Citrus Sinensis ID: 034947

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------
Protein Sequence
MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT
Secondary Structure (PSIPRED)
cccccccEEEEccHHHHHHHHHcccEEEEEEEEccccEEEEEEEEHHHHHHHHHcccEEEEEccccccccEEEEcccc
Secondary Structure Prediction (SSPRO)
cccccEEEEEccHHHHHHHHHHcccEEEEEEEEcccEEEEEEEEccHHHHHEEEcccEEEEcccccccEccEcccccc
Coil and Loop (DISEMBL)
MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLddaeevhikkntrkplgffskett
Flexible Loop (DISEMBL)
mastkvqrimtqpINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDaeevhikkntrkplgffskett
Low Complexity Region (SEG)
MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT
Disordered region (IsUnstruct)
*******RIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK***************
Disordered Region (DISOPRED)
**********TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV***********FF*****
Disordered Region (DISEMBL)
MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT
Disordered Region (DISPRO)
****KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFF*****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT
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	78	2.2.26 [Sep-21-2011]
Q7ZUG0	92	Small nuclear ribonucleop	yes	no	0.858	0.728	0.731	3e-25
A1XQR9	92	Small nuclear ribonucleop	yes	no	0.884	0.75	0.695	2e-24
P62305	92	Small nuclear ribonucleop	yes	no	0.858	0.728	0.716	2e-24
P62304	92	Small nuclear ribonucleop	yes	no	0.858	0.728	0.716	2e-24
P62303	92	Small nuclear ribonucleop	yes	no	0.858	0.728	0.716	2e-24
A4FUI2	92	Small nuclear ribonucleop	yes	no	0.858	0.728	0.716	2e-24
Q9VLV5	94	Probable small nuclear ri	yes	no	0.897	0.744	0.642	6e-23
A8XDT0	90	Probable small nuclear ri	N/A	no	0.910	0.788	0.549	4e-19
Q9XTU6	90	Probable small nuclear ri	yes	no	0.910	0.788	0.535	1e-18
Q9USZ3	84	Small nuclear ribonucleop	yes	no	0.846	0.785	0.545	1e-15

>sp|Q7ZUG0|RUXE_DANRE Small nuclear ribonucleoprotein E OS=Danio rerio GN=snrpe PE=3 SV=1

 Score =  113 bits (283), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 49/67 (73%), Positives = 60/67 (89%)

Query: 5  KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
          KVQ++M QPINLIFR+LQ+++RI +WL+EQ ++RIEG IIGFDEYMNLVLDDAEEVH+K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRISVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKT 68

Query: 65 NTRKPLG 71
            RKPLG
Sbjct: 69 KNRKPLG 75

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.
Danio rerio (taxid: 7955)

>sp|A1XQR9|RUXE_PIG Small nuclear ribonucleoprotein E OS=Sus scrofa GN=SNRPE PE=3 SV=1

 Score =  111 bits (277), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 48/69 (69%), Positives = 61/69 (88%)

Query: 3  STKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI 62
          + KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H 
Sbjct: 7  AQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHS 66

Query: 63 KKNTRKPLG 71
          K  +RK LG
Sbjct: 67 KTKSRKQLG 75

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.

Sus scrofa (taxid: 9823)

>sp|P62305|RUXE_MOUSE Small nuclear ribonucleoprotein E OS=Mus musculus GN=Snrpe PE=2 SV=1

 Score =  110 bits (275), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query: 5  KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
          KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query: 65 NTRKPLG 71
           +RK LG
Sbjct: 69 KSRKQLG 75

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|P62304|RUXE_HUMAN Small nuclear ribonucleoprotein E OS=Homo sapiens GN=SNRPE PE=1 SV=1

 Score =  110 bits (275), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query: 5  KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
          KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query: 65 NTRKPLG 71
           +RK LG
Sbjct: 69 KSRKQLG 75

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|P62303|RUXE_CHICK Small nuclear ribonucleoprotein E OS=Gallus gallus GN=SNRPE PE=3 SV=1

 Score =  110 bits (275), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query: 5  KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
          KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query: 65 NTRKPLG 71
           +RK LG
Sbjct: 69 KSRKQLG 75

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

Gallus gallus (taxid: 9031)

>sp|A4FUI2|RUXE_BOVIN Small nuclear ribonucleoprotein E OS=Bos taurus GN=SNRPE PE=3 SV=1

 Score =  110 bits (275), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query: 5  KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
          KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query: 65 NTRKPLG 71
           +RK LG
Sbjct: 69 KSRKQLG 75

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

Bos taurus (taxid: 9913)

>sp|Q9VLV5|RUXE_DROME Probable small nuclear ribonucleoprotein E OS=Drosophila melanogaster GN=SmE PE=3 SV=1

 Score =  105 bits (263), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 45/70 (64%), Positives = 59/70 (84%)

Query: 2  ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVH 61
           + KVQ++M QPINLIFR+LQ+++R+Q+WL+E   LRIEG I+GFDEYMNLVLDDAEEV+
Sbjct: 5  GNPKVQKVMVQPINLIFRYLQNRSRVQVWLYENISLRIEGHIVGFDEYMNLVLDDAEEVY 64

Query: 62 IKKNTRKPLG 71
          +K   R+ LG
Sbjct: 65 VKTRQRRNLG 74

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

Drosophila melanogaster (taxid: 7227)

>sp|A8XDT0|RUXE_CAEBR Probable small nuclear ribonucleoprotein E OS=Caenorhabditis briggsae GN=snr-6 PE=3 SV=1

 Score = 93.2 bits (230), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 39/71 (54%), Positives = 56/71 (78%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          M+  K+Q++M QP+NLIFR+LQ++ R+QIWL+E    R+EG IIGFDE+MN+V D+AEEV
Sbjct: 1  MSQRKIQKVMVQPVNLIFRYLQNRTRVQIWLYEDVTHRLEGYIIGFDEFMNVVFDEAEEV 60

Query: 61 HIKKNTRKPLG 71
          ++K   R  +G
Sbjct: 61 NMKTKGRNKIG 71

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

Caenorhabditis briggsae (taxid: 6238)

>sp|Q9XTU6|RUXE_CAEEL Probable small nuclear ribonucleoprotein E OS=Caenorhabditis elegans GN=snr-6 PE=3 SV=1

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 38/71 (53%), Positives = 56/71 (78%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          M++ K+ ++M QP+NLIFR+LQ++ R+QIWL+E    R+EG IIGFDE+MN+V D+AEEV
Sbjct: 1  MSTRKLNKVMVQPVNLIFRYLQNRTRVQIWLYEDVTHRLEGYIIGFDEFMNVVFDEAEEV 60

Query: 61 HIKKNTRKPLG 71
          ++K   R  +G
Sbjct: 61 NMKTKGRNKIG 71

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

Caenorhabditis elegans (taxid: 6239)

>sp|Q9USZ3|RUXE_SCHPO Small nuclear ribonucleoprotein E OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=sme1 PE=1 SV=1

 Score = 82.0 bits (201), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 36/66 (54%), Positives = 49/66 (74%)

Query: 3  STKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI 62
          S +VQ++M  PIN IF+ LQ    + IWLFEQ D+R++G+I GFDE+MN+VLDDA +V  
Sbjct: 2  SGRVQKVMIPPINFIFKLLQQHTPVSIWLFEQTDIRLQGQIRGFDEFMNIVLDDAVQVDA 61

Query: 63 KKNTRK 68
          K N R+
Sbjct: 62 KNNKRE 67

Involved in pre-mRNA splicing. Binds and is required for the stability of snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Involved in cap modification.

