.707	0.957	4e-30
255544228	99	conserved hypothetical protein [Ricinus	0.625	0.707	0.957	4e-30
297814702	99	hypothetical protein ARALYDRAFT_484298 [	0.625	0.707	0.957	4e-30
294463208	98	unknown [Picea sitchensis]	0.625	0.714	0.942	7e-30

>gi|294464784|gb|ADE77898.1| unknown [Picea sitchensis]

 Score =  145 bits (365), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 71/80 (88%), Positives = 74/80 (92%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKF+DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA+EFLRD DDPLKT
Sbjct: 1   MSGRKETVLDLAKFIDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAIEFLRDQDDPLKT 60

Query: 93  TDQTRQLGLIGNCCDACVTN 112
           TDQTR LGLI NC  AC +N
Sbjct: 61  TDQTRPLGLIRNCSHACCSN 80

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  137 bits (345), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 69/70 (98%), Positives = 70/70 (100%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT
Sbjct: 1   MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 60

Query: 93  TDQTRQLGLI 102
           TDQTR+LGLI
Sbjct: 61  TDQTRRLGLI 70

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 =  135 bits (341), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 68/70 (97%), Positives = 68/70 (97%)

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

Query: 93  TDQTRQLGLI 102
           TDQTR LGLI
Sbjct: 61  TDQTRNLGLI 70

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  135 bits (341), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 68/70 (97%), Positives = 68/70 (97%)

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

Query: 93  TDQTRQLGLI 102
           TDQTR LGLI
Sbjct: 61  TDQTRPLGLI 70

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  135 bits (341), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 68/70 (97%), Positives = 68/70 (97%)

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

Query: 93  TDQTRQLGLI 102
           TDQTR LGLI
Sbjct: 61  TDQTRSLGLI 70

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 =  135 bits (341), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 68/70 (97%), Positives = 68/70 (97%)

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

Query: 93  TDQTRQLGLI 102
           TDQTR LGLI
Sbjct: 61  TDQTRNLGLI 70

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15227722|ref|NP_178480.1| U6 snRNA-associated Sm-like protein LSm7 [Arabidopsis thaliana] gi|30678085|ref|NP_849931.1| U6 snRNA-associated Sm-like protein LSm7 [Arabidopsis thaliana] gi|4582434|gb|AAD24820.1| putative snRNP splicing factor [Arabidopsis thaliana] gi|27765062|gb|AAO23652.1| At2g03870 [Arabidopsis thaliana] gi|110742944|dbj|BAE99367.1| putative snRNP splicing factor [Arabidopsis thaliana] gi|330250666|gb|AEC05760.1| U6 snRNA-associated Sm-like protein LSm7 [Arabidopsis thaliana] gi|330250667|gb|AEC05761.1| U6 snRNA-associated Sm-like protein LSm7 [Arabidopsis thaliana]

 Score =  135 bits (339), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 67/70 (95%), Positives = 69/70 (98%)

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

Query: 93  TDQTRQLGLI 102
           TDQTR+LGLI
Sbjct: 61  TDQTRRLGLI 70

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  135 bits (339), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 67/70 (95%), Positives = 69/70 (98%)

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

Query: 93  TDQTRQLGLI 102
           TDQTR+LGLI
Sbjct: 61  TDQTRRLGLI 70

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  135 bits (339), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 67/70 (95%), Positives = 69/70 (98%)

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

Query: 93  TDQTRQLGLI 102
           TDQTR+LGLI
Sbjct: 61  TDQTRRLGLI 70

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294463208|gb|ADE77140.1| unknown [Picea sitchensis]

 Score =  134 bits (337), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 66/70 (94%), Positives = 68/70 (97%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
           MSGRKETVLDLAKF+DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA+EFLRD DDPLKT
Sbjct: 1   MSGRKETVLDLAKFIDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAIEFLRDQDDPLKT 60

Query: 93  TDQTRQLGLI 102
           TDQTR LGLI
Sbjct: 61  TDQTRPLGLI 70

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	112
TAIR|locus:2056825	99	EMB2816 "AT2G03870" [Arabidops	0.625	0.707	0.957	2.3e-30
FB|FBgn0261068	110	LSm7 [Drosophila melanogaster	0.633	0.645	0.583	2.2e-18
DICTYBASE|DDB_G0289499	97	lsm7 "putative U6 small nuclea	0.598	0.690	0.611	3.6e-18
UNIPROTKB|Q9UK45	103	LSM7 "U6 snRNA-associated Sm-l	0.633	0.689	0.549	5.8e-18
ZFIN|ZDB-GENE-030131-8284	103	lsm7 "LSM7 homolog, U6 small n	0.598	0.650	0.552	1.6e-17
WB|WBGene00003081	104	lsm-7 [Caenorhabditis elegans	0.598	0.644	0.552	1.8e-16
UNIPROTKB|Q23543	104	lsm-7 "Protein LSM-7" [Caenorh	0.598	0.644	0.552	1.8e-16
UNIPROTKB|G4NLE3	146	MGG_02938 "Uncharacterized pro	0.562	0.431	0.567	1.1e-14
POMBASE|SPCC285.12	113	lsm7 "U6 snRNP-associated prot	0.589	0.584	0.537	1.8e-14
ASPGD|ASPL0000056132	136	AN0767 [Emericella nidulans (t	0.562	0.463	0.582	3e-14

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

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 67/70 (95%), Positives = 69/70 (98%)

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

Query:    93 TDQTRQLGLI 102
             TDQTR+LGLI
Sbjct:    61 TDQTRRLGLI 70

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 = 222 (83.2 bits), Expect = 2.2e-18, P = 2.2e-18
 Identities = 42/72 (58%), Positives = 57/72 (79%)

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-QTRQLGLI 102
              T+ QTR LGL+
Sbjct:    73 LTEEQTRSLGLV 84

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

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

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 41/67 (61%), Positives = 54/67 (80%)

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 TRQLGLI 102
              R LGL+
Sbjct:    68 KRFLGLV 74

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

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

 Score = 218 (81.8 bits), Expect = 5.8e-18, P = 5.8e-18
 Identities = 39/71 (54%), Positives = 55/71 (77%)

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 TTDQTRQLGLI 102
              T+ TRQLGL+
Sbjct:    64 LTEDTRQLGLV 74

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 = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 37/67 (55%), Positives = 53/67 (79%)

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 TRQLGLI 102
             TRQLGL+
Sbjct:    68 TRQLGLV 74

GO:0003674 "molecular_function" evidence=ND

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

 Score = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 37/67 (55%), Positives = 53/67 (79%)

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 TRQLGLI 102
             TRQLGLI
Sbjct:    69 TRQLGLI 75

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 = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 37/67 (55%), Positives = 53/67 (79%)

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 TRQLGLI 102
             TRQLGLI
Sbjct:    69 TRQLGLI 75

GO:0005515 "protein binding" evidence=IPI

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

 Score = 187 (70.9 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 38/67 (56%), Positives = 49/67 (73%)

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

Query:    96 TRQLGLI 102
             +R LGL+
Sbjct:   110 SRPLGLV 116

GO:0003674 "molecular_function" evidence=ND

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

 Score = 185 (70.2 bits), Expect = 1.8e-14, P = 1.8e-14
 Identities = 36/67 (53%), Positives = 51/67 (76%)

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 TRQLGLI 102
              R+LGL+
Sbjct:    80 IRKLGLV 86

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

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

 Score = 183 (69.5 bits), Expect = 3.0e-14, P = 3.0e-14
 Identities = 39/67 (58%), Positives = 51/67 (76%)

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 TRQLGLI 102
              R LGLI
Sbjct:   103 -RALGLI 108

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

---

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)
Q9UK45	LSM7_HUMAN	No assigned EC number	0.5492	0.6339	0.6893	yes	no
Q9CQQ8	LSM7_MOUSE	No assigned EC number	0.5492	0.6339	0.6893	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_Genewise1_v1.C_LG_I1870	SubName- Full=Putative uncharacterized protein; (99 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.X.1452.1	annotation not avaliable (75 aa)			•	•	•	•	•		0.712
	estExt_fgenesh4_pm.C_LG_VIII0306	SubName- Full=Putative uncharacterized protein; (92 aa)			•	•	•	•	•		0.709
	grail3.0053017102	SubName- Full=Putative uncharacterized protein; (88 aa)				•	•	•	•		0.701
	eugene3.00090932	SubName- Full=Putative uncharacterized protein; (88 aa)				•	•	•	•		0.701
	eugene3.00180816	hypothetical protein (88 aa)			•	•	•		•		0.633
	estExt_fgenesh4_kg.C_LG_III0001	SubName- Full=Putative uncharacterized protein; (93 aa)				•	•	•	•		0.597
	estExt_fgenesh4_kg.C_1630004	SubName- Full=Putative uncharacterized protein; (93 aa)				•	•	•	•		0.597
	estExt_Genewise1_v1.C_1580060	hypothetical protein (128 aa)			•	•	•	•	•		0.550
	grail3.0053017202	SubName- Full=Putative uncharacterized protein; (99 aa)				•	•		•	•	0.500
	fgenesh4_pg.C_scaffold_11374000001	hypothetical protein (255 aa)			•						0.463

---

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	112
cd01729	89	cd01729, LSm7, Like-Sm protein 7	2e-39
cd01719	70	cd01719, Sm_G, Sm protein G	4e-16
smart00651	67	smart00651, Sm, snRNP Sm proteins	1e-13
pfam01423	66	pfam01423, LSM, LSM domain	1e-12
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	3e-11
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	7e-10
cd00600	63	cd00600, Sm_like, Sm and related proteins	2e-09
cd01727	91	cd01727, LSm8, Like-Sm protein 8	6e-09
cd01730	82	cd01730, LSm3, Like-Sm protein 3	2e-08
cd06168	73	cd06168, LSMD1, LSM domain containing 1	3e-08
cd01717	80	cd01717, Sm_B, Sm protein B	1e-07
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	3e-07
cd01726	68	cd01726, LSm6, Like-Sm protein 6	4e-06
cd01728	74	cd01728, LSm1, Like-Sm protein 1	6e-06
cd11679	65	cd11679, archaeal_Sm_like, archaeal Sm-related pro	2e-05
cd01722	69	cd01722, Sm_F, Sm protein F	3e-04
cd01718	79	cd01718, Sm_E, Sm protein E	0.001

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

 Score =  126 bits (318), Expect = 2e-39
 Identities = 45/66 (68%), Positives = 57/66 (86%)

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

Query: 97  RQLGLI 102
           R LGL+
Sbjct: 61  RSLGLV 66

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 89

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

 Score = 66.8 bits (164), Expect = 4e-16
 Identities = 21/40 (52%), Positives = 32/40 (80%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          +L K++DK + +KL G R+V+G L+G+D  +NLVLD+AVE
Sbjct: 4  ELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVE 43

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|197820 smart00651, Sm, snRNP Sm proteins

 Score = 60.2 bits (147), Expect = 1e-13
 Identities = 25/62 (40%), Positives = 38/62 (61%), Gaps = 7/62 (11%)

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 LI 102
           L+
Sbjct: 54  LV 55

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

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

 Score = 57.6 bits (140), Expect = 1e-12
 Identities = 22/47 (46%), Positives = 31/47 (65%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADD 88
           L K + K V V+L  GR++ GTLKG+DQ +NLVLD+  E ++D   
Sbjct: 2  FLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKV 48

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

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

 Score = 54.6 bits (132), Expect = 3e-11
 Identities = 21/39 (53%), Positives = 27/39 (69%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          L K ++K V VKL  GR+  GTL G+DQ +NLVLD+  E
Sbjct: 12 LKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEE 50

Length = 79

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

 Score = 50.7 bits (122), Expect = 7e-10
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 8/60 (13%)

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

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

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

 Score = 49.6 bits (119), Expect = 2e-09
 Identities = 26/60 (43%), Positives = 35/60 (58%), Gaps = 8/60 (13%)

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

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|212474 cd01727, LSm8, Like-Sm protein 8

 Score = 48.7 bits (117), Expect = 6e-09
 Identities = 18/39 (46%), Positives = 24/39 (61%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          L  +++K V V  T GR + GTLKG+DQ  NL+L    E
Sbjct: 4  LEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHE 42

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|212477 cd01730, LSm3, Like-Sm protein 3

 Score = 47.2 bits (113), Expect = 2e-08
 Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 41 LDLAKF-VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          LDL +  +D+ V VKL G R++ G L  YDQ LN++L +  E
Sbjct: 3  LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEE 44

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|212486 cd06168, LSMD1, LSM domain containing 1

 Score = 46.8 bits (112), Expect = 3e-08
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 3/63 (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 GLI 102
           GL+
Sbjct: 58  GLV 60

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 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|212464 cd01717, Sm_B, Sm protein B

 Score = 44.8 bits (107), Expect = 1e-07
 Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 3/63 (4%)

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

Query: 100 GLI 102
           GL+
Sbjct: 65  GLV 67

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|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional

 Score = 44.2 bits (105), Expect = 3e-07
 Identities = 21/42 (50%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 41 LD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          LD L   ++  V V+L GGR+  G L+GYD  +NLVLD A E
Sbjct: 6  LDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEE 47

Length = 72

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

 Score = 40.6 bits (96), Expect = 4e-06
 Identities = 16/40 (40%), Positives = 22/40 (55%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF 82
          L K + K V VKL  G +  G L   D  +NLVL++  E+
Sbjct: 6  LKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEY 45

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|212475 cd01728, LSm1, Like-Sm protein 1

 Score = 40.6 bits (96), 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 = 39.2 bits (92), 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|212469 cd01722, Sm_F, Sm protein F

 Score = 36.0 bits (84), 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|212465 cd01718, Sm_E, Sm protein E

 Score = 34.5 bits (80), Expect = 0.001
 Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 7/40 (17%)

Query: 63  GTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           G + G+D+ +NLVLD+A E        LK T+  + LG I
Sbjct: 35  GKIIGFDEYMNLVLDDAEEV------HLK-TNTRKPLGRI 67

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	112
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.84
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.83
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.82
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.79
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.79
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.78
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.78
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.78
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.77
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.76
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.75
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.74
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.73
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.67
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.65
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.64
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.61
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.6
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.6
KOG3168	177	consensus U1 snRNP component [Transcription]	99.58
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.56
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	99.47
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.46
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	99.41
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	99.4
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.33
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	99.2
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	98.74
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	98.72
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	98.44
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	98.16
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.98
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	97.87
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	97.7
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.52
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	96.08
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	95.66
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	95.54
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	95.05
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	95.02
PRK14638	150	hypothetical protein; Provisional	94.82
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	94.8
PRK14639	140	hypothetical protein; Provisional	94.42
PRK14091	165	RNA-binding protein Hfq; Provisional	94.17
PRK02001	152	hypothetical protein; Validated	94.12
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	94.06
PRK14091	165	RNA-binding protein Hfq; Provisional	93.92
PRK14644	136	hypothetical protein; Provisional	93.33
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	92.42
PRK14633	150	hypothetical protein; Provisional	91.53
PRK14640	152	hypothetical protein; Provisional	91.17
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	91.04
PRK14642	197	hypothetical protein; Provisional	90.91
COG1923	77	Hfq Uncharacterized host factor I protein [General	90.73
PRK14645	154	hypothetical protein; Provisional	90.56
PRK14636	176	hypothetical protein; Provisional	90.21
PRK00092	154	ribosome maturation protein RimP; Reviewed	90.1
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	90.04
PRK14634	155	hypothetical protein; Provisional	89.77
PRK14643	164	hypothetical protein; Provisional	89.45
PRK14632	172	hypothetical protein; Provisional	89.39
PRK14646	155	hypothetical protein; Provisional	89.15
PRK14647	159	hypothetical protein; Provisional	88.07
PRK14631	174	hypothetical protein; Provisional	87.77
PRK14637	151	hypothetical protein; Provisional	86.06
PRK14641	173	hypothetical protein; Provisional	85.87
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	84.88
PRK06955	300	biotin--protein ligase; Provisional	84.71
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	82.7
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	80.27