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

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	78
145329170	78	putative small nuclear ribonucleoprotein	1.0	1.0	0.948	8e-36
242051601	88	hypothetical protein SORBIDRAFT_03g00195	0.910	0.806	0.943	6e-32
15224217	88	putative small nuclear ribonucleoprotein	0.910	0.806	0.957	6e-32
282848216	88	small nuclear ribonucleoprotein polypept	0.910	0.806	0.943	2e-31
195606896	88	small nuclear ribonucleoprotein E [Zea m	0.910	0.806	0.929	2e-31
357145040	88	PREDICTED: small nuclear ribonucleoprote	0.910	0.806	0.929	2e-31
225455956	88	PREDICTED: small nuclear ribonucleoprote	0.910	0.806	0.929	2e-31
195638708	88	small nuclear ribonucleoprotein E [Zea m	0.910	0.806	0.929	2e-31
255581898	86	Small nuclear ribonucleoprotein E, putat	0.910	0.825	0.943	2e-31
357146132	88	PREDICTED: small nuclear ribonucleoprote	0.910	0.806	0.929	3e-31

>gi|145329170|ref|NP_001077914.1| putative small nuclear ribonucleoprotein [Arabidopsis thaliana] gi|330251707|gb|AEC06801.1| putative small nuclear ribonucleoprotein [Arabidopsis thaliana]

 Score =  154 bits (388), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 74/78 (94%), Positives = 76/78 (97%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRI GFDEYMNLVLD+AEEV
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRITGFDEYMNLVLDEAEEV 60

Query: 61 HIKKNTRKPLGFFSKETT 78
           IKKNTRKPLGF+SKETT
Sbjct: 61 SIKKNTRKPLGFYSKETT 78

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242051601|ref|XP_002454946.1| hypothetical protein SORBIDRAFT_03g001950 [Sorghum bicolor] gi|241926921|gb|EES00066.1| hypothetical protein SORBIDRAFT_03g001950 [Sorghum bicolor]

 Score =  141 bits (355), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 67/71 (94%), Positives = 70/71 (98%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEE+
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEI 60

Query: 61 HIKKNTRKPLG 71
          ++KKNTRK LG
Sbjct: 61 NVKKNTRKSLG 71

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15224217|ref|NP_179464.1| putative small nuclear ribonucleoprotein [Arabidopsis thaliana] gi|297836770|ref|XP_002886267.1| hypothetical protein ARALYDRAFT_900374 [Arabidopsis lyrata subsp. lyrata] gi|4185140|gb|AAD08943.1| putative small nuclear ribonucleoprotein E [Arabidopsis thaliana] gi|21592486|gb|AAM64436.1| putative small nuclear ribonucleoprotein E [Arabidopsis thaliana] gi|26452632|dbj|BAC43399.1| putative small nuclear ribonucleoprotein E [Arabidopsis thaliana] gi|28973515|gb|AAO64082.1| putative small nuclear ribonucleoprotein E [Arabidopsis thaliana] gi|297332107|gb|EFH62526.1| hypothetical protein ARALYDRAFT_900374 [Arabidopsis lyrata subsp. lyrata] gi|330251706|gb|AEC06800.1| putative small nuclear ribonucleoprotein [Arabidopsis thaliana]

 Score =  141 bits (355), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 68/71 (95%), Positives = 69/71 (97%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRI GFDEYMNLVLD+AEEV
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRITGFDEYMNLVLDEAEEV 60

Query: 61 HIKKNTRKPLG 71
           IKKNTRKPLG
Sbjct: 61 SIKKNTRKPLG 71

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|282848216|gb|ADB02889.1| small nuclear ribonucleoprotein polypeptide [Jatropha curcas]

 Score =  139 bits (350), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 67/71 (94%), Positives = 69/71 (97%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60

Query: 61 HIKKNTRKPLG 71
          ++KK TRK LG
Sbjct: 61 NVKKKTRKSLG 71

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|195606896|gb|ACG25278.1| small nuclear ribonucleoprotein E [Zea mays] gi|195611048|gb|ACG27354.1| small nuclear ribonucleoprotein E [Zea mays] gi|413947730|gb|AFW80379.1| small nuclear ribonucleoprotein E [Zea mays]

 Score =  139 bits (350), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 66/71 (92%), Positives = 70/71 (98%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL+DAEE+
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLEDAEEI 60

Query: 61 HIKKNTRKPLG 71
          ++KKNTRK LG
Sbjct: 61 NVKKNTRKSLG 71

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357145040|ref|XP_003573502.1| PREDICTED: small nuclear ribonucleoprotein E-like [Brachypodium distachyon]

 Score =  139 bits (350), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 66/71 (92%), Positives = 70/71 (98%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL+DAEE+
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLEDAEEI 60

Query: 61 HIKKNTRKPLG 71
          ++KKNTRK LG
Sbjct: 61 NVKKNTRKSLG 71

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225455956|ref|XP_002278114.1| PREDICTED: small nuclear ribonucleoprotein E [Vitis vinifera] gi|297734216|emb|CBI15463.3| unnamed protein product [Vitis vinifera]

 Score =  139 bits (350), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 66/71 (92%), Positives = 70/71 (98%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          MA+TKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV
Sbjct: 1  MATTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60

Query: 61 HIKKNTRKPLG 71
          ++KKNT+K LG
Sbjct: 61 NVKKNTKKTLG 71

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|195638708|gb|ACG38822.1| small nuclear ribonucleoprotein E [Zea mays] gi|223945527|gb|ACN26847.1| unknown [Zea mays] gi|414875728|tpg|DAA52859.1| TPA: Small nuclear ribonucleoprotein E isoform 1 [Zea mays] gi|414875729|tpg|DAA52860.1| TPA: Small nuclear ribonucleoprotein E isoform 2 [Zea mays]

 Score =  139 bits (350), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 66/71 (92%), Positives = 70/71 (98%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL+DAEE+
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLEDAEEI 60

Query: 61 HIKKNTRKPLG 71
          ++KKNTRK LG
Sbjct: 61 NVKKNTRKTLG 71

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255581898|ref|XP_002531748.1| Small nuclear ribonucleoprotein E, putative [Ricinus communis] gi|223528618|gb|EEF30637.1| Small nuclear ribonucleoprotein E, putative [Ricinus communis]

 Score =  139 bits (350), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 67/71 (94%), Positives = 69/71 (97%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60

Query: 61 HIKKNTRKPLG 71
          ++KK TRK LG
Sbjct: 61 NVKKKTRKTLG 71

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357146132|ref|XP_003573886.1| PREDICTED: small nuclear ribonucleoprotein E-like [Brachypodium distachyon]

 Score =  139 bits (349), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 66/71 (92%), Positives = 70/71 (98%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKD+RIEGRIIGFDEYMNLVL+DAEE+
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDMRIEGRIIGFDEYMNLVLEDAEEI 60

Query: 61 HIKKNTRKPLG 71
          +IKKNTRK LG
Sbjct: 61 NIKKNTRKSLG 71

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	78
TAIR|locus:2053989	88	AT2G18740 "AT2G18740" [Arabido	0.910	0.806	0.957	4.2e-31
TAIR|locus:2118781	88	AT4G30330 "AT4G30330" [Arabido	0.910	0.806	0.943	1.8e-30
ZFIN|ZDB-GENE-040426-1112	92	snrpe "small nuclear ribonucle	0.858	0.728	0.731	1.8e-23
UNIPROTKB|P62303	92	SNRPE "Small nuclear ribonucle	0.858	0.728	0.716	7.8e-23
UNIPROTKB|A4FUI2	92	SNRPE "Small nuclear ribonucle	0.858	0.728	0.716	7.8e-23
UNIPROTKB|P62304	92	SNRPE "Small nuclear ribonucle	0.858	0.728	0.716	7.8e-23
UNIPROTKB|A1XQR9	92	SNRPE "Small nuclear ribonucle	0.858	0.728	0.716	7.8e-23
UNIPROTKB|I3LDW9	92	SNRPE "Small nuclear ribonucle	0.858	0.728	0.716	7.8e-23
MGI|MGI:98346	92	Snrpe "small nuclear ribonucle	0.858	0.728	0.716	7.8e-23
RGD|2321675	92	Snrpe "small nuclear ribonucle	0.858	0.728	0.716	7.8e-23

TAIR|locus:2053989 AT2G18740 "AT2G18740" [Arabidopsis thaliana (taxid:3702)]

 Score = 342 (125.4 bits), Expect = 4.2e-31, P = 4.2e-31
 Identities = 68/71 (95%), Positives = 69/71 (97%)

Query:     1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
             MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRI GFDEYMNLVLD+AEEV
Sbjct:     1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRITGFDEYMNLVLDEAEEV 60

Query:    61 HIKKNTRKPLG 71
              IKKNTRKPLG
Sbjct:    61 SIKKNTRKPLG 71

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0008150 "biological_process" evidence=ND

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2118781 AT4G30330 "AT4G30330" [Arabidopsis thaliana (taxid:3702)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 67/71 (94%), Positives = 68/71 (95%)

Query:     1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
             MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRI GFDEYMNLVLD+AEEV
Sbjct:     1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRITGFDEYMNLVLDEAEEV 60

Query:    61 HIKKNTRKPLG 71
              IKK TRKPLG
Sbjct:    61 SIKKKTRKPLG 71

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0005829 "cytosol" evidence=RCA

GO:0016925 "protein sumoylation" evidence=RCA

ZFIN|ZDB-GENE-040426-1112 snrpe "small nuclear ribonucleoprotein polypeptide E" [Danio rerio (taxid:7955)]