>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=99.89  E-value=5.9e-23  Score=136.89  Aligned_cols=74  Identities=64%  Similarity=0.992  Sum_probs=63.6

Q ss_pred             CChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        38 ~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ..+++|.++++++|+|+|+|||+++|+|.|||+||||+|++|+|+...++++.....+.+.+|+++|||++|+.
T Consensus         2 ~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~   75 (81)
T cd01729           2 ESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVL   75 (81)
T ss_pred             cchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEE
Confidence            45788999999999999999999999999999999999999999987643322222467899999999999973

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

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

Probab=99.86  E-value=1.7e-21  Score=128.68  Aligned_cols=71  Identities=25%  Similarity=0.440  Sum_probs=61.0

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCC--CccccceEeeeeEEEeCCceec
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~--~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      +.|.+|++++|+|+|+|||.+.|+|.|||+||||+|++|+|++....+.  .....++|.+|+++|||++||.
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~   75 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVS   75 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEE
Confidence            4689999999999999999999999999999999999999998754321  1122468899999999999984

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

>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.85  E-value=5.2e-21  Score=125.86  Aligned_cols=68  Identities=31%  Similarity=0.375  Sum_probs=60.5

Q ss_pred             ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      +.++|+++++|+|.|+|+|||.+.|+|.|||+|||++|++|.|+...++.     ..++.+|+++|||++|+.
T Consensus         3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~-----~~~~~lG~~viRG~~V~~   70 (74)
T cd01728           3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDK-----YGDIPRGIFIIRGENVVL   70 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCc-----cceeEeeEEEEECCEEEE
Confidence            47789999999999999999999999999999999999999999865321     246889999999999974

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.

>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=99.85  E-value=7e-21  Score=124.41  Aligned_cols=64  Identities=36%  Similarity=0.647  Sum_probs=58.2

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      .++|+++++|+|+|+|++|+.++|+|.|||+||||+|++|.|+...        .+.+.+|.++|||++|+.
T Consensus         2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~--------~~~~~lg~v~IRG~~I~~   65 (72)
T cd01719           2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG--------GEKNNIGMVVIRGNSIVM   65 (72)
T ss_pred             chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC--------CceeEeceEEECCCEEEE
Confidence            4689999999999999999999999999999999999999999742        257899999999999973

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.

>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=99.84  E-value=1.5e-20  Score=123.93  Aligned_cols=69  Identities=23%  Similarity=0.360  Sum_probs=61.2

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ..|++|++++|+|+|+|||.|.|+|.|||+||||+|++|.|++....+.  ...+.|.+|+++|||++|+.
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~--~~~~~r~lGlv~IrG~~Iv~   71 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSF--SPTEPRVLGLVMIPGHHIVS   71 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCcc--CCccEEEeeeEEEeCCeEEE
Confidence            5789999999999999999999999999999999999999999765432  22478999999999999974

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.

>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=99.84  E-value=9.5e-21  Score=126.12  Aligned_cols=71  Identities=28%  Similarity=0.418  Sum_probs=59.6

Q ss_pred             hh-HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCC-----ccccceEeeeeEEEeCCceec
Q 033737           41 LD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        41 ~~-L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~-----~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ++ |+..++++|.|+|+|||.++|+|.|||+||||+|+||+|++...+++.     ......|.+|+++||||+||.
T Consensus         3 l~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~   79 (82)
T cd01730           3 LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVIL   79 (82)
T ss_pred             hHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEE
Confidence            44 577799999999999999999999999999999999999987643321     112367899999999999984

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.84  E-value=1.2e-20  Score=123.00  Aligned_cols=64  Identities=38%  Similarity=0.521  Sum_probs=57.1

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ...|.++++++|+|+|+||+.|+|+|.|||+|||++|+||.|...+        +..+.+|.++|||++|+.
T Consensus         6 ~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~~V~~   69 (72)
T PRK00737          6 LDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG--------EVVRKLGKVVIRGDNVVY   69 (72)
T ss_pred             HHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC--------CeEeEcCcEEEeCCEEEE
Confidence            4458999999999999999999999999999999999999997532        256889999999999973

>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=99.84  E-value=1.4e-20  Score=123.05  Aligned_cols=66  Identities=35%  Similarity=0.473  Sum_probs=58.7

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      +.|++|++++|+|+++|||.++|+|.|||+|||++|++|.|+....+.+    ...+.+|+++|||++|+
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~----~~~~~lG~~~iRG~~I~   67 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEG----VEQVVLGLYIIRGDNIA   67 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCC----ceeeEeceEEECCCEEE
Confidence            5799999999999999999999999999999999999999997643321    35778999999999997

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.

>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=99.83  E-value=5e-20  Score=121.69  Aligned_cols=66  Identities=18%  Similarity=0.323  Sum_probs=57.5

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      .-|+++++++|+|+++|||.++|+|.|||+|||++|++|.|++..++.     .+.+.+|.++|||++|+.
T Consensus         6 ~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~-----~~~~~lg~v~iRG~nV~~   71 (76)
T cd01732           6 ELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEG-----RKITKLDQILLNGNNICM   71 (76)
T ss_pred             HHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCC-----ceeeEcCeEEEeCCeEEE
Confidence            346899999999999999999999999999999999999999853221     256889999999999973

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.

>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=99.82  E-value=4.5e-20  Score=118.62  Aligned_cols=62  Identities=39%  Similarity=0.508  Sum_probs=56.7

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ..|++++|++|+|+|+||+.|.|+|.|||+||||+|++|+|++.+.        +.+.+|.++|||++|+
T Consensus         3 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~--------~~~~lg~~~iRG~~I~   64 (68)
T cd01731           3 DVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGE--------PVRKYGRVVIRGDNVL   64 (68)
T ss_pred             HHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCC--------eEeEcCcEEEeCCEEE
Confidence            4588999999999999999999999999999999999999987542        5788999999999997

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.

>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=99.79  E-value=4.4e-19  Score=120.02  Aligned_cols=69  Identities=19%  Similarity=0.312  Sum_probs=57.3

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCC-----ccccceEeeeeEEEeCCceec
Q 033737           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        43 L~~~i--~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~-----~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      |...+  +++|.|+|++|+.+.|+|.|||+||||+|+||+|++...+++.     ......+.+|.++||||+||.
T Consensus         7 L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~   82 (87)
T cd01720           7 LTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVIL   82 (87)
T ss_pred             HHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEE
Confidence            46665  8999999999999999999999999999999999987643221     112357789999999999983

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

>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.79  E-value=5.3e-19  Score=113.54  Aligned_cols=61  Identities=21%  Similarity=0.302  Sum_probs=55.4

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      .|++++|++|+|+|++|++|+|+|.|||+|||++|++|+|....        .+.+.+|.++|||++|+
T Consensus         4 ~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~--------~~~~~~~~v~IRG~~I~   64 (67)
T cd01726           4 FLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNG--------QLKNKYGDAFIRGNNVL   64 (67)
T ss_pred             HHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCC--------ceeeEeCCEEEECCEEE
Confidence            47899999999999999999999999999999999999987542        25778999999999986

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

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

Probab=99.78  E-value=5.6e-19  Score=113.81  Aligned_cols=63  Identities=30%  Similarity=0.382  Sum_probs=56.1

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ..|++++|++|+|.|+||++|.|+|.|||+|||++|++|.|+...        ...+.+|.++|||++|+.
T Consensus         4 ~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~--------~~~~~lg~~~IRG~~I~~   66 (68)
T cd01722           4 PFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG--------KSTGNLGEVLIRCNNVLY   66 (68)
T ss_pred             HHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC--------ccccCcCcEEEECCEEEE
Confidence            458899999999999999999999999999999999999998542        246779999999999873

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.

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

Probab=99.78  E-value=2e-20  Score=128.98  Aligned_cols=84  Identities=55%  Similarity=0.848  Sum_probs=76.0

Q ss_pred             ccccccCCCCCChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCC
Q 033737           28 LKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCD  107 (112)
Q Consensus        28 ~~~~~ms~~~~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd  107 (112)
                      ++.-.+++++.+.++|.+|++|+|+|++.+||+..|+|.|||+.|||||++++||..+++++.....+.|.+|++++||.
T Consensus         7 ~~~~~e~~kkEsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGT   86 (108)
T KOG1781|consen    7 QRKKFEKPKKESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGT   86 (108)
T ss_pred             ccccccccchhHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEccc
Confidence            34445678889999999999999999999999999999999999999999999999998888776677899999999999


Q ss_pred             ceec
Q 033737          108 ACVT  111 (112)
Q Consensus       108 ~iv~  111 (112)
                      .+|.
T Consensus        87 alvl   90 (108)
T KOG1781|consen   87 ALVL   90 (108)
T ss_pred             EEEE
Confidence            8873

>smart00651 Sm snRNP Sm proteins

Probab=99.78  E-value=1.6e-18  Score=109.76  Aligned_cols=63  Identities=41%  Similarity=0.639  Sum_probs=57.7

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      .|++++|++|+|.|+||+.+.|+|.|||+|||++|++|.|+....       .+.+.+|.++|||++|+.
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-------~~~~~~~~~~IrG~~I~~   64 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-------EKKRKLGLVFIRGNNIVY   64 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC-------cEEeEeCCEEEcCCEEEE
Confidence            588999999999999999999999999999999999999998652       268899999999999973

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

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

Probab=99.77  E-value=1.9e-18  Score=109.51  Aligned_cols=63  Identities=35%  Similarity=0.518  Sum_probs=58.0

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      .|++++|++|+|.|+||+.++|+|.+||+|||++|++|.|+.....       +.+.+|.++|||++|+.
T Consensus         2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-------~~~~~~~~~irG~~I~~   64 (67)
T PF01423_consen    2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-------EKRSLGLVFIRGSNIRY   64 (67)
T ss_dssp             HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-------EEEEEEEEEEEGGGEEE
T ss_pred             hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-------cEeECcEEEEECCEEEE
Confidence            5889999999999999999999999999999999999999987531       68899999999999974

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 ....

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

Probab=99.76  E-value=8.7e-19  Score=115.30  Aligned_cols=63  Identities=41%  Similarity=0.701  Sum_probs=58.0

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ++|++|++|++.++|+.||...|+|+|||.|||+||++++|...+        ..+..+|.++|||++||.
T Consensus         7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~--------~~~~~ig~~vIrgnsiv~   69 (77)
T KOG1780|consen    7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD--------GDKNNIGMVVIRGNSIVM   69 (77)
T ss_pred             chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc--------CCcceeeeEEEeccEEEE
Confidence            399999999999999999999999999999999999999998664        256789999999999984

>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=99.75  E-value=5.5e-18  Score=112.98  Aligned_cols=64  Identities=28%  Similarity=0.394  Sum_probs=54.7

Q ss_pred             hhhHHhhcCC--eEEEEEc--CCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           40 VLDLAKFVDK--GVQVKLT--GGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        40 ~~~L~~~i~k--~V~V~L~--dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ...+.+|+++  +|.|+++  +|+.++|+|.|||+||||+|+||+|+....       .+.+.+|+++||||+|+
T Consensus         8 ~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~-------~~~~~lG~iliRGnnV~   75 (79)
T cd01718           8 INLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKT-------KTRKPLGRILLKGDNIT   75 (79)
T ss_pred             HHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCC-------ceEeEcCcEEEeCCEEE
Confidence            3447899998  6677766  999999999999999999999999997531       25788999999999997

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.

>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=99.74  E-value=1.4e-17  Score=103.98  Aligned_cols=60  Identities=37%  Similarity=0.581  Sum_probs=55.4

Q ss_pred             HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        43 L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      |++++|++|+|.|+||+.+.|+|.|||+|||++|++|.|+...        ...+.+|.++|||++|+
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~--------~~~~~~~~~~irG~~I~   60 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE--------GKKRVLGLVLIRGDNVR   60 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC--------CcEEECCeEEEECCEEE
Confidence            5678999999999999999999999999999999999999765        25789999999999986

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.

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

Probab=99.73  E-value=2.3e-17  Score=108.75  Aligned_cols=68  Identities=37%  Similarity=0.483  Sum_probs=55.6

Q ss_pred             ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ....|+++++++|.|+|++|+++.|+|.|||+|||++|++|.|+...... .   ...+..|.++|||++|+
T Consensus         8 ~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~-~---~~~~~~~~~~IRG~~I~   75 (79)
T COG1958           8 PLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGE-K---NVRRLGGEVLIRGDNIV   75 (79)
T ss_pred             cHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCc-c---ccceeccEEEEECCcEE
Confidence            35568999999999999999999999999999999999999999851110 0   12344449999999986

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.67  E-value=2.8e-16  Score=106.88  Aligned_cols=63  Identities=27%  Similarity=0.443  Sum_probs=52.5

Q ss_pred             hHHhhcCC--eEEEEEcC--CeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           42 DLAKFVDK--GVQVKLTG--GRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        42 ~L~~~i~k--~V~V~L~d--gr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      .+.+++..  +|.|++.|  +++++|+|.|||+||||+|+||+|++.+.       ++.+.+|+++||||+|+.
T Consensus        18 ~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~-------~~~~~lG~ilIRGnnV~~   84 (89)
T PTZ00138         18 QIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKK-------NTRKDLGRILLKGDNITL   84 (89)
T ss_pred             HHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCC-------ceeeEcCeEEEcCCEEEE
Confidence            36778776  66777767  59999999999999999999999987532       257899999999999973

>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=99.65  E-value=7.6e-16  Score=99.84  Aligned_cols=61  Identities=21%  Similarity=0.133  Sum_probs=53.5

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      -|.+..|++|.|.|+||.+|.|+|.++|+|||++|++|.+...+.        +...+|.++|||++|.
T Consensus         4 ~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g--------~~~~~~~v~IRG~nI~   64 (70)
T cd01721           4 LLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDG--------RVSQLEQVYIRGSKIR   64 (70)
T ss_pred             HHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCC--------cEeEcCcEEEeCCEEE
Confidence            468889999999999999999999999999999999998754331        3567899999999985

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=99.64  E-value=9.2e-16  Score=100.80  Aligned_cols=62  Identities=19%  Similarity=0.187  Sum_probs=53.7

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      -|+++.|++|.|.|++|+.+.|+|.+||+|||++|++|.|...+.       +....+|.++|||++|.
T Consensus         5 ~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g-------~~~~~~~~v~IRG~~I~   66 (76)
T cd01723           5 LLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDG-------DKFWKMPECYIRGNTIK   66 (76)
T ss_pred             HHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCC-------cEeeeCCcEEEeCCEEE
Confidence            368899999999999999999999999999999999999874332       13456799999999986

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=99.61  E-value=2.5e-15  Score=102.04  Aligned_cols=62  Identities=23%  Similarity=0.264  Sum_probs=55.7

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ..|+++.|++|+|.|++|..|+|+|.++|.|||++|+||.++..+        .....+|.++|||++|.
T Consensus         4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~--------~~~~~~~~v~IRG~nI~   65 (90)
T cd01724           4 RFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG--------RNPVPLDTLSIRGNNIR   65 (90)
T ss_pred             HHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC--------CceeEcceEEEeCCEEE
Confidence            457899999999999999999999999999999999999988543        24678999999999985

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.