 Score = 270 (100.1 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 49/67 (73%), Positives = 60/67 (89%)

Query:     5 KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
             KVQ++M QPINLIFR+LQ+++RI +WL+EQ ++RIEG IIGFDEYMNLVLDDAEEVH+K 
Sbjct:     9 KVQKVMVQPINLIFRYLQNRSRISVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKT 68

Query:    65 NTRKPLG 71
               RKPLG
Sbjct:    69 KNRKPLG 75

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

UNIPROTKB|P62303 SNRPE "Small nuclear ribonucleoprotein E" [Gallus gallus (taxid:9031)]

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query:     5 KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
             KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct:     9 KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query:    65 NTRKPLG 71
              +RK LG
Sbjct:    69 KSRKQLG 75

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005683 "U7 snRNP" evidence=IEA

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

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

UNIPROTKB|A4FUI2 SNRPE "Small nuclear ribonucleoprotein E" [Bos taurus (taxid:9913)]

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query:     5 KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
             KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct:     9 KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query:    65 NTRKPLG 71
              +RK LG
Sbjct:    69 KSRKQLG 75

GO:0005683 "U7 snRNP" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|P62304 SNRPE "Small nuclear ribonucleoprotein E" [Homo sapiens (taxid:9606)]

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query:     5 KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
             KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct:     9 KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query:    65 NTRKPLG 71
              +RK LG
Sbjct:    69 KSRKQLG 75

GO:0003723 "RNA binding" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=NAS

GO:0005681 "spliceosomal complex" evidence=NAS

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

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0005683 "U7 snRNP" evidence=IDA

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

GO:0000387 "spliceosomal snRNP assembly" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006397 "mRNA processing" evidence=TAS

GO:0008334 "histone mRNA metabolic process" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0034660 "ncRNA metabolic process" evidence=TAS

UNIPROTKB|A1XQR9 SNRPE "Small nuclear ribonucleoprotein E" [Sus scrofa (taxid:9823)]

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query:     5 KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
             KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct:     9 KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query:    65 NTRKPLG 71
              +RK LG
Sbjct:    69 KSRKQLG 75

GO:0005683 "U7 snRNP" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|I3LDW9 SNRPE "Small nuclear ribonucleoprotein E" [Sus scrofa (taxid:9823)]

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query:     5 KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
             KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct:     9 KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query:    65 NTRKPLG 71
              +RK LG
Sbjct:    69 KSRKQLG 75

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

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

GO:0005683 "U7 snRNP" evidence=IEA

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

MGI|MGI:98346 Snrpe "small nuclear ribonucleoprotein E" [Mus musculus (taxid:10090)]

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query:     5 KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
             KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct:     9 KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query:    65 NTRKPLG 71
              +RK LG
Sbjct:    69 KSRKQLG 75

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005683 "U7 snRNP" evidence=ISO

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

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

RGD|2321675 Snrpe "small nuclear ribonucleoprotein polypeptide E" [Rattus norvegicus (taxid:10116)]

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query:     5 KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
             KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct:     9 KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query:    65 NTRKPLG 71
              +RK LG
Sbjct:    69 KSRKQLG 75

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

GO:0005683 "U7 snRNP" evidence=IEA;ISO

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
A4FUI2	RUXE_BOVIN	No assigned EC number	0.7164	0.8589	0.7282	yes	no
Q9XTU6	RUXE_CAEEL	No assigned EC number	0.5352	0.9102	0.7888	yes	no
P62305	RUXE_MOUSE	No assigned EC number	0.7164	0.8589	0.7282	yes	no
P62304	RUXE_HUMAN	No assigned EC number	0.7164	0.8589	0.7282	yes	no
Q9VLV5	RUXE_DROME	No assigned EC number	0.6428	0.8974	0.7446	yes	no
P62303	RUXE_CHICK	No assigned EC number	0.7164	0.8589	0.7282	yes	no
Q7ZUG0	RUXE_DANRE	No assigned EC number	0.7313	0.8589	0.7282	yes	no
Q9USZ3	RUXE_SCHPO	No assigned EC number	0.5454	0.8461	0.7857	yes	no
A1XQR9	RUXE_PIG	No assigned EC number	0.6956	0.8846	0.75	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:
	AT2G18740	small nuclear ribonucleoprotein E, putative / snRNP-E, putative / Sm protein E, putative; small nuclear ribonucleoprotein E, putative / snRNP-E, putative / Sm protein E, putative; FUNCTIONS IN- molecular_function unknown; INVOLVED IN- biological_process unknown; LOCATED IN- small nucleolar ribonucleoprotein complex, nucleus; EXPRESSED IN- 22 plant structures; EXPRESSED DURING- 13 growth stages; CONTAINS InterPro DOMAIN/s- Like-Sm ribonucleoprotein, core (InterPro-IPR001163), Like-Sm ribonucleoprotein, eukaryotic and archaea-type, core (InterPro-IPR006649), Like-Sm ribonucleoprotein-rel [...] (88 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	AT2G03870	small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative; small nucle [...] (99 aa)				•	•		•		0.980
	AT3G59810	small nuclear ribonucleoprotein F, putative / U6 snRNA-associated Sm-like protein, putative / S [...] (91 aa)				•	•		•		0.970
	RUXF	RUXF (SMALL NUCLEAR RIBONUCLEOPROTEIN F); SMALL NUCLEAR RIBONUCLEOPROTEIN F (RUXF); FUNCTIONS I [...] (88 aa)				•	•		•		0.965
	AT2G30000	unknown protein; LOCATED IN- cellular_component unknown; EXPRESSED IN- 24 plant structures; EXP [...] (110 aa)				•			•		0.906
	AT1G07170	unknown protein; LOCATED IN- cellular_component unknown; EXPRESSED IN- 24 plant structures; EXP [...] (110 aa)				•			•		0.906
	AT3G55220	splicing factor, putative; splicing factor, putative; FUNCTIONS IN- nucleic acid binding; INVOL [...] (1214 aa)				•			•		0.871
	AT3G55200	splicing factor, putative; splicing factor, putative; FUNCTIONS IN- nucleic acid binding; INVOL [...] (1214 aa)				•			•		0.871
	SNRNP-G	SNRNP-G (PROBABLE SMALL NUCLEAR RIBONUCLEOPROTEIN G); PROBABLE SMALL NUCLEAR RIBONUCLEOPROTEIN [...] (80 aa)				•	•		•		0.870
	AT3G07590	small nuclear ribonucleoprotein D1, putative / snRNP core protein D1, putative / Sm protein D1, [...] (114 aa)				•	•		•		0.869
	SAD1	SAD1 (SUPERSENSITIVE TO ABA AND DROUGHT 1); RNA binding; SAD1 encodes a polypeptide similar to [...] (88 aa)			•	•	•		•	•	0.847

---

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	78
cd01718	79	cd01718, Sm_E, Sm protein E	8e-44
PTZ00138	89	PTZ00138, PTZ00138, small nuclear ribonucleoprotei	6e-36
pfam01423	66	pfam01423, LSM, LSM domain	1e-11
smart00651	67	smart00651, Sm, snRNP Sm proteins	1e-10
cd00600	63	cd00600, Sm_like, Sm and related proteins	2e-07
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	4e-07
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	7e-07
cd01719	70	cd01719, Sm_G, Sm protein G	1e-06
cd01739	63	cd01739, LSm11_M, Like-Sm protein 11, middle domai	2e-06
cd01732	76	cd01732, LSm5, Like-Sm protein 5	9e-06
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	1e-05
cd01726	68	cd01726, LSm6, Like-Sm protein 6	1e-04
cd01722	69	cd01722, Sm_F, Sm protein F	2e-04
cd01717	80	cd01717, Sm_B, Sm protein B	3e-04
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	0.001

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

 Score =  135 bits (342), Expect = 8e-44
 Identities = 52/65 (80%), Positives = 62/65 (95%)

Query: 7  QRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNT 66
          Q++M QPINLIFR+LQ+K+R+QIWL+EQ D+RIEG+IIGFDEYMNLVLDDAEEVH+K NT
Sbjct: 1  QKVMVQPINLIFRYLQNKSRVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNT 60

Query: 67 RKPLG 71
          RKPLG
Sbjct: 61 RKPLG 65

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

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

 Score =  115 bits (291), Expect = 6e-36
 Identities = 49/71 (69%), Positives = 59/71 (83%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          M   K+Q+IMTQPIN IFRF   K R+QIWL++  +LRIEG+I+GFDEYMN+VLDDAEEV
Sbjct: 3  MTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEV 62