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

Probab=99.60  E-value=1.2e-15  Score=100.33  Aligned_cols=62  Identities=34%  Similarity=0.407  Sum_probs=56.9

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      +.|+.+.||+|.|+|++|.+|+|+|.+.|.||||.|.+|+|++..        .....+|.++||.++|-
T Consensus        11 pFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG--------~~~g~lGEilIRCNNvl   72 (79)
T KOG3482|consen   11 PFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG--------VSTGNLGEILIRCNNVL   72 (79)
T ss_pred             HHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc--------cccccceeEEEEeccEE
Confidence            358999999999999999999999999999999999999999876        35778999999999974

>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=99.60  E-value=5.3e-15  Score=98.06  Aligned_cols=62  Identities=23%  Similarity=0.216  Sum_probs=54.3

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ..|+...|+.|.|.|+||..|.|+|.++|+|||++|+||.+...+        .....+|.++|||++|.
T Consensus        12 ~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~--------~~~~~~~~v~IRG~nI~   73 (78)
T cd01733          12 ILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN--------GKQVQVEEIMVTGRNIR   73 (78)
T ss_pred             HHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC--------CceeECCcEEEECCEEE
Confidence            346889999999999999999999999999999999999876433        23557999999999986

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.

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=99.58  E-value=2.2e-16  Score=117.78  Aligned_cols=72  Identities=25%  Similarity=0.446  Sum_probs=64.0

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCC--CccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~--~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ...|.+++|++++|.++|||.++|.+.+||+|||++|.+|+|++..+.+.  ..+++++|-+|++++||++||.
T Consensus         6 sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs   79 (177)
T KOG3168|consen    6 SSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVS   79 (177)
T ss_pred             hhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEE
Confidence            45688999999999999999999999999999999999999998875443  2346799999999999999984

>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=99.56  E-value=1.4e-14  Score=96.40  Aligned_cols=64  Identities=20%  Similarity=0.108  Sum_probs=53.8

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ..|+++.|++|+|.|++|..|.|+|.++|.|||++|++|.+...+..      .....+|.++|||++|.
T Consensus         4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~------~~~~~~~~v~IRG~~I~   67 (81)
T cd01725           4 SFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKY------PHMLSVKNCFIRGSVVR   67 (81)
T ss_pred             HHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCc------ccccccCeEEEECCEEE
Confidence            34788999999999999999999999999999999999987643221      12456799999999985

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.

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

Probab=99.47  E-value=1.6e-14  Score=97.20  Aligned_cols=72  Identities=28%  Similarity=0.374  Sum_probs=59.5

Q ss_pred             ChhhHH-hhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCC-----ccccceEeeeeEEEeCCcee
Q 033737           39 TVLDLA-KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        39 ~~~~L~-~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~-----~~~~~~r~lGlvvIRGd~iv  110 (112)
                      .|++|. -+++.+|.|+++++|.+.|+|.|||+|.||+|.+++|.+..-+...     ..+..+|.+.++++|||+|+
T Consensus         5 ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vi   82 (91)
T KOG3460|consen    5 EPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVI   82 (91)
T ss_pred             ccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEE
Confidence            466754 4599999999999999999999999999999999999987533211     12357889999999999986

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

Probab=99.46  E-value=1.1e-14  Score=95.65  Aligned_cols=70  Identities=23%  Similarity=0.252  Sum_probs=61.1

Q ss_pred             cCCCCCChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        33 ms~~~~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ||.+......|++.+|++|.|+|.+|-.|.|+|.+.|.|||+.|+.+.|+...        +.++++|.++|||++|-
T Consensus         1 ~s~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ng--------ql~n~ygdaFirGnnVl   70 (77)
T KOG1783|consen    1 MSEGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNG--------QLKNKYGDAFIRGNNVL   70 (77)
T ss_pred             CCcccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcC--------cccccccceeeccccEE
Confidence            55444445568999999999999999999999999999999999999999754        36788999999999874

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

Probab=99.41  E-value=2.6e-14  Score=101.93  Aligned_cols=67  Identities=28%  Similarity=0.389  Sum_probs=59.9

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      +.+|.+++++++.|.|+|||.+.|.|++||||.|++|+.|+|++...+.     .-.+..|..+|||+|||-
T Consensus        11 t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~-----Y~di~~glfiIRGENVvl   77 (129)
T KOG1782|consen   11 TTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNK-----YCDIPRGLFIIRGENVVL   77 (129)
T ss_pred             hhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecce-----ecccCceEEEEecCcEEE
Confidence            4568999999999999999999999999999999999999999986432     466778999999999983

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

Probab=99.40  E-value=2.5e-13  Score=92.63  Aligned_cols=65  Identities=29%  Similarity=0.430  Sum_probs=58.1

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCce
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDAC  109 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~i  109 (112)
                      +.|+.|++++|.|...|||.+.|.|.||||-.||+|+++-|++.....    ..++..+|+.+|||+|+
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~----gv~q~~lGlyiirgeNv   67 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETE----GVEQIVLGLYIIRGENV   67 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhc----chhheeeEEEEEecCcc
Confidence            468999999999999999999999999999999999999999875332    24678899999999986

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

Probab=99.33  E-value=1.1e-12  Score=87.15  Aligned_cols=68  Identities=21%  Similarity=0.369  Sum_probs=57.9

Q ss_pred             CChhhH-HhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           38 ETVLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        38 ~~~~~L-~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ..|++| .+.+|.+++|.++++|++.|+|.|||.|.|++|+|+.||-.....     ....+++.+++.|++|-
T Consensus         6 llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~eg-----r~~tk~~~iLLnGNni~   74 (84)
T KOG1775|consen    6 LLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEG-----RRMTKLDQILLNGNNIT   74 (84)
T ss_pred             cccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCc-----ceeeeeeeeeecCCcEE
Confidence            446665 588999999999999999999999999999999999999765432     35668999999999873

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

Probab=99.20  E-value=1.2e-11  Score=83.08  Aligned_cols=62  Identities=31%  Similarity=0.455  Sum_probs=49.7

Q ss_pred             hHHhhcCC--eEEEEEc--CCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           42 DLAKFVDK--GVQVKLT--GGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        42 ~L~~~i~k--~V~V~L~--dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      .+-+|+..  +|.|+|.  -|..++|.++|||+|||+||++|+|.....+       ..+.+|.++++||+|-
T Consensus        16 ~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~-------~rk~lGRilLKGDnIt   81 (88)
T KOG1774|consen   16 LIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTK-------SRKELGRILLKGDNIT   81 (88)
T ss_pred             HHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccccc-------CCCccccEEEcCCcEE
Confidence            34677775  5556664  4899999999999999999999999866432       3458999999999984

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

Probab=98.74  E-value=1.8e-09  Score=75.94  Aligned_cols=86  Identities=16%  Similarity=0.217  Sum_probs=67.5

Q ss_pred             cccccccccCCCCCChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCC---C--ccccceEee
Q 033737           25 LGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP---L--KTTDQTRQL   99 (112)
Q Consensus        25 ~~~~~~~~ms~~~~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~---~--~~~~~~r~l   99 (112)
                      ..-.+..+|..+|.+...-..--...|.|.++|++.+-|++.|||.|.|++|+++.|.+....++   .  ......|.+
T Consensus        13 ~~~~e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~i   92 (114)
T KOG3459|consen   13 LEVPEEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFI   92 (114)
T ss_pred             cccccccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhh
Confidence            45566777777776655555456678999999999999999999999999999999998764332   1  112458999


Q ss_pred             eeEEEeCCcee
Q 033737          100 GLIGNCCDACV  110 (112)
Q Consensus       100 GlvvIRGd~iv  110 (112)
                      |.++||||+|+
T Consensus        93 sK~flRGdsvI  103 (114)
T KOG3459|consen   93 SKMFLRGDSVI  103 (114)
T ss_pred             heeeecCCeEE
Confidence            99999999986

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

Probab=98.72  E-value=5.9e-08  Score=66.19  Aligned_cols=63  Identities=24%  Similarity=0.152  Sum_probs=50.8

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCce
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDAC  109 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~i  109 (112)
                      ...+.++|++|.|.|+++..|.|+|.+.|+|.|+-|.|..-...++   .   ..-..+-.++|||..|
T Consensus         5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~k---y---Phm~Sv~ncfIRGSvv   67 (96)
T KOG3448|consen    5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDK---Y---PHMLSVKNCFIRGSVV   67 (96)
T ss_pred             HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCccc---C---CCeeeeeeEEEeccEE
Confidence            3467889999999999999999999999999999999976553321   1   2345567899999875

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

Probab=98.44  E-value=3.9e-07  Score=65.45  Aligned_cols=60  Identities=22%  Similarity=0.198  Sum_probs=52.0

Q ss_pred             HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCce
Q 033737           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDAC  109 (112)
Q Consensus        43 L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~i  109 (112)
                      |+..-+.++.|.|++|.+|.|.|+..|.+|||.|.+++++..+.+       .--.+..+.|||.+|
T Consensus         7 L~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgd-------kf~r~pEcYirGttI   66 (134)
T KOG3293|consen    7 LKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGD-------KFFRMPECYIRGTTI   66 (134)
T ss_pred             HHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCC-------ceeecceeEEeccee
Confidence            455678999999999999999999999999999999999877643       345578999999987

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

Probab=98.16  E-value=1e-05  Score=56.88  Aligned_cols=61  Identities=21%  Similarity=0.280  Sum_probs=51.5

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCce
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDAC  109 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~i  109 (112)
                      ...|+++.+.+++|.|++|..+.|++.+.|.+||..|.++.-....         ++..+-.+.|||++|
T Consensus         4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~---------~pv~l~~lsirgnni   64 (109)
T KOG3428|consen    4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG---------EPVRLDTLSIRGNNI   64 (109)
T ss_pred             HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC---------CceeEEEEEeecceE
Confidence            3467889999999999999999999999999999999987765432         345677888999987

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

Probab=97.98  E-value=5.6e-06  Score=53.58  Aligned_cols=37  Identities=27%  Similarity=0.425  Sum_probs=30.5

Q ss_pred             CeEEEEEcC--C--eEEEEEEEeecCccceeecceEEEeec
Q 033737           49 KGVQVKLTG--G--RQVTGTLKGYDQLLNLVLDEAVEFLRD   85 (112)
Q Consensus        49 k~V~V~L~d--g--r~i~G~L~~fD~~mNlvL~~a~E~~~~   85 (112)
                      .+|+|.++.  |  -.++|.|.|||+|+||+|.|+.|....
T Consensus         9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~   49 (66)
T cd01739           9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK   49 (66)
T ss_pred             cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence            577777653  2  378999999999999999999998765

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=97.87  E-value=3.5e-05  Score=50.03  Aligned_cols=67  Identities=15%  Similarity=0.173  Sum_probs=41.1

Q ss_pred             HHhhcCCeEEEEEcCCeEEEEEEEeecC---ccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQ---LLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        43 L~~~i~k~V~V~L~dgr~i~G~L~~fD~---~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      +..++|++|.|+++||..|+|.|.+++.   -+.++|.-|........++ ...........++|+++.||
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            5678999999999999999999999988   8899998888765432211 11123445567788888776

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

Probab=97.70  E-value=0.00017  Score=50.92  Aligned_cols=59  Identities=20%  Similarity=0.128  Sum_probs=49.6

Q ss_pred             HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCce
Q 033737           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDAC  109 (112)
Q Consensus        43 L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~i  109 (112)
                      |.+.-|.-|++.+..|..|.|+|.-.|..||++|+|..-...+.        ....+-.++|||+.|
T Consensus        10 LhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg--------~vs~le~V~IRGS~I   68 (119)
T KOG3172|consen   10 LHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDG--------RVSQLEQVFIRGSKI   68 (119)
T ss_pred             eecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCC--------cceeeeeEEEecCeE
Confidence            34456778999999999999999999999999999998876543        455678999999976

>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=96.52  E-value=0.015  Score=34.72  Aligned_cols=35  Identities=20%  Similarity=0.300  Sum_probs=30.4

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEeecCccceeecceEE
Q 033737           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE   81 (112)
Q Consensus        46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E   81 (112)
                      ++|++|++.+ ++..++|+..++|....|+++....
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g   35 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG   35 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence            4799999999 6677799999999999999977555

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 ....

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

Probab=96.08  E-value=0.032  Score=38.38  Aligned_cols=66  Identities=9%  Similarity=0.065  Sum_probs=47.3

Q ss_pred             HhhcCCeEEEEEcCCeEEEEEEEeecC-ccceeecceEEEeecCCC-CCccccceEeeeeEEEeCCce
Q 033737           44 AKFVDKGVQVKLTGGRQVTGTLKGYDQ-LLNLVLDEAVEFLRDADD-PLKTTDQTRQLGLIGNCCDAC  109 (112)
Q Consensus        44 ~~~i~k~V~V~L~dgr~i~G~L~~fD~-~mNlvL~~a~E~~~~~~~-~~~~~~~~r~lGlvvIRGd~i  109 (112)
                      .+|+|++|.+..+++-+|+|+|...|. ...|.|.++.-+-..... +...-....-...++.||..|
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDI   71 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDI   71 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTE
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEcccc
Confidence            358999999999999999999999996 589999998776543211 110001233467888888765

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

Probab=95.66  E-value=0.024  Score=36.21  Aligned_cols=32  Identities=22%  Similarity=0.408  Sum_probs=27.6

Q ss_pred             cCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (112)
Q Consensus        47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~   78 (112)
                      -..+|.|.|.+|-.++|.+.|||+|+=++-.+
T Consensus        10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716          10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence            34689999999999999999999998776555

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=95.54  E-value=0.028  Score=35.92  Aligned_cols=32  Identities=25%  Similarity=0.380  Sum_probs=27.4

Q ss_pred             cCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (112)
Q Consensus        47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~   78 (112)
                      -..+|+|.|.+|-.+.|.+.|||+|+=++-.+
T Consensus        14 ~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383        14 ERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            34689999999999999999999998776544

This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.

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

Probab=95.05  E-value=0.22  Score=32.93  Aligned_cols=65  Identities=8%  Similarity=0.057  Sum_probs=47.6

Q ss_pred             hhcCCeEEEEEcCCeEEEEEEEeecCc-cceeecceEEEeecCCCC--CccccceEeeeeEEEeCCce
Q 033737           45 KFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIGNCCDAC  109 (112)
Q Consensus        45 ~~i~k~V~V~L~dgr~i~G~L~~fD~~-mNlvL~~a~E~~~~~~~~--~~~~~~~r~lGlvvIRGd~i  109 (112)
                      +|+|+++.+.-+.+-+|+|+|..+|.. .-+.|.++.-+-......  .+.-....-+..++.||..|
T Consensus         3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDI   70 (74)
T cd01736           3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDI   70 (74)
T ss_pred             cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcc
Confidence            589999999999999999999999966 567799987665432211  10112344567899999876

Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=95.02  E-value=0.046  Score=36.61  Aligned_cols=33  Identities=18%  Similarity=0.406  Sum_probs=28.1

Q ss_pred             cCCeEEEEEcCCeEEEEEEEeecCccceeecce
Q 033737           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (112)
Q Consensus        47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a   79 (112)
                      -..+|.|.|.+|-.+.|.+.|||+|.=|+-.+.
T Consensus        18 ~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g   50 (79)
T PRK00395         18 ERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG   50 (79)
T ss_pred             cCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence            446899999999999999999999987766554

>PRK14638 hypothetical protein; Provisional

Probab=94.82  E-value=0.083  Score=38.72  Aligned_cols=38  Identities=13%  Similarity=0.310  Sum_probs=32.0

Q ss_pred             ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeec
Q 033737           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~   77 (112)
                      .+.++.+++|++|+|++.+++.++|+|.++|.- ++.|.
T Consensus        91 ~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         91 GPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             CHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            366789999999999999999999999999863 44443

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

Probab=94.80  E-value=0.054  Score=40.74  Aligned_cols=43  Identities=26%  Similarity=0.394  Sum_probs=32.8

Q ss_pred             CChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCc-cceeecceEE
Q 033737           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVE   81 (112)
Q Consensus        38 ~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~-mNlvL~~a~E   81 (112)
                      .+|.....|++|.|+|++.| +++.|-+..+|.- .|+||-+-.|
T Consensus         7 ~~p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e   50 (166)
T PF06372_consen    7 KSPLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE   50 (166)
T ss_dssp             S-HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred             CCHHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence            45788999999999999999 9999999999966 6898885444

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.

>PRK14639 hypothetical protein; Provisional

Probab=94.42  E-value=0.12  Score=37.46  Aligned_cols=37  Identities=19%  Similarity=0.302  Sum_probs=31.9

Q ss_pred             ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceee
Q 033737           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL   76 (112)
                      .+.+..+++|++|+|++.+++.+.|+|.++|.- ++.|
T Consensus        79 ~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l  115 (140)
T PRK14639         79 KIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL  115 (140)
T ss_pred             CHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            366789999999999999999999999999883 4444

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=94.17  E-value=0.23  Score=37.41  Aligned_cols=73  Identities=21%  Similarity=0.269  Sum_probs=47.2

Q ss_pred             eEEEeeEEEEEEecccccccccccccccccCCCCCChhh--HHhhcC--CeEEEEEcCCeEEEEEEEeecCccceeecce
Q 033737            4 FVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLD--LAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (112)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ms~~~~~~~~--L~~~i~--k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a   79 (112)
                      .+==||.|=+.-.+..-  +... .+...++++.....+  |+.+..  .+|.|.|.+|-.+.|.+.|||+|.=|+-.+.
T Consensus        59 LIYKHAISTI~p~~~i~--~~~~-~~~~~~~~~~~nlQd~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g  135 (165)
T PRK14091         59 LVYKHAISTIMPAHPLD--LSRF-SKSLDANKKSRLLQDVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG  135 (165)
T ss_pred             EEEeeeeeeecccCCcc--hhhh-cchhhhcccccccHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            34447777666555542  2222 244445544455444  555533  4888999999999999999999986666554

>PRK02001 hypothetical protein; Validated

Probab=94.12  E-value=0.15  Score=37.68  Aligned_cols=37  Identities=22%  Similarity=0.396  Sum_probs=31.7

Q ss_pred             ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceee
Q 033737           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL   76 (112)
                      .+.+..+++|+.|+|++.+++.++|+|.++|.- ++.|
T Consensus        81 ~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l  117 (152)
T PRK02001         81 VPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL  117 (152)
T ss_pred             CHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence            356789999999999999999999999999864 4444

>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=94.06  E-value=0.15  Score=32.46  Aligned_cols=36  Identities=11%  Similarity=0.170  Sum_probs=30.3

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEeecCccceeecceEE
Q 033737           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE   81 (112)
Q Consensus        46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E   81 (112)
                      .+|..|++++-.|.+|+|.+.+||.-.++++=.|.+
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            478999999999999999999999887776554433

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.

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=93.92  E-value=0.13  Score=38.72  Aligned_cols=49  Identities=18%  Similarity=0.313  Sum_probs=36.3

Q ss_pred             cccCCCCCChhh--HHhhcC--CeEEEEEcCCeEEEEEEEeecCccceeecce
Q 033737           31 LKMSGRKETVLD--LAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (112)
Q Consensus        31 ~~ms~~~~~~~~--L~~~i~--k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a   79 (112)
                      -.|++++....+  |+.+..  .+|.|.|.+|-.++|.+.+||+|.=|+-.+.
T Consensus         3 ~~m~~~~~nlQD~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g   55 (165)
T PRK14091          3 ANMAEKVNNLQDIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG   55 (165)
T ss_pred             ccccccccchHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            357766666555  555543  4788899999999999999999986665453

>PRK14644 hypothetical protein; Provisional

Probab=93.33  E-value=0.34  Score=35.08  Aligned_cols=41  Identities=17%  Similarity=0.208  Sum_probs=32.5

Q ss_pred             CCCChhhHHhhcCCeEEEEEcCC----eEEEEEEEeecCccceeec
Q 033737           36 RKETVLDLAKFVDKGVQVKLTGG----RQVTGTLKGYDQLLNLVLD   77 (112)
Q Consensus        36 ~~~~~~~L~~~i~k~V~V~L~dg----r~i~G~L~~fD~~mNlvL~   77 (112)
                      +|....++.+++|+.|.|+|++.    +.++|.|.++|.. ++.|.
T Consensus        73 RpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         73 MDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             CCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            33444578999999999999877    9999999999873 45553

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

Probab=92.42  E-value=0.52  Score=30.88  Aligned_cols=37  Identities=38%  Similarity=0.502  Sum_probs=30.0

Q ss_pred             ChhhHHhhcCCeEEEEEc---CC-eEEEEEEEeecCccceee
Q 033737           39 TVLDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQLLNLVL   76 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~---dg-r~i~G~L~~fD~~mNlvL   76 (112)
                      .+.++.+++|+.|.|+++   +| +.+.|.|.++|.- ++.|
T Consensus        16 ~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l   56 (83)
T cd01734          16 KEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL   56 (83)
T ss_pred             CHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence            356789999999999997   55 6899999999874 3444

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

>PRK14633 hypothetical protein; Provisional

Probab=91.53  E-value=0.62  Score=34.07  Aligned_cols=37  Identities=16%  Similarity=0.281  Sum_probs=30.2

Q ss_pred             ChhhHHhhcCCeEEEEE----cCCeEEEEEEEeecCccceee
Q 033737           39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL   76 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L----~dgr~i~G~L~~fD~~mNlvL   76 (112)
                      .+.++.+++|++|.|++    .+++.++|+|.++|.. ++.|
T Consensus        85 ~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l  125 (150)
T PRK14633         85 NIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL  125 (150)
T ss_pred             CHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence            35678999999999998    4679999999999874 4444

>PRK14640 hypothetical protein; Provisional

Probab=91.17  E-value=0.7  Score=33.82  Aligned_cols=38  Identities=24%  Similarity=0.386  Sum_probs=30.8

Q ss_pred             ChhhHHhhcCCeEEEEE----cCCeEEEEEEEeecCccceeec
Q 033737           39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVLD   77 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L----~dgr~i~G~L~~fD~~mNlvL~   77 (112)
                      .+.++.+++|++|.|++    .+++.++|+|.++|.. ++.|.
T Consensus        88 ~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~  129 (152)
T PRK14640         88 KVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT  129 (152)
T ss_pred             CHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence            36678999999999999    5679999999999874 44443

>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=91.04  E-value=0.66  Score=33.09  Aligned_cols=36  Identities=31%  Similarity=0.556  Sum_probs=27.1

Q ss_pred             hhhHHhhcCCeEEEEE----cCCeEEEEEEEeecCccceee
Q 033737           40 VLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL   76 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L----~dgr~i~G~L~~fD~~mNlvL   76 (112)
                      ..++.+++|++|.|++    .+.+.+.|+|.++|. -.++|
T Consensus        79 ~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   79 PRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             HHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             HHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            5578999999999999    455789999999998 34444

; PDB: 1IB8_A.

>PRK14642 hypothetical protein; Provisional

Probab=90.91  E-value=0.7  Score=35.62  Aligned_cols=37  Identities=16%  Similarity=0.327  Sum_probs=30.7

Q ss_pred             ChhhHHhhcCCeEEEEEc-------------CCeEEEEEEEeecCccceee
Q 033737           39 TVLDLAKFVDKGVQVKLT-------------GGRQVTGTLKGYDQLLNLVL   76 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~-------------dgr~i~G~L~~fD~~mNlvL   76 (112)
                      ...++.+++|+.|.|+|+             +.+.++|+|.++|.. ++.|
T Consensus        91 ~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         91 HEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             CHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            366789999999999998             679999999999874 4434

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

Probab=90.73  E-value=0.51  Score=31.46  Aligned_cols=31  Identities=19%  Similarity=0.401  Sum_probs=25.9

Q ss_pred             cCCeEEEEEcCCeEEEEEEEeecCccceeec
Q 033737           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (112)
Q Consensus        47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~   77 (112)
                      -..+|.|-|.||-.+.|.+.|||+|.=|+=.
T Consensus        18 ~~i~VtIfLvNG~~L~G~V~sfD~f~VlL~~   48 (77)
T COG1923          18 EKIPVTIFLVNGFKLQGQVESFDNFVVLLKN   48 (77)
T ss_pred             cCCeEEEEEEcCEEEEEEEEeeeeEEEEEEc
Confidence            3458999999999999999999999754433

>PRK14645 hypothetical protein; Provisional

Probab=90.56  E-value=0.76  Score=33.89  Aligned_cols=35  Identities=17%  Similarity=0.295  Sum_probs=29.0

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceee
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL   76 (112)
                      +.++.+++|++|.|++ +++.++|+|.++|.- .+.|
T Consensus        94 ~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l  128 (154)
T PRK14645         94 ARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF  128 (154)
T ss_pred             HHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence            5678999999999986 789999999999874 3444

>PRK14636 hypothetical protein; Provisional

Probab=90.21  E-value=0.87  Score=34.28  Aligned_cols=37  Identities=27%  Similarity=0.499  Sum_probs=30.0

Q ss_pred             ChhhHHhhcCCeEEEEEc---CC-eEEEEEEEeecCccceee
Q 033737           39 TVLDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQLLNLVL   76 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~---dg-r~i~G~L~~fD~~mNlvL   76 (112)
                      .+.++.+++|++|.|+++   +| +.++|+|.++|.- ++.|
T Consensus        89 ~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         89 RPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             CHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            366789999999999997   55 6999999999873 4444

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=90.10  E-value=1  Score=32.81  Aligned_cols=31  Identities=32%  Similarity=0.594  Sum_probs=27.9

Q ss_pred             hhhHHhhcCCeEEEEE----cCCeEEEEEEEeecC
Q 033737           40 VLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQ   70 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L----~dgr~i~G~L~~fD~   70 (112)
                      +.++.+++|+.|+|++    .+++.++|+|.++|.
T Consensus        90 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         90 ARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             HHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence            5679999999999997    578899999999987

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.04  E-value=1.3  Score=32.89  Aligned_cols=33  Identities=27%  Similarity=0.477  Sum_probs=30.1

Q ss_pred             hhhHHhhcCCeEEEEE----cCCeEEEEEEEeecCcc
Q 033737           40 VLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLL   72 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L----~dgr~i~G~L~~fD~~m   72 (112)
                      ..+..+++|+.|.|+|    .+++.++|+|.++|.-.
T Consensus        91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~  127 (153)
T COG0779          91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET  127 (153)
T ss_pred             HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence            5568999999999999    88999999999999876

>PRK14634 hypothetical protein; Provisional

Probab=89.77  E-value=1.1  Score=33.02  Aligned_cols=37  Identities=19%  Similarity=0.224  Sum_probs=29.5

Q ss_pred             ChhhHHhhcCCeEEEEEcC----CeEEEEEEEeecCccceee
Q 033737           39 TVLDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQLLNLVL   76 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~d----gr~i~G~L~~fD~~mNlvL   76 (112)
                      .+.+..+++|++|+|++.+    .+.++|+|.++|.- ++.|
T Consensus        91 ~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l  131 (155)
T PRK14634         91 SDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI  131 (155)
T ss_pred             CHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence            3667899999999999863    37899999999864 3444

>PRK14643 hypothetical protein; Provisional

Probab=89.45  E-value=1.1  Score=33.32  Aligned_cols=32  Identities=22%  Similarity=0.298  Sum_probs=28.0

Q ss_pred             hhhHHhhcCCeEEEEEcC----CeEEEEEEEeecCc
Q 033737           40 VLDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQL   71 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~d----gr~i~G~L~~fD~~   71 (112)
                      ..++.+++|++|.|++.+    .+.++|+|.++|.-
T Consensus        96 ~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         96 QEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             HHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            667899999999999865    68999999999865

>PRK14632 hypothetical protein; Provisional

Probab=89.39  E-value=1.1  Score=33.47  Aligned_cols=37  Identities=19%  Similarity=0.380  Sum_probs=30.1

Q ss_pred             hhhHHhhcCCeEEEEEcC-------CeEEEEEEEeecCccceeec
Q 033737           40 VLDLAKFVDKGVQVKLTG-------GRQVTGTLKGYDQLLNLVLD   77 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~d-------gr~i~G~L~~fD~~mNlvL~   77 (112)
                      ..++.+++|+.|.|++.+       .+.+.|+|.++|.- ++.|.
T Consensus        90 ~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         90 AEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             HHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            567899999999999975       57999999999853 44443

>PRK14646 hypothetical protein; Provisional

Probab=89.15  E-value=1.3  Score=32.65  Aligned_cols=37  Identities=22%  Similarity=0.202  Sum_probs=29.6

Q ss_pred             ChhhHHhhcCCeEEEEEcC----CeEEEEEEEeecCccceee
Q 033737           39 TVLDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQLLNLVL   76 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~d----gr~i~G~L~~fD~~mNlvL   76 (112)
                      ...++.+++|++|.|+|++    -+.++|+|.++|.- .+.|
T Consensus        91 ~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l  131 (155)
T PRK14646         91 SERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI  131 (155)
T ss_pred             CHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence            3567899999999999854    37789999999874 4554

>PRK14647 hypothetical protein; Provisional

Probab=88.07  E-value=1.6  Score=32.09  Aligned_cols=32  Identities=19%  Similarity=0.353  Sum_probs=27.5

Q ss_pred             ChhhHHhhcCCeEEEEEc---------CCeEEEEEEEeecC
Q 033737           39 TVLDLAKFVDKGVQVKLT---------GGRQVTGTLKGYDQ   70 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~---------dgr~i~G~L~~fD~   70 (112)
                      .+.++.+++|++|.|+++         +.+.++|+|.++|.
T Consensus        90 ~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~  130 (159)
T PRK14647         90 KEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD  130 (159)
T ss_pred             CHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence            356789999999999995         35899999999986