Query: 61 HIKKNTRKPLG 71
          + KKNTRK LG
Sbjct: 63 YTKKNTRKDLG 73

Length = 89

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

 Score = 54.1 bits (131), Expect = 1e-11
 Identities = 17/50 (34%), Positives = 26/50 (52%)

Query: 19 RFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          +FLQ     ++ +  +    + G + GFD++MNLVLDD EE        K
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNK 50

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

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

 Score = 51.3 bits (124), Expect = 1e-10
 Identities = 16/53 (30%), Positives = 28/53 (52%)

Query: 19 RFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLG 71
          +FL+     ++ +  +      G + GFD++MNLVL+D EE       ++ LG
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLG 53

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

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

 Score = 43.0 bits (102), Expect = 2e-07
 Identities = 13/42 (30%), Positives = 20/42 (47%)

Query: 27 IQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
            + +  +    + G ++ FD+YMNLVLDD  E       R 
Sbjct: 7  KTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRV 48

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|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1

 Score = 42.6 bits (101), Expect = 4e-07
 Identities = 14/36 (38%), Positives = 25/36 (69%), Gaps = 1/36 (2%)

Query: 36 DLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLG 71
             + G + GFD+++NLVL++AEE+ I+  + + LG
Sbjct: 21 GKEVRGVLKGFDQHLNLVLENAEEI-IEGESVRKLG 55

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

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

 Score = 41.9 bits (99), Expect = 7e-07
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 5/65 (7%)

Query: 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGF 72
          P++ + + L    R+ + L   ++ R  G ++GFD+YMNLVLDD EE+ I  +  K +  
Sbjct: 8  PLSFLKKLLNK--RVLVKLKNGREYR--GTLVGFDQYMNLVLDDVEEI-ISHDGEKNVRR 62

Query: 73 FSKET 77
             E 
Sbjct: 63 LGGEV 67

Length = 79

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

 Score = 41.0 bits (97), Expect = 1e-06
 Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 1/34 (2%)

Query: 38 RIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLG 71
          ++ G + GFD +MNLVLDDA E  +    + P+G
Sbjct: 22 KVSGVLRGFDPFMNLVLDDAVEE-VGDGEKTPIG 54

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

 Score = 40.3 bits (95), Expect = 2e-06
 Identities = 13/46 (28%), Positives = 30/46 (65%), Gaps = 2/46 (4%)

Query: 17 IFRFLQSKARIQIWLFEQKDLR--IEGRIIGFDEYMNLVLDDAEEV 60
          + R+++ + R+++++ + K +R   EG ++ FD++ NL L D +E 
Sbjct: 1  LHRWMRDRTRVKVYIRKAKGIRGSCEGYLVAFDKHWNLALVDVDET 46

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2-like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-membered ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing. Length = 63

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

 Score = 39.1 bits (92), Expect = 9e-06
 Identities = 16/40 (40%), Positives = 24/40 (60%)

Query: 29 IWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          IW+  + D    G ++GFD+Y+N+VL+D  E  I    RK
Sbjct: 16 IWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRK 55

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

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

 Score = 38.4 bits (90), Expect = 1e-05
 Identities = 14/28 (50%), Positives = 20/28 (71%)

Query: 41 GRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          G + G+D +MNLVLD+AEE+   +  RK
Sbjct: 29 GELQGYDIHMNLVLDNAEEIQDGEVVRK 56

Length = 72

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

 Score = 36.3 bits (85), Expect = 1e-04
 Identities = 12/28 (42%), Positives = 15/28 (53%)

Query: 41 GRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          G +   D YMNLVL+D EE    +   K
Sbjct: 26 GVLACLDGYMNLVLEDTEEYVDGQLVAK 53

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|212469 cd01722, Sm_F, Sm protein F

 Score = 35.3 bits (82), Expect = 2e-04
 Identities = 9/21 (42%), Positives = 13/21 (61%)

Query: 40 EGRIIGFDEYMNLVLDDAEEV 60
          +G ++  D YMNL L + EE 
Sbjct: 25 KGTLVSVDSYMNLQLANTEEY 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|212464 cd01717, Sm_B, Sm protein B

 Score = 35.2 bits (82), Expect = 3e-04
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 39 IEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
            G  + FD++MNLVL D EE    K  +K
Sbjct: 23 FVGTFLAFDKHMNLVLSDCEEFRKIKPKKK 52

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|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein

 Score = 33.6 bits (77), Expect = 0.001
 Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 5/48 (10%)

Query: 13 PINLIFRFLQSKARIQIWLFEQKDLR-IEGRIIGFDEYMNLVLDDAEE 59
          P   +   + S+ R+++    + D   ++GR++  D+YMNL L D  E
Sbjct: 1  PNKKVKSLVGSRIRVEM----KGDENQLQGRLVAVDDYMNLHLTDTME 44

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	78
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.94
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.93
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	99.92
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.86
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.84
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.82
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.81
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.79
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.78
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.77
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.76
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.75
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.74
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.74
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.73
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.73
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.71
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.7
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.68
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.67
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.66
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.64
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.6
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.58
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	99.37
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	99.13
KOG3168	177	consensus U1 snRNP component [Transcription]	99.03
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	98.95
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.89
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	98.77
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	98.75
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	98.75
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	98.26
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	97.93
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	97.78
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	97.76
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	97.61
COG1923	77	Hfq Uncharacterized host factor I protein [General	97.47
PRK14091	165	RNA-binding protein Hfq; Provisional	97.22
PRK14091	165	RNA-binding protein Hfq; Provisional	96.84
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	95.78
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	93.77
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	93.4
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	91.44
PRK14633	150	hypothetical protein; Provisional	91.32
PRK14634	155	hypothetical protein; Provisional	90.34
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	89.98
PRK14638	150	hypothetical protein; Provisional	89.37
PRK14636	176	hypothetical protein; Provisional	88.2
PRK14643	164	hypothetical protein; Provisional	88.18
PRK14639	140	hypothetical protein; Provisional	87.78
PRK14640	152	hypothetical protein; Provisional	87.77
PRK02001	152	hypothetical protein; Validated	87.31
PRK14632	172	hypothetical protein; Provisional	86.46
PRK14645	154	hypothetical protein; Provisional	84.88
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	84.5
PRK14647	159	hypothetical protein; Provisional	83.99
PRK14644	136	hypothetical protein; Provisional	80.74
PRK00092	154	ribosome maturation protein RimP; Reviewed	80.48

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.94  E-value=1.9e-26  Score=143.56  Aligned_cols=78  Identities=63%  Similarity=1.019  Sum_probs=73.0

Q ss_pred             CCccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947            1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus         1 ms~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      |+.|+++|.|..|+..+.+++.++.+|.||++++++++++|+|.|||+||||||+||+|+..+++..+.+|.++|||.
T Consensus         3 ~~~~~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGn   80 (89)
T PTZ00138          3 MTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGD   80 (89)
T ss_pred             CcccccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCC
Confidence            788889999999999999999999999999999999999999999999999999999999655667889999999995

>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=99.93  E-value=2.3e-25  Score=136.00  Aligned_cols=72  Identities=75%  Similarity=1.175  Sum_probs=66.2

Q ss_pred             ceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947            7 QRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus         7 ~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      +|.|..|++.+.++++++.+|.||+++++|++++|+|.|||+||||||+||+|+...+++.+.+|.++|||.
T Consensus         1 ~~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGn   72 (79)
T cd01718           1 QKVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGD   72 (79)
T ss_pred             CccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCC
Confidence            467999999999999999999999998889999999999999999999999999644567788999999995

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.