>PRK14631 hypothetical protein; Provisional

Probab=87.77  E-value=1.6  Score=32.87  Aligned_cols=31  Identities=19%  Similarity=0.375  Sum_probs=27.4

Q ss_pred             ChhhHHhhcCCeEEEEEc----CCeEEEEEEEeec
Q 033737           39 TVLDLAKFVDKGVQVKLT----GGRQVTGTLKGYD   69 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~----dgr~i~G~L~~fD   69 (112)
                      ...++.+++|+.|.|++.    +.+.++|+|.++|
T Consensus       108 ~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~  142 (174)
T PRK14631        108 QLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD  142 (174)
T ss_pred             CHHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence            366799999999999995    5599999999998

>PRK14637 hypothetical protein; Provisional

Probab=86.06  E-value=2.2  Score=31.34  Aligned_cols=38  Identities=29%  Similarity=0.349  Sum_probs=28.8

Q ss_pred             ChhhHHhhcCCeEEEEEcCCeEE-EEEEEeecCccceeec
Q 033737           39 TVLDLAKFVDKGVQVKLTGGRQV-TGTLKGYDQLLNLVLD   77 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~dgr~i-~G~L~~fD~~mNlvL~   77 (112)
                      .+.++.+++|++|.|++.+.+.+ +|+|.++|.- ++.|.
T Consensus        89 ~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~  127 (151)
T PRK14637         89 NAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT  127 (151)
T ss_pred             CHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence            36678999999999999544455 7999999874 44443

>PRK14641 hypothetical protein; Provisional

Probab=85.87  E-value=2.2  Score=32.16  Aligned_cols=30  Identities=20%  Similarity=0.294  Sum_probs=26.3

Q ss_pred             hhhHHhhcCCeEEEEEcC----CeEEEEEEEeec
Q 033737           40 VLDLAKFVDKGVQVKLTG----GRQVTGTLKGYD   69 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~d----gr~i~G~L~~fD   69 (112)
                      ..+..+++|+.|.|++.+    .+.++|+|.++|
T Consensus        96 ~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         96 PRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             HHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            567899999999999965    568999999996

>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=84.88  E-value=2.6  Score=28.16  Aligned_cols=57  Identities=16%  Similarity=0.093  Sum_probs=40.0

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCc-cceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~-mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ..|....|++|.+.|.++.+..|++.|+|.. .|+..++-. .            .-......++|...|+
T Consensus        17 r~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-T------------PlGv~~eAlLR~~DVi   74 (80)
T PF11095_consen   17 RSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-T------------PLGVQPEALLRCSDVI   74 (80)
T ss_dssp             HHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-T------------TTTEEEEEEEEGGGEE
T ss_pred             HHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-C------------CcccChhheeecCCEE
Confidence            3467778999999999999999999999966 577666522 1            1122467788887776

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.

>PRK06955 biotin--protein ligase; Provisional

Probab=84.71  E-value=4  Score=32.59  Aligned_cols=33  Identities=24%  Similarity=0.400  Sum_probs=28.9

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (112)
Q Consensus        46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~   78 (112)
                      ++|++|++...+++.+.|++.|+|....|+++.
T Consensus       247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~  279 (300)
T PRK06955        247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT  279 (300)
T ss_pred             cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence            588999997767788999999999999999853

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

Probab=82.70  E-value=2.9  Score=26.94  Aligned_cols=38  Identities=26%  Similarity=0.351  Sum_probs=28.4

Q ss_pred             ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~   78 (112)
                      .-..|++++|++|.|.+..|.. .|+|.+.... .++|+.
T Consensus        12 vyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~   49 (66)
T PF10842_consen   12 VYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEE   49 (66)
T ss_pred             HHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEe
Confidence            3456899999999999977765 9999998532 234443

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

Probab=80.27  E-value=8.1  Score=30.72  Aligned_cols=31  Identities=23%  Similarity=0.562  Sum_probs=27.0

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEeecCccceeec
Q 033737           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (112)
Q Consensus        46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~   77 (112)
                      ++|++|++... +..++|++.|+|....|++.
T Consensus       270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~  300 (319)
T PRK11886        270 FLGREVKLIIG-DKEISGIARGIDEQGALLLE  300 (319)
T ss_pred             ccCCeEEEEeC-CcEEEEEEEEECCCceEEEE
Confidence            58899999874 45799999999999999995

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	112
3swn_C	117	Structure Of The Lsm657 Complex: An Assembly Interm		1e-14
4emk_C	113	Crystal Structure Of Splsm567 Length = 113		3e-14
3cw1_G	76	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		3e-08
3bw1_A	96	Crystal Structure Of Homomeric Yeast Lsm3 Exhibitin		2e-04
4emg_A	93	Crystal Structure Of Splsm3 Length = 93		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 = 74.7 bits (182), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 36/67 (53%), Positives = 51/67 (76%), Gaps = 1/67 (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  TRQLGLI 102
            R+LGL+
Sbjct: 84  IRKLGLV 90

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

Iteration: 1
 Score = 73.2 bits (178), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/67 (53%), Positives = 50/67 (74%), Gaps = 1/67 (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  TRQLGLI 102
            R+LGL+
Sbjct: 80  IRKLGLV 86

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 8/61 (13%)
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 I 102
           +
Sbjct: 60  V 60

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 38 ETVLDLAKF-VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          ET LDL K  +D+ V +KL G R + GTL+ +D   N+VL +AVE
Sbjct: 9  ETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVE 53

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 37/63 (58%), Gaps = 3/63 (4%)
Query: 41  LDLAKF-VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQL 99
           LDL +  +D+ V VKL G R++ G L  YD+ LN VL +A E +   DD  + TD+ + L
Sbjct: 11  LDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNXVLGDAEEIVTIFDD--EETDKDKAL 68
Query: 100 GLI 102
             I
Sbjct: 69  KTI 71

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	112
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	2e-21
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	3e-19
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	6e-19
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	1e-18
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	6e-17
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	2e-16
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	8e-16
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	5e-15
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	5e-15
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	7e-14
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	1e-13
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	1e-12
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	2e-11
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	2e-10
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-10
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	3e-10
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	4e-08
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	9e-08
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	2e-06
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	6e-06
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	8e-06
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	2e-05
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	3e-05
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	1e-04

>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 = 80.8 bits (199), Expect = 2e-21
 Identities = 36/67 (53%), Positives = 51/67 (76%), Gaps = 1/67 (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  TRQLGLI 102
            R+LGL+
Sbjct: 80  IRKLGLV 86

>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 = 74.3 bits (183), Expect = 3e-19
 Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 10/70 (14%)

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  TDQTRQLGLI 102
             Q   +G++
Sbjct: 52  -GQQNNIGMV 60

>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 = 73.5 bits (181), Expect = 6e-19
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 9/71 (12%)

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

Query: 92  TTDQTRQLGLI 102
                ++LG I
Sbjct: 57  --GSGKKLGTI 65

>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 = 73.2 bits (180), Expect = 1e-18
 Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 2/68 (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  QTRQLGLI 102
             R+  ++
Sbjct: 66  SERRCEMV 73

>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 = 68.5 bits (168), Expect = 6e-17
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 10/70 (14%)

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

Query: 93  TDQTRQLGLI 102
            +  R++G +
Sbjct: 52  -EVVRKVGSV 60

>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 = 67.6 bits (165), Expect = 2e-16
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

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

Query: 93  TD--QTRQLGLI 102
            +  + R LGL+
Sbjct: 59  AEREEKRVLGLV 70

>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 = 65.5 bits (160), Expect = 8e-16
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 10/74 (13%)

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

Query: 89  PLKTTDQTRQLGLI 102
                    + G +
Sbjct: 57  ----DGNVYKRGTM 66

>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 = 63.5 bits (155), Expect = 5e-15
 Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 8/60 (13%)

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

>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 = 63.7 bits (155), Expect = 5e-15
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

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  QLGLI 102
              ++
Sbjct: 74  HYEML 78

>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 = 60.4 bits (147), Expect = 7e-14
 Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 10/70 (14%)

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  TDQTRQLGLI 102
            +  ++ G I
Sbjct: 52  -EVVKRYGKI 60

>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 = 61.2 bits (148), Expect = 1e-13
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 29  KSLKMSGRKETVLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDAD 87
            S +  G     L L  K +   + V + G ++ +G L+G+D+ +N+VLD+  E+   AD
Sbjct: 18  GSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKAD 77

Query: 88  DPLKTTDQ-------TRQLGLI 102
           +   +            +L  I
Sbjct: 78  EEDISGGNKKLKRVMVNRLETI 99

>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 = 57.3 bits (139), Expect = 1e-12
 Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 8/60 (13%)

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

>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 = 54.2 bits (131), Expect = 2e-11
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 9/61 (14%)

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 I 102
           I
Sbjct: 62  I 62

>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 = 52.1 bits (125), Expect = 2e-10
 Identities = 15/60 (25%), Positives = 22/60 (36%), Gaps = 8/60 (13%)

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

>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 = 2e-10
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 33  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF--LRDADDPL 90
           M+  K +   + + +D  ++  L  GR   GT K +D+ +NL+L +  EF  ++  +   
Sbjct: 1   MTVGKSS--KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQ 58

Query: 91  KTTDQTRQLGLI 102
              ++ R LGL+
Sbjct: 59  AEREEKRVLGLV 70

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

 Score = 51.8 bits (124), Expect = 3e-10
 Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 7/60 (11%)

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

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

 Score = 46.0 bits (109), Expect = 4e-08
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 7/52 (13%)

Query: 51  VQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLI 102
           V +      ++ G + G+D+ +NLVLD+A E           T   +QLG I
Sbjct: 33  VWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEI-------HSKTKSRKQLGRI 77

>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 = 45.2 bits (107), Expect = 9e-08
 Identities = 17/41 (41%), Positives = 20/41 (48%), Gaps = 1/41 (2%)

Query: 43 LAKFVDKGVQVKL-TGGRQVTGTLKGYDQLLNLVLDEAVEF 82
          L   V+  V VKL     +  GTL   D   NL L+EA EF
Sbjct: 26 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEF 66

>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 = 42.0 bits (99), Expect = 2e-06
 Identities = 13/49 (26%), Positives = 21/49 (42%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLK 91
          L     + + V+L  G    G L+  D  +NL L E +  + D D   +
Sbjct: 21 LNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFR 69

>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 = 41.1 bits (96), Expect = 6e-06
 Identities = 12/69 (17%), Positives = 28/69 (40%), Gaps = 6/69 (8%)

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

Query: 94  DQTRQLGLI 102
           ++ R +  +
Sbjct: 91  NKDRYISKM 99

>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 = 40.8 bits (95), Expect = 8e-06
 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

>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 = 40.0 bits (93), Expect = 2e-05
 Identities = 14/45 (31%), Positives = 22/45 (48%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDAD 87
          L K   + V ++L  G QV GT+ G D  +N  L      L++ +
Sbjct: 7  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE 51

>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 = 39.3 bits (91), Expect = 3e-05
 Identities = 8/43 (18%), Positives = 13/43 (30%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD 85
          L +     V  +   G    G L   +  +N  +       RD
Sbjct: 10 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD 52

>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 = 36.6 bits (85), Expect = 1e-04
 Identities = 8/43 (18%), Positives = 13/43 (30%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD 85
          L +     V  +   G    G L   +  +N  +       RD
Sbjct: 10 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD 52

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	112
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.88
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.85
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.85
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.85
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.85
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.85
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.84
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.84
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.84
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.84
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.83
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.83
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.83
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.82
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.82
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.82
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.8
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.8
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.79
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.77
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.77
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.74
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.67
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.66
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	98.74
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	96.82
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.56
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	96.54
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	96.2
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	96.17
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	95.85
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	95.61
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	95.12
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	94.77
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	93.78
1ycy_A	71	Conserved hypothetical protein; structural genomic	92.4
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	91.43
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	91.04
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	90.13
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	89.64
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	88.26
2xk0_A	69	Polycomb protein PCL; transcription, aromatic CAGE	82.48
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	82.44
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	81.66
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	81.52
1bia_A	321	BIRA bifunctional protein; transcription regulatio	80.88

>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=99.88  E-value=9e-23  Score=142.54  Aligned_cols=86  Identities=44%  Similarity=0.653  Sum_probs=52.8

Q ss_pred             cccccccccCCCCCChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEE
Q 033737           25 LGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGN  104 (112)
Q Consensus        25 ~~~~~~~~ms~~~~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvI  104 (112)
                      ++....-...+++.+.++|.+|+|++|+|+|+|||.|+|+|.|||+||||+|++|+|++...+.. ......|.+|+++|
T Consensus        10 ~~~~~~~~~~~kke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~-~~~~~~r~lG~v~I   88 (113)
T 4emk_C           10 PGNSSQPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDG-KLTGAIRKLGLVVV   88 (113)
T ss_dssp             ----------------------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC----------CCEEEEEEEEE
T ss_pred             CCCCCCCccCCccchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCc-ccccceeEccEEEE
Confidence            33334444556678899999999999999999999999999999999999999999998753211 12247899999999


Q ss_pred             eCCceec
Q 033737          105 CCDACVT  111 (112)
Q Consensus       105 RGd~iv~  111 (112)
                      ||++|+.
T Consensus        89 RG~nIv~   95 (113)
T 4emk_C           89 RGTTLVL   95 (113)
T ss_dssp             CTTTEEE
T ss_pred             CCCeEEE
Confidence            9999973

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

Probab=99.85  E-value=1.1e-21  Score=127.72  Aligned_cols=65  Identities=37%  Similarity=0.678  Sum_probs=49.4

Q ss_pred             ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ..+.|.+++|++|+|+|+|||.|+|+|.|||+|||++|++|.|++.+        .+.+.+|+++|||++|+.
T Consensus         5 ~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~lg~v~iRG~~I~~   69 (76)
T 3s6n_G            5 HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATS--------GQQNNIGMVVIRGNSIIM   69 (76)
T ss_dssp             ---------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC------------CBSSEEECSSSEEE
T ss_pred             chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccC--------CcEeEcCEEEECCCeEEE
Confidence            46789999999999999999999999999999999999999999764        246889999999999973

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

Probab=99.85  E-value=2.7e-21  Score=125.08  Aligned_cols=64  Identities=30%  Similarity=0.360  Sum_probs=58.7

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ...|.+++|++|+|+|+|||.|+|+|.|||+|||++|++|.|++.+        ...+.+|.++|||++|+.
T Consensus         6 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~~I~~   69 (75)
T 1h64_1            6 LDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG--------EVVKRYGKIVIRGDNVLA   69 (75)
T ss_dssp             HHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEE
T ss_pred             HHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeC--------CceeECCEEEECCCEEEE
Confidence            5568999999999999999999999999999999999999999863        368999999999999973

>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=99.85  E-value=3.1e-21  Score=126.67  Aligned_cols=71  Identities=37%  Similarity=0.461  Sum_probs=61.8