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

Probab=99.92  E-value=6.9e-26  Score=138.59  Aligned_cols=78  Identities=68%  Similarity=1.077  Sum_probs=74.0

Q ss_pred             CCccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947            1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus         1 ms~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ||++|.||.|++|++++.+|+..+.+|.|||+++-+.+++|.++|||+|||+||+||+|........+.+|.++|.|.
T Consensus         1 ms~~kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGD   78 (88)
T KOG1774|consen    1 MSREKVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGD   78 (88)
T ss_pred             CCcccccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCC
Confidence            899999999999999999999999999999999999999999999999999999999999877777779999999983

>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=99.87  E-value=8.3e-22  Score=119.32  Aligned_cols=64  Identities=30%  Similarity=0.480  Sum_probs=55.4

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEe--cCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI--KKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~--~~~~~~~lG~ilir~~   78 (78)
                      ..|+++|.++++++  |.|.+++  |+++.|+|.|||+|||++|+||+|++.  ++++.+.+|.++|||.
T Consensus         2 ~~P~~~L~~~~~~~--V~V~l~~--gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~   67 (76)
T cd01732           2 LLPLELIDKCIGSR--IWIVMKS--DKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGN   67 (76)
T ss_pred             cChHHHHHHhCCCE--EEEEECC--CeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCC
Confidence            47999999999965  7777755  999999999999999999999999963  3446788999999995

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

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.86  E-value=1.6e-21  Score=116.53  Aligned_cols=63  Identities=29%  Similarity=0.457  Sum_probs=56.9

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..|+++|.++++++  |.|++++  |+++.|+|.|||+|||++|+||+|.+ +++..+.+|.++|||.
T Consensus         3 ~~P~~~L~~~~~k~--V~V~lk~--g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~   65 (72)
T PRK00737          3 QRPLDVLNNALNSP--VLVRLKG--GREFRGELQGYDIHMNLVLDNAEEIQ-DGEVVRKLGKVVIRGD   65 (72)
T ss_pred             cchHHHHHHhCCCE--EEEEECC--CCEEEEEEEEEcccceeEEeeEEEEc-CCCeEeEcCcEEEeCC
Confidence            47999999999976  8888866  89999999999999999999999984 6677789999999994

>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=99.85  E-value=4.1e-21  Score=113.24  Aligned_cols=61  Identities=18%  Similarity=0.309  Sum_probs=55.5

Q ss_pred             hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      |+++|+++++++  |+|.|++  |++++|+|.|||.|||++|+||+|. .+++....+|.++|||.
T Consensus         1 p~~~L~~~~~~~--V~V~Lk~--g~~~~G~L~~~D~~mNlvL~~~~~~-~~~~~~~~~~~v~IRG~   61 (67)
T cd01726           1 PSEFLKAIIGRP--VVVKLNS--GVDYRGILACLDGYMNIALEQTEEY-VNGQLKNKYGDAFIRGN   61 (67)
T ss_pred             CHHHHHhhCCCe--EEEEECC--CCEEEEEEEEEccceeeEEeeEEEE-eCCceeeEeCCEEEECC
Confidence            899999999975  9999976  8999999999999999999999997 46677889999999995

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.

>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=99.85  E-value=4.8e-21  Score=116.93  Aligned_cols=63  Identities=24%  Similarity=0.435  Sum_probs=54.7

Q ss_pred             ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC------------CeeeeeeEEEEecC
Q 034947           12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK------------NTRKPLGFFSKETT   78 (78)
Q Consensus        12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~------------~~~~~lG~ilir~~   78 (78)
                      .|+++|+.+++++  |.|.+++  ||++.|+|.|||+||||+|+||+|++...            +..+.+|.++|||+
T Consensus         1 ~pl~~l~~~~~k~--V~V~l~~--gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd   75 (82)
T cd01730           1 EPLDLIRLSLDER--VYVKLRG--DRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGD   75 (82)
T ss_pred             CchHHHHHhCCCE--EEEEECC--CCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCC
Confidence            4999999999975  8888865  89999999999999999999999996431            24778999999995

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

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

Probab=99.85  E-value=7.3e-21  Score=117.88  Aligned_cols=66  Identities=20%  Similarity=0.346  Sum_probs=56.2

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC------------CeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK------------NTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~------------~~~~~lG~ilir~~   78 (78)
                      ..|+++|.+++...++|.|+|++  |+++.|+|.|||+||||+|+||+|++...            ...+.+|.+||||.
T Consensus         1 ~gPl~~L~~~~~~~~~V~V~lr~--~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd   78 (87)
T cd01720           1 TGPLSLLTQAVKNNTQVLINCRN--NKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGD   78 (87)
T ss_pred             CChHHHHHHHHcCCCEEEEEEcC--CCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCC
Confidence            37999999999655679999976  89999999999999999999999987442            13557899999994

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.

>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=99.84  E-value=1.1e-20  Score=111.54  Aligned_cols=61  Identities=26%  Similarity=0.437  Sum_probs=54.8

Q ss_pred             hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      |+++|.++++++  |.|.+++  |+++.|+|.|||+||||+|+||+|.+ .+...+.+|.++|||.
T Consensus         1 p~~~L~~~~~~~--V~V~l~~--g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~~~iRG~   61 (68)
T cd01731           1 PLDVLKDSLNKP--VLVKLKG--GKEVRGRLKSYDQHMNLVLEDAEEID-DGEPVRKYGRVVIRGD   61 (68)
T ss_pred             ChHHHHHhcCCE--EEEEECC--CCEEEEEEEEECCcceEEEeeEEEEe-cCCeEeEcCcEEEeCC
Confidence            899999999976  8888865  89999999999999999999999996 4456788999999995

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.

>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=99.84  E-value=1.3e-20  Score=111.51  Aligned_cols=62  Identities=23%  Similarity=0.335  Sum_probs=55.9

Q ss_pred             ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      .|+++|.+++++.  |.|.|++  |+++.|+|.|||+|||++|+||+|+ .++.....+|.++|||+
T Consensus         1 ~p~~~L~~~~g~~--V~V~Lk~--g~~~~G~L~~~D~~mNi~L~~~~e~-~~~~~~~~lg~~~IRG~   62 (68)
T cd01722           1 NPKPFLNDLTGKP--VIVKLKW--GMEYKGTLVSVDSYMNLQLANTEEY-IDGKSTGNLGEVLIRCN   62 (68)
T ss_pred             CHHHHHHHcCCCE--EEEEECC--CcEEEEEEEEECCCEEEEEeeEEEE-eCCccccCcCcEEEECC
Confidence            4999999999975  8888876  8999999999999999999999998 46666788999999995

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.

>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=99.82  E-value=6.4e-20  Score=109.90  Aligned_cols=61  Identities=28%  Similarity=0.493  Sum_probs=53.8

Q ss_pred             hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      |...|.++++|+  |.|.+++  |+++.|+|.|||+||||+|+||+|+. ++...+.+|.++|||.
T Consensus         1 ~~~~L~~~i~k~--V~V~L~~--g~~~~G~L~~~D~~mNlvL~~~~E~~-~~~~~~~lg~v~IRG~   61 (72)
T cd01719           1 HPPELKKYMDKK--LSLKLNG--NRKVSGILRGFDPFMNLVLDDAVEVN-SGGEKNNIGMVVIRGN   61 (72)
T ss_pred             CchhhHHhCCCe--EEEEECC--CeEEEEEEEEEcccccEEeccEEEEc-cCCceeEeceEEECCC
Confidence            557899999976  8888865  89999999999999999999999995 6667789999999994

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.

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

Probab=99.81  E-value=1.5e-19  Score=109.31  Aligned_cols=67  Identities=30%  Similarity=0.505  Sum_probs=56.2

Q ss_pred             eeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEe-cCCe-eeeee-EEEEecC
Q 034947            8 RIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI-KKNT-RKPLG-FFSKETT   78 (78)
Q Consensus         8 ~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~-~~~~-~~~lG-~ilir~~   78 (78)
                      +....|+++|.+++++  +|.|+|++  |+++.|+|.|||+|||++|+||+|+.. +++. ...+| .++|||+
T Consensus         3 ~~~~~~~~~l~~~~~~--~V~V~lk~--g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~   72 (79)
T COG1958           3 MLGPLPLSFLKKLLNK--RVLVKLKN--GREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGD   72 (79)
T ss_pred             cccCCcHHHHHHhhCC--EEEEEECC--CCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECC
Confidence            3456899999999995  49999977  899999999999999999999999963 4444 34555 9999995

>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=99.81  E-value=1.7e-19  Score=110.11  Aligned_cols=61  Identities=26%  Similarity=0.429  Sum_probs=51.6

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC-------CeeeeeeEEEEecC
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK-------NTRKPLGFFSKETT   78 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~-------~~~~~lG~ilir~~   78 (78)
                      ..-|.++++++  |.|.+++  ||++.|+|.|||+||||||+||+|+..+.       +..+.+|.++|||.
T Consensus         4 ~~~L~~~i~k~--V~V~l~~--gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~   71 (81)
T cd01729           4 ILDLSKYVDKK--IRVKFQG--GREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGT   71 (81)
T ss_pred             hhhHHHhcCCe--EEEEECC--CcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCC
Confidence            34489999976  8888855  99999999999999999999999996432       35688999999995

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.

>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=99.79  E-value=4.1e-19  Score=107.08  Aligned_cols=63  Identities=13%  Similarity=0.130  Sum_probs=56.4

Q ss_pred             ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      .|+++|+++.+++  |.|.||+  |+++.|+|.+||+|||++|+||+|...+++....+|.++|||.
T Consensus         1 ~Pl~~L~~~~g~~--V~VeLkn--g~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~   63 (76)
T cd01723           1 LPLSLLKTAQNHP--MLVELKN--GETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGN   63 (76)
T ss_pred             CchHHHHhcCCCE--EEEEECC--CCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCC
Confidence            4999999999965  9999977  8999999999999999999999998666666677899999995

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.

>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=99.78  E-value=1.5e-18  Score=104.67  Aligned_cols=63  Identities=24%  Similarity=0.329  Sum_probs=53.2

Q ss_pred             ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCC--eeeeeeEEEEecC
Q 034947           12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKN--TRKPLGFFSKETT   78 (78)
Q Consensus        12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~--~~~~lG~ilir~~   78 (78)
                      .++..|.++++++  |.|.+++  |+++.|+|.|||+|||++|+||+|+...++  ..+.+|.+++||.
T Consensus         2 ~~~~~L~~~l~k~--v~V~l~~--gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~   66 (74)
T cd01728           2 PGTASLVDDLDKK--VVVLLRD--GRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGE   66 (74)
T ss_pred             CchHHHHHhcCCE--EEEEEcC--CeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECC
Confidence            3577899999976  7777755  999999999999999999999999864432  4678999999994

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.

>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=99.77  E-value=2e-18  Score=104.54  Aligned_cols=60  Identities=25%  Similarity=0.485  Sum_probs=50.6

Q ss_pred             HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC---------CeeeeeeEEEEecC
Q 034947           15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK---------NTRKPLGFFSKETT   78 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~---------~~~~~lG~ilir~~   78 (78)
                      +-|.++++++  |.|.+++  ||++.|+|.|||+||||||+||+|++...         .+.+.+|.++|||.
T Consensus         3 ~~l~~~l~~~--V~V~l~d--gR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~   71 (79)
T cd01717           3 SKMLQLINYR--LRVTLQD--GRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGE   71 (79)
T ss_pred             chhHHHcCCE--EEEEECC--CcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCC
Confidence            3478899976  8888855  99999999999999999999999986422         35688999999995

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.

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

Probab=99.76  E-value=3.1e-18  Score=101.87  Aligned_cols=61  Identities=18%  Similarity=0.165  Sum_probs=53.9

Q ss_pred             hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      |+++|.++.++.  |+|+||+  |.++.|+|.+||.|||++|+||+|...+++ ...+|+++|||.
T Consensus         1 P~~~L~~~~g~~--V~VeLk~--g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~-~~~~~~v~IRG~   61 (70)
T cd01721           1 PIKLLHEAEGHI--VTVELKT--GEVYRGKLIEAEDNMNCQLKDVTVTARDGR-VSQLEQVYIRGS   61 (70)
T ss_pred             ChHHHhhCCCCE--EEEEECC--CcEEEEEEEEEcCCceeEEEEEEEECCCCc-EeEcCcEEEeCC
Confidence            899999999965  9999987  899999999999999999999998754544 567899999995

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.

>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=99.75  E-value=7.5e-18  Score=101.01  Aligned_cols=60  Identities=23%  Similarity=0.364  Sum_probs=50.1

Q ss_pred             HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec---CCeeeeeeEEEEecC
Q 034947           15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK---KNTRKPLGFFSKETT   78 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~---~~~~~~lG~ilir~~   78 (78)
                      ..|.++++++  |.|.+  .+|+.+.|+|.|||+|||++|++|+|+...   +...+.+|.++|||.
T Consensus         2 ~~L~~~l~~~--V~V~l--~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~   64 (74)
T cd01727           2 STLEDYLNKT--VSVIT--VDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGD   64 (74)
T ss_pred             hhHHHhcCCE--EEEEE--CCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCC
Confidence            3578899976  76766  559999999999999999999999998542   335778999999995

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.

>smart00651 Sm snRNP Sm proteins

Probab=99.74  E-value=8.1e-18  Score=97.87  Aligned_cols=59  Identities=25%  Similarity=0.486  Sum_probs=52.3

Q ss_pred             HHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        16 ~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      +|.++++++  |.|.+++  |+.+.|+|.+||+|||++|+||+|+..+......+|.++|||.
T Consensus         2 ~L~~~~~~~--V~V~l~~--g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~   60 (67)
T smart00651        2 FLKKLIGKR--VLVELKN--GREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN   60 (67)
T ss_pred             hhHHhCCcE--EEEEECC--CcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCC
Confidence            688999975  8888866  8999999999999999999999999755467889999999995

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

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

Probab=99.74  E-value=4e-18  Score=102.69  Aligned_cols=58  Identities=22%  Similarity=0.482  Sum_probs=50.8

Q ss_pred             HHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        16 ~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      -|++|++|+  +.++|  +++|.+.|+|+|||.|||+||+||+|.. ..+.+.++|.++|||.
T Consensus         8 eLkkymdKk--i~lkl--nG~r~v~GiLrGyD~FmNiVlde~vE~~-~~~~~~~ig~~vIrgn   65 (77)
T KOG1780|consen    8 ELKKYMDKK--IVLKL--NGGRKVTGILRGYDPFMNIVLDETVEPN-GDGDKNNIGMVVIRGN   65 (77)
T ss_pred             hHHHhhhhe--EEEEe--CCCcEEEEEEeccchHHhhhhhhceeec-CcCCcceeeeEEEecc
Confidence            789999987  55555  8899999999999999999999999995 5556788999999983

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

Probab=99.73  E-value=2.2e-17  Score=96.18  Aligned_cols=60  Identities=23%  Similarity=0.479  Sum_probs=52.3

Q ss_pred             HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ++|.++++++  |.|.+++  |+.+.|+|.+||+|||++|+||.|...++.+.+.+|.++|||.
T Consensus         1 ~~L~~~~g~~--V~V~l~~--g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~   60 (67)
T PF01423_consen    1 NFLQKLIGKR--VRVELKN--GRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGS   60 (67)
T ss_dssp             HHHHHTTTSE--EEEEETT--SEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGG
T ss_pred             ChhHHhCCcE--EEEEEeC--CEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECC
Confidence            4789999965  8888855  9999999999999999999999999644448899999999994

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 ....

>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=99.73  E-value=3.4e-17  Score=98.95  Aligned_cols=60  Identities=17%  Similarity=0.241  Sum_probs=51.5

Q ss_pred             HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec-----CCeeeeeeEEEEecC
Q 034947           15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK-----KNTRKPLGFFSKETT   78 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~-----~~~~~~lG~ilir~~   78 (78)
                      +.|.++++++  |.|.+++  ||.+.|+|.+||+||||+|+||.|+..+     ..+.+.+|.++|||.
T Consensus         3 ~~L~~~l~~~--v~V~l~d--gR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~   67 (75)
T cd06168           3 QKLRSLLGRT--MRIHMTD--GRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGH   67 (75)
T ss_pred             hHHHHhcCCe--EEEEEcC--CeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCC
Confidence            4688899976  7777754  9999999999999999999999999743     246889999999995

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.

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

Probab=99.71  E-value=1.7e-17  Score=99.84  Aligned_cols=62  Identities=24%  Similarity=0.297  Sum_probs=58.1

Q ss_pred             ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEe
Q 034947           10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKE   76 (78)
Q Consensus        10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir   76 (78)
                      ..+|..||+...+|  +|.|+||+  |.+|+|+|++.|.||||.|.+|+|+ .++....++|+|+||
T Consensus         6 PvNPKpFL~~l~gk--~V~vkLKw--g~eYkG~LvsvD~YmNlqL~~~eE~-idG~~~g~lGEilIR   67 (79)
T KOG3482|consen    6 PVNPKPFLNGLTGK--PVLVKLKW--GQEYKGTLVSVDNYMNLQLANAEEY-IDGVSTGNLGEILIR   67 (79)
T ss_pred             cCCchHHHhhccCC--eEEEEEec--CcEEEEEEEEecchhheehhhhhhh-hcccccccceeEEEE
Confidence            46999999999996  59999988  8999999999999999999999999 699999999999998

>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=99.70  E-value=8.9e-17  Score=99.97  Aligned_cols=61  Identities=21%  Similarity=0.301  Sum_probs=54.7

Q ss_pred             hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      |+.||.++.++.  |+|+||+  |..|.|+|.++|.|||++|+||+|.. +++....+|.++|||.
T Consensus         2 ~~~fL~~l~g~~--V~VeLKn--g~~~~G~L~~vD~~MNl~L~~a~~~~-~~~~~~~~~~v~IRG~   62 (90)
T cd01724           2 LVRFLMKLTNET--VTIELKN--GTIVHGTITGVDPSMNTHLKNVKLTL-KGRNPVPLDTLSIRGN   62 (90)
T ss_pred             HhHHHHhCCCCE--EEEEECC--CCEEEEEEEEEcCceeEEEEEEEEEc-CCCceeEcceEEEeCC
Confidence            788999999965  9999987  88999999999999999999999984 5666788999999995

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.