Q ss_pred             cCCCCCChh-hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           33 MSGRKETVL-DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        33 ms~~~~~~~-~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      |+..+..|. .|.+++|++|+|+|+|||.|+|+|.|||+|||++|++|.|++.+        ...+.+|.++|||++|+.
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            555544444 58999999999999999999999999999999999999999854        357899999999999873

>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=99.85  E-value=4.1e-21  Score=130.24  Aligned_cols=71  Identities=27%  Similarity=0.362  Sum_probs=61.5

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ...|.+++|++|+|+|+|||.|+|+|.|||+||||+|++|+|++...+++. .....|.+|+++|||++|+.
T Consensus        12 ~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~-~~~~~r~lG~v~IRG~nVv~   82 (96)
T 3bw1_A           12 LDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEE-LSESERRCEMVFIRGDTVTL   82 (96)
T ss_dssp             HHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTC-CCEEEEEEEEEEECGGGEEE
T ss_pred             HHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccc-cCcceeEcCEEEECCCEEEE
Confidence            556899999999999999999999999999999999999999987654321 12468999999999999973

>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=99.85  E-value=3.1e-21  Score=128.85  Aligned_cols=72  Identities=25%  Similarity=0.377  Sum_probs=59.8

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCC--CccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~--~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ...|.+++|++|+|+|+|||.|+|+|.|||+||||+|++|+|++....++  .......+.+|+++|||++|+.
T Consensus         6 ~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~   79 (91)
T 1d3b_B            6 SSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVS   79 (91)
T ss_dssp             -CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEE
T ss_pred             hHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEE
Confidence            45789999999999999999999999999999999999999986432211  1123578999999999999973

>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=99.84  E-value=6e-21  Score=123.83  Aligned_cols=64  Identities=36%  Similarity=0.485  Sum_probs=58.6

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ...|.+++|++|+|+|+||+.|.|+|.|||+|||++|++|.|++.+        ...+.+|.++|||++|+.
T Consensus         6 ~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~~I~~   69 (77)
T 1i4k_A            6 LDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG--------EVVRKVGSVVIRGDTVVF   69 (77)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEE
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecC--------CcEeECCEEEECCCEEEE
Confidence            4568999999999999999999999999999999999999999864        368899999999999873

>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=4.8e-21  Score=124.27  Aligned_cols=63  Identities=24%  Similarity=0.301  Sum_probs=57.4

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ...|.+++|++|+|+|+||+.|+|+|.|||+|||++|++|+|+...        .+.+.+|.++|||++|+
T Consensus         6 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~~I~   68 (75)
T 4emk_B            6 NEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNG--------KKTNVYGDAFIRGNNVL   68 (75)
T ss_dssp             HHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETT--------EEEEEEEEEEEEGGGSS
T ss_pred             HHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecC--------CcccEecEEEEcCCeEE
Confidence            4558999999999999999999999999999999999999998743        35789999999999986

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

Probab=99.84  E-value=1e-20  Score=127.85  Aligned_cols=74  Identities=31%  Similarity=0.399  Sum_probs=58.0

Q ss_pred             CChhhH-HhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCC-----ccccceEeeeeEEEeCCceec
Q 033737           38 ETVLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        38 ~~~~~L-~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~-----~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ..|.+| ..++|++|+|+|+|||.|.|+|.|||+||||+|++|+|++...+++.     ..+.+.|.+|+++|||++|+.
T Consensus         8 ~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nVv~   87 (93)
T 4emg_A            8 AEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVIL   87 (93)
T ss_dssp             -CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGEEE
T ss_pred             CCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeEEE
Confidence            446675 55599999999999999999999999999999999999987533211     122468999999999999973

>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=99.84  E-value=1.5e-20  Score=127.64  Aligned_cols=65  Identities=22%  Similarity=0.333  Sum_probs=57.9

Q ss_pred             hhh-HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~-L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      |.+ |.++++++|+|+|+|||+|+|+|.|||+||||+|+||+|+....       .+.+.+|.++|||++|+.
T Consensus        21 Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~-------~~~~~lg~v~IRG~nI~~   86 (94)
T 4emk_A           21 PLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVT-------GVTEKHSEMLLNGNGMCM   86 (94)
T ss_dssp             HHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTT-------CCEEEEEEEEECSTTEEE
T ss_pred             CHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCC-------CcEeEcCEEEEcCCEEEE
Confidence            444 78999999999999999999999999999999999999998321       358899999999999973

>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=99.83  E-value=1.1e-20  Score=125.88  Aligned_cols=69  Identities=26%  Similarity=0.295  Sum_probs=58.8

Q ss_pred             cCCCCCChh-hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           33 MSGRKETVL-DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        33 ms~~~~~~~-~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ||. |..|. .|.+++|++|+|+|+||+.|+|+|.|||+|||++|++|.|+...        ...+.+|.++|||++|+
T Consensus         1 ms~-~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g--------~~~~~lg~v~IRG~nI~   70 (86)
T 3s6n_F            1 MSL-PLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDG--------ALSGHLGEVLIRCNNVL   70 (86)
T ss_dssp             --C-CCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEESSEEECGGGEE
T ss_pred             CCc-CcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCC--------ceeeEccEEEEeCCeEE
Confidence            554 34444 48999999999999999999999999999999999999998642        25789999999999997

>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=99.83  E-value=2.2e-20  Score=123.33  Aligned_cols=64  Identities=34%  Similarity=0.468  Sum_probs=58.7

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ...|.+++|++|+|+|+||+.|.|+|.|||+|||++|+||+|++.+        ...+.+|.++|||++|+.
T Consensus        17 ~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~IRG~~I~~   80 (83)
T 1mgq_A           17 LDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG--------EVTRRLGTVLIRGDNIVY   80 (83)
T ss_dssp             THHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEE
T ss_pred             HHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecC--------CcccCCCEEEECCCEEEE
Confidence            4568999999999999999999999999999999999999999853        368999999999999873

>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=99.83  E-value=1.2e-20  Score=132.14  Aligned_cols=93  Identities=16%  Similarity=0.220  Sum_probs=55.2

Q ss_pred             cccccccccccccccccCCCCCChhhHHhhc--CCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCC----
Q 033737           17 RSARVSFNLGFLKSLKMSGRKETVLDLAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL----   90 (112)
Q Consensus        17 ~~~~~~~~~~~~~~~~ms~~~~~~~~L~~~i--~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~----   90 (112)
                      ||+++..+....+..++...|  ...|.+++  +++|+|+|+|||.|.|+|.|||+||||+|+||+|++...+++.    
T Consensus         8 ~~~~~~~~~~~~e~~~~~~~P--l~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~   85 (118)
T 1b34_B            8 KSEMTPEELQKREEEEFNTGP--LSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKK   85 (118)
T ss_dssp             ------------------CCH--HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC------------
T ss_pred             hhhcChhhhhhhhhhhcccCh--HHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccc
Confidence            577776666667777776543  33467888  5999999999999999999999999999999999986532210    


Q ss_pred             --ccccceEeeeeEEEeCCceec
Q 033737           91 --KTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        91 --~~~~~~r~lGlvvIRGd~iv~  111 (112)
                        ......|.+|.++|||++|+.
T Consensus        86 ~~~~~~~~r~lg~v~IRG~nVv~  108 (118)
T 1b34_B           86 KSKPVNKDRYISKMFLRGDSVIV  108 (118)
T ss_dssp             -------CEEEEEEEECGGGEEE
T ss_pred             cccccccccCcCeEEEcCCEEEE
Confidence              011246789999999999973

>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=99.82  E-value=2.4e-20  Score=122.50  Aligned_cols=63  Identities=27%  Similarity=0.375  Sum_probs=57.1

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ...|.++++++|+|+|+|||.|.|+|.|||+|||++|+||.|+ ..        ...+.+|.++|||++|+.
T Consensus        13 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~--------~~~~~lg~v~iRG~~I~~   75 (81)
T 1i8f_A           13 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-ID--------GNVYKRGTMVVRGENVLF   75 (81)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ET--------TEEEEEEEEEECGGGEEE
T ss_pred             HHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cC--------CcccCCCEEEECCCEEEE
Confidence            4458999999999999999999999999999999999999999 32        368999999999999973

>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=99.82  E-value=3e-20  Score=120.79  Aligned_cols=63  Identities=30%  Similarity=0.428  Sum_probs=58.2

Q ss_pred             hhhHHhhcCCeEEEEEcCC-eEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           40 VLDLAKFVDKGVQVKLTGG-RQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dg-r~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ...|.++++++|+|+|+|| ++++|+|.|||+|||++|++|+|+...        ...+.+|.++|||++|+
T Consensus         7 ~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~nI~   70 (77)
T 1ljo_A            7 NQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE--------EKVRSLGEIVLRGNNVV   70 (77)
T ss_dssp             HHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEE
T ss_pred             HHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecC--------CcEeECCeEEEeCCeEE
Confidence            5568999999999999999 999999999999999999999999852        36889999999999987

>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=99.82  E-value=2.7e-20  Score=143.72  Aligned_cols=72  Identities=25%  Similarity=0.377  Sum_probs=61.7

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCC--CccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~--~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ..+|.+|+||+|+|+|+|||+|+|+|+|||+||||||+||+|++..+.++  ..+.+++|.+|+++||||+||.
T Consensus         6 ~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~   79 (231)
T 3pgw_B            6 SSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVS   79 (231)
T ss_pred             hHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEE
Confidence            56799999999999999999999999999999999999999998532221  2233578999999999999984

>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=99.80  E-value=6.4e-20  Score=123.99  Aligned_cols=72  Identities=21%  Similarity=0.370  Sum_probs=59.7

Q ss_pred             cCCCCCChhh-HHhhcCCeEEEEE----cCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCC
Q 033737           33 MSGRKETVLD-LAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCD  107 (112)
Q Consensus        33 ms~~~~~~~~-L~~~i~k~V~V~L----~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd  107 (112)
                      |.+-+..|.+ |.++++++++|++    +|||+|+|+|.|||+||||+|+||+|+..+.       ++.+.+|+++|||+
T Consensus        10 ~~~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~-------~~~~~lg~v~iRG~   82 (92)
T 3s6n_E           10 VQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT-------KSRKQLGRIMLKGD   82 (92)
T ss_dssp             ----CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSS-------CCEEEEEEEEECGG
T ss_pred             cceeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCC-------CceeEcCeEEEeCC
Confidence            3333445666 6899999999999    9999999999999999999999999997532       35789999999999


Q ss_pred             ceec
Q 033737          108 ACVT  111 (112)
Q Consensus       108 ~iv~  111 (112)
                      +|+.
T Consensus        83 nV~~   86 (92)
T 3s6n_E           83 NITL   86 (92)
T ss_dssp             GEEE
T ss_pred             EEEE
Confidence            9973

>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=99.80  E-value=1e-19  Score=123.01  Aligned_cols=63  Identities=33%  Similarity=0.363  Sum_probs=55.8

Q ss_pred             hhhHHhhcCCeEEEEEcCC-eEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           40 VLDLAKFVDKGVQVKLTGG-RQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dg-r~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ...|.+++|++|+|+|+|| ++|+|+|.|||+||||+|++|+|+..+        .+.+.+|.++|||++|+
T Consensus        23 ~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~--------~~~~~lg~v~IRG~nI~   86 (93)
T 1n9r_A           23 KPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG--------VSHGTLGEIFIRCNNVL   86 (93)
T ss_dssp             ---CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETT--------EEEEECCSEEECGGGEE
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCC--------CeEeEcCEEEEcCCeEE
Confidence            3458999999999999999 999999999999999999999999742        35789999999999987

>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=99.79  E-value=6.8e-20  Score=128.84  Aligned_cols=72  Identities=25%  Similarity=0.390  Sum_probs=57.3

Q ss_pred             hhh-HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCC--CCCcc-----ccceEeeeeEEEeCCceec
Q 033737           40 VLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDAD--DPLKT-----TDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~-L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~--~~~~~-----~~~~r~lGlvvIRGd~iv~  111 (112)
                      |.+ |.++++++|+|.|+|||.|+|+|.|||+||||+|+||+|++.+.+  +....     +...+.+|+++|||++|+.
T Consensus        29 Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~nVv~  108 (121)
T 2fwk_A           29 PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAM  108 (121)
T ss_dssp             HHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEEE
T ss_pred             cHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCEEEE
Confidence            444 689999999999999999999999999999999999999986411  10000     1127899999999999973

>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=99.77  E-value=1.4e-18  Score=112.96  Aligned_cols=62  Identities=16%  Similarity=0.043  Sum_probs=56.2

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ..|++++|++|+|+|++|++|+|+|.|||+|||++|++|+|+..+        .+.+.+|.++|||++|.
T Consensus         8 ~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~--------~~~~~lg~v~IRG~nI~   69 (75)
T 1d3b_A            8 KVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD--------GRVAQLEQVYIRGCKIR   69 (75)
T ss_dssp             HHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTT--------SCEEEEEEEEECGGGEE
T ss_pred             HHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCC--------CcEEEcCeEEEeCCEEE
Confidence            347899999999999999999999999999999999999998643        24789999999999986

>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=99.77  E-value=9.8e-19  Score=120.78  Aligned_cols=62  Identities=23%  Similarity=0.255  Sum_probs=51.2

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      .|.+++|++|+|+|+||++|+|+|.|||+||||+|++|+|+..+.       +..+.+|.++|||++|+
T Consensus        20 lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg-------~~~~~lg~v~IRG~nI~   81 (105)
T 4emh_A           20 LLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDG-------DKFFRLPECYIRGNNIK   81 (105)
T ss_dssp             ------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTS-------CEEEEEEEEEECGGGEE
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCC-------ceeeEcCeEEEeCCeEE
Confidence            378999999999999999999999999999999999999986432       25789999999999986

>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=99.74  E-value=4.8e-18  Score=119.15  Aligned_cols=63  Identities=27%  Similarity=0.307  Sum_probs=57.1

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ...|.++++++|+|+|+||++|+|+|.+||+||||+|+||+|+..+        .+.+.+|.++|||++|+
T Consensus         4 ~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~--------~~~~~lg~v~IRG~nI~   66 (119)
T 1b34_A            4 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKN--------REPVQLETLSIRGNNIR   66 (119)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTT--------SCCEEEEEEEECGGGEE
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCC--------CceeEcceEEEcCCeEE
Confidence            4568999999999999999999999999999999999999998643        24689999999999996

>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=99.67  E-value=6.7e-17  Score=115.28  Aligned_cols=58  Identities=26%  Similarity=0.319  Sum_probs=53.5

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ..|.+++|++|+|+|+||+.|.|+|.|||+||||+|+||.|+.            .+.+|.++|||++|+
T Consensus         3 ~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~------------~~~lg~v~IRG~nI~   60 (130)
T 1m5q_A            3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA------------GEKFNRVFIMYRYIV   60 (130)
T ss_dssp             HHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT------------CCEEEEEEECGGGEE
T ss_pred             hHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc------------CCEeceEEEeCCeEE
Confidence            5689999999999999999999999999999999999999962            257899999999986

>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=99.66  E-value=2.3e-16  Score=111.95  Aligned_cols=63  Identities=16%  Similarity=0.080  Sum_probs=56.7