>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=99.68  E-value=2.4e-16  Score=90.42  Aligned_cols=57  Identities=30%  Similarity=0.515  Sum_probs=49.3

Q ss_pred             HHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           17 IFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        17 L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      |.++++++  |.|.+++  |+.+.|+|.+||+|||++|+||.|...+ .....+|.++|||.
T Consensus         1 l~~~~g~~--V~V~l~~--g~~~~G~L~~~D~~~Ni~L~~~~~~~~~-~~~~~~~~~~irG~   57 (63)
T cd00600           1 LKDLVGKT--VRVELKD--GRVLEGVLVAFDKYMNLVLDDVEETIKE-GKKRVLGLVLIRGD   57 (63)
T ss_pred             ChHHCCCE--EEEEECC--CcEEEEEEEEECCCCCEEECCEEEEecC-CcEEECCeEEEECC
Confidence            45778865  8888866  8999999999999999999999999643 66788999999995

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.

>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=99.67  E-value=2.7e-16  Score=95.93  Aligned_cols=63  Identities=16%  Similarity=0.213  Sum_probs=53.3

Q ss_pred             ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC-CeeeeeeEEEEecC
Q 034947           12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK-NTRKPLGFFSKETT   78 (78)
Q Consensus        12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~-~~~~~lG~ilir~~   78 (78)
                      .|++||.++.++.  |+|.||+  |..+.|+|.++|.|||++|+||++...++ .....+|.++|||.
T Consensus         1 l~~~fL~~l~g~~--V~VeLKn--g~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~   64 (81)
T cd01725           1 LFFSFFKTLVGKE--VTVELKN--DLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGS   64 (81)
T ss_pred             ChhHHHHhCCCCE--EEEEECC--CcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECC
Confidence            4889999999865  9999987  88999999999999999999998874333 23456799999995

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

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

Probab=99.66  E-value=4.8e-16  Score=94.41  Aligned_cols=63  Identities=16%  Similarity=0.235  Sum_probs=54.5

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..+..+|..+.++.  |+|.||+  |..|.|+|.++|.|||++|+||++.. .++....+|.++|||.
T Consensus         8 ~tl~~~L~~l~g~~--V~VeLKn--g~~~~G~L~~vD~~MNl~L~~~~~~~-~~~~~~~~~~v~IRG~   70 (78)
T cd01733           8 NTLIILLQGLQGKV--VTVELRN--ETTVTGRIASVDAFMNIRLAKVTIID-RNGKQVQVEEIMVTGR   70 (78)
T ss_pred             chHHHHHHHCCCCE--EEEEECC--CCEEEEEEEEEcCCceeEEEEEEEEc-CCCceeECCcEEEECC
Confidence            46788999999865  9999987  78999999999999999999999884 4445568999999995

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.

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

Probab=99.64  E-value=1.2e-16  Score=97.01  Aligned_cols=65  Identities=29%  Similarity=0.554  Sum_probs=56.8

Q ss_pred             ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec--CCeeeeeeEEEEecC
Q 034947           10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK--KNTRKPLGFFSKETT   78 (78)
Q Consensus        10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~--~~~~~~lG~ilir~~   78 (78)
                      ...|++++.++++.+    ||+..++++++.|+|.|||.|.|+||+|++||..+  ++...++++++++|.
T Consensus         5 ~llPlEliDkcIgsk----i~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGN   71 (84)
T KOG1775|consen    5 TLLPLELIDKCIGSK----IWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGN   71 (84)
T ss_pred             hcccHHHHHHhcCce----EEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCC
Confidence            368999999999987    66666779999999999999999999999999754  457889999999983

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

Probab=99.60  E-value=6.5e-17  Score=102.13  Aligned_cols=65  Identities=26%  Similarity=0.357  Sum_probs=54.5

Q ss_pred             ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC-------CeeeeeeEEEEecC
Q 034947           10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK-------NTRKPLGFFSKETT   78 (78)
Q Consensus        10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~-------~~~~~lG~ilir~~   78 (78)
                      -...+--|.+|++|+    |++|..+||+..|+|.|||+.|||||+|++|+-.+.       ++.+.||.+++|||
T Consensus        15 kkEsilDLsky~Dk~----Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGT   86 (108)
T KOG1781|consen   15 KKESILDLSKYLDKK----IRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGT   86 (108)
T ss_pred             chhHHhhHHHhhccc----eEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEccc
Confidence            345567899999988    555558899999999999999999999999995442       35699999999998

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

Probab=99.58  E-value=2.1e-16  Score=95.09  Aligned_cols=63  Identities=17%  Similarity=0.341  Sum_probs=57.9

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..|-+||.+++++.  |.|+|  ++|..|.|+|...|.|||+.|+.++|+ .+++..+++|++||||+
T Consensus         5 ~~~~~fl~~iiGr~--V~VKl--~sgvdyrG~l~~lDgymNiaLe~tee~-~ngql~n~ygdaFirGn   67 (77)
T KOG1783|consen    5 SMPGEFLKAIIGRT--VVVKL--NSGVDYRGTLVCLDGYMNIALESTEEY-VNGQLKNKYGDAFIRGN   67 (77)
T ss_pred             cCcHHHHHHHhCCe--EEEEe--cCCccccceehhhhhHHHHHHHHHHHH-hcCcccccccceeeccc
Confidence            57999999999975  77777  779999999999999999999999999 59999999999999995

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

Probab=99.37  E-value=1e-13  Score=85.37  Aligned_cols=65  Identities=25%  Similarity=0.426  Sum_probs=53.8

Q ss_pred             ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec--C----------CeeeeeeEEEEec
Q 034947           10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK--K----------NTRKPLGFFSKET   77 (78)
Q Consensus        10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~--~----------~~~~~lG~ilir~   77 (78)
                      +..|+++|+-+++++  |-|+++  ++|++.|+|.|||+|+|++|.||+|....  .          ..++.+-.+|+||
T Consensus         3 v~ePldllrlsLdEr--VyVKlr--~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRG   78 (91)
T KOG3460|consen    3 VEEPLDLLRLSLDER--VYVKLR--SDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRG   78 (91)
T ss_pred             ccccHHHHhhcccce--EEEEec--CChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeC
Confidence            678999999999976  666665  49999999999999999999999998531  1          2457788899998


Q ss_pred             C
Q 034947           78 T   78 (78)
Q Consensus        78 ~   78 (78)
                      .
T Consensus        79 d   79 (91)
T KOG3460|consen   79 D   79 (91)
T ss_pred             C
Confidence            3

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

Probab=99.13  E-value=8.5e-11  Score=76.95  Aligned_cols=63  Identities=16%  Similarity=0.138  Sum_probs=57.4

Q ss_pred             ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      .|+.+|..+-+  .|+.|.||+  |-.|.|.|..+|.+|||.|.+++++..|+..--.+-++-||||
T Consensus         2 lPLsLL~~aq~--~pmlvELKN--get~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGt   64 (134)
T KOG3293|consen    2 LPLSLLKTAQN--HPMLVELKN--GETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGT   64 (134)
T ss_pred             cchhHHHhcCC--CeEEEEecC--CCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecc
Confidence            69999999988  579999998  6679999999999999999999999888888788889999997

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=99.03  E-value=2.5e-11  Score=82.93  Aligned_cols=57  Identities=26%  Similarity=0.454  Sum_probs=46.5

Q ss_pred             HHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEe---------cCCeeeeeeEEEEecC
Q 034947           18 FRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI---------KKNTRKPLGFFSKETT   78 (78)
Q Consensus        18 ~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~---------~~~~~~~lG~ilir~~   78 (78)
                      -+.+|-+  ..|.+  +++|.+.|.+.+||.|||+||.||+|+..         +.++++.+|.+++||.
T Consensus        10 l~~iNyr--~rv~~--qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRge   75 (177)
T KOG3168|consen   10 LQHINYR--MRVRL--QDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGE   75 (177)
T ss_pred             HHhhcce--EEEEe--ccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCC
Confidence            3455655  55555  66999999999999999999999999842         3578999999999983

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

Probab=98.95  E-value=7.2e-10  Score=69.28  Aligned_cols=59  Identities=19%  Similarity=0.371  Sum_probs=50.0