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ...|.++++++|+|+|++|++|.|+|.+||+|||++|+||+|+..+.        +...+|.++|||++|+
T Consensus         7 ~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g--------~~~~l~~v~IRGnnI~   69 (126)
T 2y9a_D            7 IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG--------RVAQLEQVYIRGSKIR   69 (126)
T ss_dssp             HHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTS--------CCEEEEEEEECGGGEE
T ss_pred             HHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCC--------cEeecccEEEeCCEEE
Confidence            45589999999999999999999999999999999999999986431        4688999999999986

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

Probab=98.74  E-value=3e-08  Score=66.23  Aligned_cols=59  Identities=19%  Similarity=0.203  Sum_probs=48.8

Q ss_pred             CChhhHHhhcCCeEEEEEcCCeEEEEEEEeec-CccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        38 ~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD-~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      .+|.++++|+||+|.|+|.||++|.|.|.+|| .-.|++|.++    ..+          .....++|.|..|.
T Consensus         7 ~~p~el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~----~~~----------~~~~~~iI~G~aI~   66 (86)
T 1y96_A            7 KGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF----LED----------GSMSVTGIMGHAVQ   66 (86)
T ss_dssp             SCHHHHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE----CTT----------SCEEEEEECGGGEE
T ss_pred             CCHHHHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec----ccC----------CeEEEEEEecceEE
Confidence            46889999999999999999999999999999 7899999998    111          11356778787664

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

Probab=96.82  E-value=0.0022  Score=41.83  Aligned_cols=46  Identities=30%  Similarity=0.381  Sum_probs=31.7

Q ss_pred             cCCCCCChhh--HHhhc--CCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737           33 MSGRKETVLD--LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (112)
Q Consensus        33 ms~~~~~~~~--L~~~i--~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~   78 (112)
                      |+.+.....+  |+.+.  +.+|+|.|.+|-.++|.+.+||+|+=++-.+
T Consensus         4 ~~~~~~nlQd~fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~~~   53 (78)
T 3ahu_A            4 GSMKPINIQDQFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLESE   53 (78)
T ss_dssp             ------CHHHHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEESS
T ss_pred             ccccccChHHHHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEEEEC
Confidence            4444455444  55554  6799999999999999999999998666543

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

Probab=96.56  E-value=0.0025  Score=41.65  Aligned_cols=43  Identities=26%  Similarity=0.454  Sum_probs=29.9

Q ss_pred             cCCCCCChhh--HHhhcC--CeEEEEEcCCeEEEEEEEeecCcccee
Q 033737           33 MSGRKETVLD--LAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (112)
Q Consensus        33 ms~~~~~~~~--L~~~i~--k~V~V~L~dgr~i~G~L~~fD~~mNlv   75 (112)
                      |++++....+  |+.+..  .+|.|.|.+|-.++|.+.+||+|+=++
T Consensus         1 m~~~~~nlQd~fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL   47 (79)
T 3sb2_A            1 MSNKGQLLQDPFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL   47 (79)
T ss_dssp             -----CTTHHHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             CCccccchHHHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            4444444444  666644  479999999999999999999998655

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

Probab=96.54  E-value=0.0032  Score=40.60  Aligned_cols=35  Identities=23%  Similarity=0.445  Sum_probs=29.8

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEeecCccceeec
Q 033737           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (112)
Q Consensus        43 L~~~i--~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~   77 (112)
                      |+.+.  ..+|+|.|.+|-.++|.+.+||+|+=++-+
T Consensus        14 L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL~~   50 (74)
T 2ylb_A           14 LNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKN   50 (74)
T ss_dssp             HHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEES
T ss_pred             HHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEEC
Confidence            66665  679999999999999999999999866543

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

Probab=96.20  E-value=0.011  Score=38.42  Aligned_cols=36  Identities=25%  Similarity=0.418  Sum_probs=30.2

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (112)
Q Consensus        43 L~~~i--~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~   78 (112)
                      |+.+.  ..+|.|.|.+|-.++|.+.+||+|+=++-.+
T Consensus        12 Ln~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~~~   49 (77)
T 1kq1_A           12 LENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQ   49 (77)
T ss_dssp             HHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             HHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEEEC
Confidence            56665  6799999999999999999999998666543

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

Probab=96.17  E-value=0.0079  Score=39.55  Aligned_cols=34  Identities=24%  Similarity=0.441  Sum_probs=28.4

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEeecCccceee
Q 033737           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (112)
Q Consensus        43 L~~~i--~k~V~V~L~dgr~i~G~L~~fD~~mNlvL   76 (112)
                      |+.+.  ..+|+|.|.+|-.++|.+.+||+|+=++-
T Consensus        12 Ln~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~   47 (82)
T 1u1s_A           12 LNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK   47 (82)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEe
Confidence            55443  66999999999999999999999986554

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

Probab=95.85  E-value=0.015  Score=37.30  Aligned_cols=32  Identities=19%  Similarity=0.210  Sum_probs=27.8

Q ss_pred             cCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (112)
Q Consensus        47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~   78 (112)
                      -+.+|+|.|.+|-.++|.+.|||+|+=++-.+
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   55 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSNYEIMVKVG   55 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceEEEEEeC
Confidence            45689999999999999999999998766544

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

Probab=95.61  E-value=0.014  Score=39.85  Aligned_cols=36  Identities=22%  Similarity=0.458  Sum_probs=29.4

Q ss_pred             HHhhcCC--eEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737           43 LAKFVDK--GVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (112)
Q Consensus        43 L~~~i~k--~V~V~L~dgr~i~G~L~~fD~~mNlvL~~   78 (112)
                      |+.+..+  +|.|.|.+|-.++|++.+||+|+=++-++
T Consensus        14 Ln~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~~~   51 (104)
T 2y90_A           14 LNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNT   51 (104)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEESS
T ss_pred             HHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEECC
Confidence            6666544  89999999999999999999998665543

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

Probab=95.12  E-value=0.16  Score=33.63  Aligned_cols=66  Identities=12%  Similarity=0.083  Sum_probs=48.6

Q ss_pred             HhhcCCeEEEEEcCCeEEEEEEEeecCc-cceeecceEEEeecCCCC-CccccceEeeeeEEEeCCce
Q 033737           44 AKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFLRDADDP-LKTTDQTRQLGLIGNCCDAC  109 (112)
Q Consensus        44 ~~~i~k~V~V~L~dgr~i~G~L~~fD~~-mNlvL~~a~E~~~~~~~~-~~~~~~~r~lGlvvIRGd~i  109 (112)
                      ..|+|+++.+..+.+-+|+|+|...|.. .-+.|.++.-+-...... .+.-....-+..++.||..|
T Consensus         9 ~~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDI   76 (88)
T 2vxe_A            9 LPELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDI   76 (88)
T ss_dssp             SCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTE
T ss_pred             CcccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCc
Confidence            3589999999999999999999999955 688999987775432211 11112334568899999876

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

Probab=94.77  E-value=0.037  Score=38.95  Aligned_cols=37  Identities=27%  Similarity=0.453  Sum_probs=31.2

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceee--cce
Q 033737           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL--DEA   79 (112)
Q Consensus        42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL--~~a   79 (112)
                      ...+|+|+.|.|+|+||..++|++..+|.- +|.|  .+|
T Consensus         6 ~~sqFlGy~V~v~LkDgs~~qG~I~~vd~k-~LtL~~~~a   44 (125)
T 4a53_A            6 SVADFYGSNVEVLLNNDSKARGVITNFDSS-NSILQLRLA   44 (125)
T ss_dssp             CHHHHTTCEEEEEETTSCEEEEEEEEEETT-TTEEEEEET
T ss_pred             cHHHhcCceEEEEECCCCEeeEEEEeecCC-eeEEecccc
Confidence            467899999999999999999999999843 4555  665

>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=93.78  E-value=0.15  Score=34.23  Aligned_cols=68  Identities=9%  Similarity=0.037  Sum_probs=46.9

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEeecCc-cceeecceEEEeecCCC-CCccccceEeeeeEEEeCCce
Q 033737           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFLRDADD-PLKTTDQTRQLGLIGNCCDAC  109 (112)
Q Consensus        42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~-mNlvL~~a~E~~~~~~~-~~~~~~~~r~lGlvvIRGd~i  109 (112)
                      .-..|+|+++.+..+.+-+|+|+|...|.. .-+.|.++.-+-..... +.+.-....-+..++.||..|
T Consensus        13 ~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDI   82 (95)
T 2fb7_A           13 GGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDI   82 (95)
T ss_dssp             ---CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTE
T ss_pred             ccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCc
Confidence            346799999999999999999999999954 67888887665433211 111112333467888999876

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

Probab=92.40  E-value=0.19  Score=31.76  Aligned_cols=44  Identities=25%  Similarity=0.499  Sum_probs=34.0

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeec
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD   85 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~   85 (112)
                      ..|.++.|+||-+.......|+|+|.-||.-. +.|.|+..+.-.
T Consensus         9 ktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~GN   52 (71)
T 1ycy_A            9 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGN   52 (71)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEE
T ss_pred             HHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHhcc
Confidence            34899999999999999999999999999874 678888877543

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

Probab=91.43  E-value=0.29  Score=35.15  Aligned_cols=32  Identities=25%  Similarity=0.254  Sum_probs=27.6

Q ss_pred             hhhHHhhcCCeEEEEE----cCCeEEEEEEEeecCc
Q 033737           40 VLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQL   71 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L----~dgr~i~G~L~~fD~~   71 (112)
                      +.++.+++|+.|.|++    .+.+.++|+|.++|.-
T Consensus        96 ~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T 1ib8_A           96 KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED  131 (164)
T ss_dssp             HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             HHHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCC
Confidence            5568899999999999    4559999999999865

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

Probab=91.04  E-value=0.39  Score=31.58  Aligned_cols=36  Identities=14%  Similarity=0.230  Sum_probs=33.6

Q ss_pred             hhcCCeEEEEEcCCe-EEEEEEEeecCc-cceeecceE
Q 033737           45 KFVDKGVQVKLTGGR-QVTGTLKGYDQL-LNLVLDEAV   80 (112)
Q Consensus        45 ~~i~k~V~V~L~dgr-~i~G~L~~fD~~-mNlvL~~a~   80 (112)
                      +|+|+.|.+...++- .|+|.+..+|.. .+|.|.++.
T Consensus         6 ~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f   43 (84)
T 2vc8_A            6 DWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF   43 (84)
T ss_dssp             TTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE
T ss_pred             cccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh
Confidence            699999999999998 999999999987 689999994

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

Probab=90.13  E-value=0.37  Score=36.88  Aligned_cols=34  Identities=32%  Similarity=0.488  Sum_probs=30.5

Q ss_pred             cCCeEEEEEcCCeEEEEEEEeecCccceeecceE
Q 033737           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV   80 (112)
Q Consensus        47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~   80 (112)
                      +|++|++.+.+|..+.|+..|+|....|+|+...
T Consensus       223 ~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~~  256 (270)
T 3rux_A          223 IGSRVRVELPGGQDVVGIARDIDDQGRLCLDVGG  256 (270)
T ss_dssp             TTSEEEEECTTSCEEEEEEEEECTTSCEEEEETT
T ss_pred             cCCEEEEEECCCeEEEEEEEEECCCCeEEEEECC
Confidence            6899999988899999999999999999997543

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

Probab=89.64  E-value=0.55  Score=29.79  Aligned_cols=43  Identities=21%  Similarity=0.228  Sum_probs=33.8

Q ss_pred             CCCCChhhHHhhcC--CeEEEEEcCCeEEEEEEEeecCccceeec
Q 033737           35 GRKETVLDLAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (112)
Q Consensus        35 ~~~~~~~~L~~~i~--k~V~V~L~dgr~i~G~L~~fD~~mNlvL~   77 (112)
                      .+-.+...|++|+-  ..|.|+|.+|..++|.+.-+|++.=++-+
T Consensus         6 t~lPsvR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L~~   50 (70)
T 3hfo_A            6 SGLPSVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLVD   50 (70)
T ss_dssp             CSCHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEC
T ss_pred             CCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEEEc
Confidence            33344566888864  58999999999999999999998766554

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

Probab=88.26  E-value=0.75  Score=29.29  Aligned_cols=41  Identities=24%  Similarity=0.372  Sum_probs=32.5

Q ss_pred             CChhhHHhhcC--CeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737           38 ETVLDLAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (112)
Q Consensus        38 ~~~~~L~~~i~--k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~   78 (112)
                      .+...|++|+.  ..|.|+|.+|..++|++.-+|.+.=++.++
T Consensus        11 PsvR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L~~~   53 (72)
T 3hfn_A           11 PSIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIADE   53 (72)
T ss_dssp             HHHHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEEEC-
T ss_pred             CcHHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEEEcC
Confidence            34566888876  488999999999999999999987555543

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

Probab=82.48  E-value=3.3  Score=26.14  Aligned_cols=39  Identities=23%  Similarity=0.292  Sum_probs=29.3

Q ss_pred             cCCeEEEEEcCCeEEEEEEEeecCcccee-ecceEEEeec
Q 033737           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLV-LDEAVEFLRD   85 (112)
Q Consensus        47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlv-L~~a~E~~~~   85 (112)
                      +|..|.++-+||+.|-|+++...+.-=+| .+|-.|.+..
T Consensus        18 ~geDVL~rw~DG~fYLGtIVd~~~~~ClV~FeD~S~~Wv~   57 (69)
T 2xk0_A           18 LQEDVFIKCNDGRFYLGTIIDQTSDQYLIRFDDQSEQWCE   57 (69)
T ss_dssp             TTCEEEEECTTSCEEEEEEEEECSSCEEEEETTCCEEEEC
T ss_pred             cCCeEEEEecCCCEEEEEEEecCCceEEEEecCCcceeee
Confidence            88999999999999999997766554333 3566666654

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

Probab=82.44  E-value=2.7  Score=27.54  Aligned_cols=57  Identities=16%  Similarity=0.130  Sum_probs=42.2

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCc-cceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~-mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ..|....|++|.+.|.++.+..|++.|+|.. .|+..++-.-             .-..+...++|+..|+
T Consensus        22 r~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T-------------PiGv~~eAlLR~~Dii   79 (85)
T 1y96_B           22 RSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQT-------------PIGVQAEALLRCSDII   79 (85)
T ss_dssp             HHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEECC-------------TTCCEEEEEEEGGGEE
T ss_pred             HHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcCC-------------CcccchhhhhhcCCEE
Confidence            3456778999999999999999999999955 6777665221             1123567788887664

>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=81.66  E-value=1.1  Score=33.42  Aligned_cols=31  Identities=19%  Similarity=0.265  Sum_probs=26.6

Q ss_pred             cCCeEEEEEcCCeEEEEEEEeecCccceeecce
Q 033737           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (112)
Q Consensus        47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a   79 (112)
                      +|++|++...++  +.|+..|+|....|+++..
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            789999976554  9999999999999999753

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

Probab=81.52  E-value=3.2  Score=30.84  Aligned_cols=32  Identities=19%  Similarity=0.208  Sum_probs=28.4

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (112)
Q Consensus        46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~   78 (112)
                      ++|++|++...++..+.|+..|+|....|+ +.
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            379999999888877999999999999998 64

>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=80.88  E-value=3  Score=32.14  Aligned_cols=33  Identities=21%  Similarity=0.520  Sum_probs=28.2

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEeecCccceeecce
Q 033737           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (112)
Q Consensus        46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a   79 (112)
                      ++|++|++... +..+.|+..|+|....|+++..
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            37899999865 5689999999999999999753

---

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	112
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	1e-16
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	8e-14
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	1e-12
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	3e-12
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	8e-12
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	9e-12
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	4e-11
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	5e-11
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	1e-10
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-10
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	2e-10
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	1e-07
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	4e-07

>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 = 66.4 bits (162), Expect = 1e-16
 Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

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

Query: 101 LI 102
           L+
Sbjct: 63  LV 64

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Length = 92

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

 Score = 59.9 bits (145), Expect = 8e-14
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 7/67 (10%)

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

Query: 96  TRQLGLI 102
             +L  I
Sbjct: 70  VNRLETI 76

>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 = 55.9 bits (135), Expect = 1e-12
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 9/71 (12%)

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

Query: 92  TTDQTRQLGLI 102
                ++LG I
Sbjct: 55  --GSGKKLGTI 63

>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]

 Score = 55.1 bits (133), Expect = 3e-12
 Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 8/60 (13%)

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

>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 = 54.5 bits (131), Expect = 8e-12
 Identities = 12/69 (17%), Positives = 28/69 (40%), Gaps = 6/69 (8%)

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

Query: 94  DQTRQLGLI 102
           ++ R +  +
Sbjct: 66  NKDRYISKM 74

>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 = 53.9 bits (130), Expect = 9e-12
 Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 8/60 (13%)

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

>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 = 52.4 bits (126), Expect = 4e-11
 Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 8/60 (13%)

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

>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 = 52.0 bits (125), Expect = 5e-11
 Identities = 16/50 (32%), Positives = 26/50 (52%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKT 92
          L   + K V VKL    ++ G L+ +DQ +NL+L++A E +        T
Sbjct: 7  LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGT 56

>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 = 51.2 bits (123), Expect = 1e-10
 Identities = 20/61 (32%), Positives = 24/61 (39%), Gaps = 9/61 (14%)

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

Query: 102 I 102
           I
Sbjct: 53  I 53

>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 = 50.9 bits (122), Expect = 1e-10
 Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 9/61 (14%)

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 I 102
           I
Sbjct: 62  I 62

>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 = 2e-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 = 43.1 bits (102), Expect = 1e-07
 Identities = 14/43 (32%), Positives = 21/43 (48%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD 85
          L K   + V ++L  G QV GT+ G D  +N  L      L++
Sbjct: 6  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKN 48

>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 = 41.7 bits (98), Expect = 4e-07
 Identities = 8/43 (18%), Positives = 13/43 (30%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD 85
          L +     V  +   G    G L   +  +N  +       RD
Sbjct: 7  LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD 49

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	112
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.88
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.83
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.83
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.82
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.82
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.81
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.8
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.8
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.78
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.78
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.7
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.6
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.52
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	96.63
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	95.76
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	94.9
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	93.63
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	93.62
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	90.48

>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=99.88  E-value=3.5e-23  Score=134.96  Aligned_cols=70  Identities=26%  Similarity=0.403  Sum_probs=60.6

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCC--CccccceEeeeeEEEeCCceec
Q 033737           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~--~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      +|.+|+|++|+|+|+|||.|.|+|.|||+||||+|++|+|++.....+  ..+..+.|.+|+++|||++||.
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~   73 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVS   73 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEE
Confidence            578999999999999999999999999999999999999997654332  2233578999999999999984

>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=99.83  E-value=6.1e-21  Score=121.73  Aligned_cols=63  Identities=25%  Similarity=0.376  Sum_probs=57.7

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      .+.|++++|++|+|+|+||+.|+|+|.+||+|||++|++|.|+..+         +.+.+|.++|||++|+.
T Consensus         4 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~---------~~~~~g~v~iRG~~I~~   66 (71)
T d1i8fa_           4 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG---------NVYKRGTMVVRGENVLF   66 (71)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETT---------EEEEEEEEEECGGGEEE
T ss_pred             hHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECC---------CEEEcceEEEeCCeEEE
Confidence            4579999999999999999999999999999999999999998653         57889999999999973

>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=99.83  E-value=7.9e-21  Score=121.08  Aligned_cols=62  Identities=37%  Similarity=0.503  Sum_probs=56.6

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      .-|.+++|++|+|.|+||+.|.|+|.|||+|||++|++|.|+...        ...+.+|.++|||++|+
T Consensus         6 ~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~~g~~~IRG~~I~   67 (72)
T d1i4k1_           6 DVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG--------EVVRKVGSVVIRGDTVV   67 (72)
T ss_dssp             HHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSS--------SEEEEEEEEEECGGGEE
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecC--------CeEeEcceEEEeCCeEE
Confidence            348999999999999999999999999999999999999998653        35788999999999996

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

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

Probab=99.82  E-value=2.2e-20  Score=118.46  Aligned_cols=64  Identities=33%  Similarity=0.422  Sum_probs=57.5

Q ss_pred             hhh-HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~-L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      |.+ |++++|++|+|.|+||+.|+|+|.|||+||||+|++|.|+...        ...+.+|.++|||++|+.
T Consensus         3 Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~l~~~~IRG~~I~~   67 (71)
T d1h641_           3 PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG--------EVVKRYGKIVIRGDNVLA   67 (71)
T ss_dssp             HHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEE
T ss_pred             chHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecC--------CcEeEcCcEEEECCeEEE
Confidence            344 7899999999999999999999999999999999999998653        367899999999999973

>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=99.82  E-value=2.1e-20  Score=120.26  Aligned_cols=63  Identities=37%  Similarity=0.499  Sum_probs=57.3

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      .-|.+++|++|+|.|+||+.|+|+|.|||+|||++|++|.|+..+        .+.+.+|.++|||++|+.
T Consensus        10 ~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~~~~v~iRG~~I~~   72 (76)
T d1th7a1          10 KVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD--------GSGKKLGTIVIRGDNVIL   72 (76)
T ss_dssp             HHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSS--------SCEEEEEEEEECGGGEEE
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecC--------CcccCcceEEEECCEEEE
Confidence            448899999999999999999999999999999999999998654        357899999999999974

>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=99.81  E-value=8.3e-21  Score=125.90  Aligned_cols=71  Identities=23%  Similarity=0.363  Sum_probs=57.8

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCC-------CccccceEeeeeEEEeCCceec
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP-------LKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~-------~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ..|.++++++|+|.|+|||.|.|+|.|||+||||+|+||.|++....++       ....+..|.+|+++|||++|+.
T Consensus         8 ~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~Vv~   85 (92)
T d2fwka1           8 ALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAM   85 (92)
T ss_dssp             HHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEEE
T ss_pred             HHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEEEE
Confidence            3489999999999999999999999999999999999999998654321       1123467899999999999974

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

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

Probab=99.80  E-value=3.2e-20  Score=123.95  Aligned_cols=69  Identities=19%  Similarity=0.322  Sum_probs=52.4

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCc------cccceEeeeeEEEeCCceec
Q 033737           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLK------TTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        43 L~~~i--~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~------~~~~~r~lGlvvIRGd~iv~  111 (112)
                      |.+++  +++|+|.|+|||.+.|+|.|||+||||+|+||+|++...+++..      ...+.|.+|+++||||+||.
T Consensus         7 l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnVv~   83 (93)
T d1b34b_           7 LTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIV   83 (93)
T ss_dssp             HHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEEE
T ss_pred             HHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEEEE
Confidence            55666  89999999999999999999999999999999999876443211      11357899999999999984

>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=99.80  E-value=1.1e-19  Score=116.32  Aligned_cols=64  Identities=34%  Similarity=0.468  Sum_probs=57.7

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ...|.+++|++|.|.|+||+.|.|+|.|||+|||++|++|.|+..+        .+.+.+|.++|||++|+.
T Consensus         8 l~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~--------~~~~~~~~~~IRG~~I~~   71 (74)
T d1mgqa_           8 LDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG--------EVTRRLGTVLIRGDNIVY   71 (74)
T ss_dssp             THHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEE
T ss_pred             HHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCC--------CeEeEcceEEEeCCEEEE
Confidence            3448999999999999999999999999999999999999998653        367899999999999863

>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=99.78  E-value=1.3e-19  Score=114.67  Aligned_cols=61  Identities=34%  Similarity=0.441  Sum_probs=54.4

Q ss_pred             HHhhcCCeEEEEEc-CCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           43 LAKFVDKGVQVKLT-GGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        43 L~~~i~k~V~V~L~-dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      |++++|++|.|+|+ +|+.|+|+|.+||+|||++|++|.|+..+        ...+.+|.++|||++|+.
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~lg~~~IRG~nI~~   62 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG--------VSHGTLGEIFIRCNNVLY   62 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETT--------EEEEECCSEEECGGGEEE
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecC--------CcccCcCeEEEECCEEEE
Confidence            57899999999999 56889999999999999999999998653        357889999999999973

>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=99.78  E-value=2.9e-19  Score=115.00  Aligned_cols=64  Identities=30%  Similarity=0.415  Sum_probs=56.6

Q ss_pred             hhhHHhhcCCeEEEEEcCC-eEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737           40 VLDLAKFVDKGVQVKLTGG-RQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT  111 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dg-r~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~  111 (112)
                      ...|.+++|++|+|+|++| |.|.|+|.|||+|||++|+||.|+..+        ...+.+|.++|||++|+.
T Consensus         7 ~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~~g~~~IRG~~I~~   71 (75)
T d1ljoa_           7 NQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE--------EKVRSLGEIVLRGNNVVL   71 (75)
T ss_dssp             HHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETT--------EEEEEEEEEEECGGGEEE
T ss_pred             HHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCC--------CcEeEcceEEEeCCEEEE
Confidence            3458999999999999865 899999999999999999999998654        367899999999999963

>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=99.70  E-value=2.7e-17  Score=104.61  Aligned_cols=60  Identities=17%  Similarity=0.072  Sum_probs=54.6

Q ss_pred             HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        43 L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      |.+..|++|+|+|+||++|+|+|.++|.|||++|++|.++..+        .+.+.+|.++|||++|.
T Consensus         7 L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~--------~~~~~~~~v~IRG~~I~   66 (72)
T d1d3ba_           7 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD--------GRVAQLEQVYIRGCKIR   66 (72)
T ss_dssp             HHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTT--------SCEEEEEEEEECGGGEE
T ss_pred             HHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCC--------CcEeEcCeEEEECCEEE
Confidence            7889999999999999999999999999999999999987543        25678999999999985

>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=99.60  E-value=1e-15  Score=99.12  Aligned_cols=62  Identities=26%  Similarity=0.294  Sum_probs=55.4

Q ss_pred             hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      ..|+++.|++|.|.|+||..|.|+|.++|.|||+.|++|.+...+        .+...+|.++|||++|-
T Consensus         4 ~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~--------~~~~~~~~v~IRG~~Ir   65 (80)
T d1b34a_           4 RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKN--------REPVQLETLSIRGNNIR   65 (80)
T ss_dssp             HHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTT--------SCCEEEEEEEECGGGEE
T ss_pred             HHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCC--------CCEEEcccEEEcCCEEE
Confidence            458899999999999999999999999999999999999997554        24678999999999974

>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=99.52  E-value=1.4e-14  Score=101.46  Aligned_cols=59  Identities=27%  Similarity=0.334  Sum_probs=52.3

Q ss_pred             hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV  110 (112)
Q Consensus        40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv  110 (112)
                      .++|++++|++|.|.|+||+.|.|+|.++|+|||++|+||.+...            -.++.++|||++|+
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~~------------~k~~~v~IRG~~I~   60 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAG------------EKFNRVFIMYRYIV   60 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETTC------------CEEEEEEECGGGEE
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECCC------------CcccEEEEeCCeEE
Confidence            467999999999999999999999999999999999999987421            14788999999985

>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=96.63  E-value=0.0034  Score=35.39  Aligned_cols=35  Identities=23%  Similarity=0.507  Sum_probs=29.8

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEeecCccceeecceEE
Q 033737           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE   81 (112)
Q Consensus        46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E   81 (112)
                      |+|++|+|.. .++.++|+..|+|....|+|+....
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t~~g   35 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQDGI   35 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEETTE
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEECCC
Confidence            6899999975 5588999999999999999975433

>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=95.76  E-value=0.035  Score=34.76  Aligned_cols=64  Identities=9%  Similarity=0.066  Sum_probs=48.3

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEeecCc-cceeecceEEEeecCCCC-CccccceEeeeeEEEeCCce
Q 033737           46 FVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFLRDADDP-LKTTDQTRQLGLIGNCCDAC  109 (112)
Q Consensus        46 ~i~k~V~V~L~dgr~i~G~L~~fD~~-mNlvL~~a~E~~~~~~~~-~~~~~~~r~lGlvvIRGd~i  109 (112)
                      |+|+++.+..+.+-+|+|+|...|.. .-+.|.|+.-+-....++ .+.-....-++.++.||+.|
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDI   67 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDI   67 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTE
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCc
Confidence            79999999999999999999999966 568899988775443221 11112344678999999876

>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=94.90  E-value=0.024  Score=33.76  Aligned_cols=34  Identities=21%  Similarity=0.310  Sum_probs=28.6

Q ss_pred             cCCeEEEEEcCCeEEEEEEEeecCccceeecceE
Q 033737           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV   80 (112)
Q Consensus        47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~   80 (112)
                      -..+|.|.|.+|-.++|.+.|||+|.=++-.+..
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            3468999999999999999999999877755543

>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=93.63  E-value=0.046  Score=32.72  Aligned_cols=34  Identities=26%  Similarity=0.218  Sum_probs=28.7

Q ss_pred             ChhhHHhhcCCeEEEEEc----CCeEEEEEEEeecCcc
Q 033737           39 TVLDLAKFVDKGVQVKLT----GGRQVTGTLKGYDQLL   72 (112)
Q Consensus        39 ~~~~L~~~i~k~V~V~L~----dgr~i~G~L~~fD~~m   72 (112)
                      ...++.+|+|+.|.|+|+    +-+.++|+|.++|.-.
T Consensus         5 ~~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~   42 (74)
T d1ib8a1           5 TKDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE   42 (74)
T ss_dssp             SHHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE
T ss_pred             CHHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCCe
Confidence            366899999999999984    3479999999999754

>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=93.62  E-value=0.048  Score=32.93  Aligned_cols=29  Identities=24%  Similarity=0.476  Sum_probs=25.1

Q ss_pred             cCCeEEEEEcCCeEEEEEEEeecCcccee
Q 033737           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (112)
Q Consensus        47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlv   75 (112)
                      -...|.|.|.+|-.++|.+.|||+|.=|+
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            34689999999999999999999996544

>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=90.48  E-value=0.23  Score=29.51  Aligned_cols=43  Identities=26%  Similarity=0.527  Sum_probs=33.5

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeec
Q 033737           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD   85 (112)
Q Consensus        42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~   85 (112)
                      .|+++.|++|-|.......|.|+|.-||.-. +.|.|+..+.-.
T Consensus         6 tL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~GN   48 (66)
T d1ycya1           6 VLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGN   48 (66)
T ss_dssp             HHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEE
T ss_pred             HHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHhcc
Confidence            4889999999999999999999999999874 678888877543