Q ss_pred             HHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec---CCeeeeeeEEEEecC
Q 034947           16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK---KNTRKPLGFFSKETT   78 (78)
Q Consensus        16 ~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~---~~~~~~lG~ilir~~   78 (78)
                      -|..|+++.    |.+..++||-+.|.|.|||+-.||+|+|+.|+..+   +.+...+|.=+|||.
T Consensus         4 ~L~~y~n~~----V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirge   65 (96)
T KOG1784|consen    4 TLEDYMNQR----VSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGE   65 (96)
T ss_pred             hHHHHhhce----EEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecC
Confidence            478899987    55566889999999999999999999999999644   346788999999983

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

Probab=98.89  E-value=8.8e-10  Score=65.17  Aligned_cols=45  Identities=27%  Similarity=0.478  Sum_probs=38.1

Q ss_pred             HHhhcCcceEEEEEEecCCe--EEEEEEEEeccccceeEeceEEEEe
Q 034947           18 FRFLQSKARIQIWLFEQKDL--RIEGRIIGFDEYMNLVLDDAEEVHI   62 (78)
Q Consensus        18 ~~~~~k~~~V~V~lk~~~~~--~~~G~L~gfD~~mNlvL~da~E~~~   62 (78)
                      .+++..+.+|.|.++..++.  .++|.|++||.||||+|.|+.|.+.
T Consensus         2 ~~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~   48 (66)
T cd01739           2 HRCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR   48 (66)
T ss_pred             chhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence            45667778999999876663  5899999999999999999999973

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.

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

Probab=98.77  E-value=3.8e-08  Score=61.37  Aligned_cols=62  Identities=19%  Similarity=0.203  Sum_probs=48.1

Q ss_pred             hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCC-eeeeeeEEEEecC
Q 034947           13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKN-TRKPLGFFSKETT   78 (78)
Q Consensus        13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~-~~~~lG~ilir~~   78 (78)
                      -.+|++..+++.  |.|.||+  +..+.|+|.+.|+|+|+-|+|..-...+.- --...-.++|||.
T Consensus         3 FysfFkslvg~~--V~VeLKn--d~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGS   65 (96)
T KOG3448|consen    3 FYSFFKSLVGKE--VVVELKN--DLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGS   65 (96)
T ss_pred             hHHHHHHhcCCe--EEEEEcC--CcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEecc
Confidence            367899999976  9999998  899999999999999999999876632211 1223456788884

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

Probab=98.75  E-value=8.5e-10  Score=72.13  Aligned_cols=58  Identities=26%  Similarity=0.438  Sum_probs=49.0

Q ss_pred             HHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCC--eeeeeeEEEEecC
Q 034947           17 IFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKN--TRKPLGFFSKETT   78 (78)
Q Consensus        17 L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~--~~~~lG~ilir~~   78 (78)
                      +..+++++  +.|-|++  ||.+.|.|++||+|-|++|++|+|...-++  -....|..+|||.
T Consensus        14 l~~~~dkK--llVlLRD--GR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGE   73 (129)
T KOG1782|consen   14 LVEYLDKK--LLVLLRD--GRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGE   73 (129)
T ss_pred             HHHHhcce--EEEEEec--CcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecC
Confidence            77889987  8899977  999999999999999999999999865332  2456799999983

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

Probab=98.75  E-value=7.7e-10  Score=71.12  Aligned_cols=64  Identities=16%  Similarity=0.320  Sum_probs=56.9

Q ss_pred             ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec------CC------eeeeeeEEEEec
Q 034947           12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK------KN------TRKPLGFFSKET   77 (78)
Q Consensus        12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~------~~------~~~~lG~ilir~   77 (78)
                      .|++.+...+....+|+|.+++  ++.+.|++.|||.|.|++|+++.|.|.+      +.      ..+.+|.++|||
T Consensus        24 Gpls~~~~~~~~~~~vLi~cRn--n~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRG   99 (114)
T KOG3459|consen   24 GPLSVLPASVKNNTQVLINCRN--NVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRG   99 (114)
T ss_pred             CchhhhHHHhhcCceeEEEecc--cHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecC
Confidence            8999999999999999999987  7889999999999999999999998742      11      256789999999

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

Probab=98.26  E-value=2.3e-06  Score=55.11  Aligned_cols=64  Identities=16%  Similarity=0.121  Sum_probs=52.7

Q ss_pred             ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      +.-|+.+|+.+-+.  -|++.+.+  |-.|.|+|.-.+.+||++|+|.+-...+ .....+-.|+|||.
T Consensus         3 ~gvpiKlLhEaqGh--IVt~Et~t--Ge~YRGkliEaeDnmNcql~di~vT~~d-g~vs~le~V~IRGS   66 (119)
T KOG3172|consen    3 VGVPIKLLHEAQGH--IVTVETKT--GEVYRGKLIEAEDNMNCQLRDITVTARD-GRVSQLEQVFIRGS   66 (119)
T ss_pred             cccceeeeecccCc--EEEEEecC--CceeeeeeEEeccccccEEEEEEEEccC-CcceeeeeEEEecC
Confidence            34689999999884  47777755  7889999999999999999999877544 45677899999984

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

Probab=97.93  E-value=7.3e-05  Score=48.08  Aligned_cols=58  Identities=21%  Similarity=0.223  Sum_probs=47.3

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEec
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKET   77 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~   77 (78)
                      ..+|.++.++.  |+|.|++  +....|++.+.|.+||..|.++.-.. .+ +...+-.+.+||
T Consensus         4 vr~L~kl~~e~--vtIeLkn--gt~v~G~I~~Vd~~Mn~~l~~v~~t~-~~-~pv~l~~lsirg   61 (109)
T KOG3428|consen    4 VRFLKKLLNER--VTIELKN--GTIVHGTIDSVDVQMNTHLKHVKMTV-KG-EPVRLDTLSIRG   61 (109)
T ss_pred             HHHHHHhhCCe--EEEEecC--CcEEeeeEEEEEhhheeEEEEEEEec-CC-CceeEEEEEeec
Confidence            46888998865  9999988  78899999999999999999877553 44 445677787777

>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=97.78  E-value=9.5e-05  Score=43.22  Aligned_cols=37  Identities=22%  Similarity=0.493  Sum_probs=32.2

Q ss_pred             HHHHHhhcCcceEEEEEEecCCeEEEEEEEEecccccee
Q 034947           15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLV   53 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlv   53 (78)
                      .+|+.+-.++.+|+|.|.+  |.+++|.+.|||+|+=++
T Consensus         2 ~fln~~r~~~~~Vtv~L~N--G~~l~G~I~~fD~ftVll   38 (61)
T cd01716           2 QFLNAARKEKIPVTIYLVN--GVQLKGQIESFDNFTVLL   38 (61)
T ss_pred             HHHHHHHHcCCcEEEEEeC--CcEEEEEEEEEcceEEEE
Confidence            3678888888999999988  899999999999999443

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=97.76  E-value=0.00011  Score=42.96  Aligned_cols=37  Identities=16%  Similarity=0.486  Sum_probs=32.4

Q ss_pred             HHHHHhhcCcceEEEEEEecCCeEEEEEEEEecccccee
Q 034947           15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLV   53 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlv   53 (78)
                      .+|+.+-.++.+|+|.|.+  |..++|.+.|||.|+=++
T Consensus         6 ~fln~~r~~~~~Vti~L~n--G~~l~G~I~~fD~ftVll   42 (61)
T TIGR02383         6 QFLNTLRKERIPVTVFLVN--GVQLKGVIESFDNFTVLL   42 (61)
T ss_pred             HHHHHHHHcCCcEEEEEeC--CcEEEEEEEEEeeeEEEE
Confidence            4788888888999999987  899999999999999444

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

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=97.61  E-value=0.00022  Score=43.65  Aligned_cols=41  Identities=17%  Similarity=0.479  Sum_probs=34.0

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD   56 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d   56 (78)
                      -.+|+.+-.++.+|+|.|.+  |.++.|.+.|||.|+=|+-.+
T Consensus         9 d~fLn~lr~~~~~VtifL~N--G~~l~G~I~~fD~ftVll~~~   49 (79)
T PRK00395          9 DPFLNALRKERVPVTIYLVN--GIKLQGQIESFDNFVVLLRNT   49 (79)
T ss_pred             HHHHHHHHHcCCCEEEEEeC--CcEEEEEEEEEccEEEEEEEC
Confidence            35788888888999999988  899999999999999444333

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

Probab=97.47  E-value=0.00049  Score=41.86  Aligned_cols=39  Identities=18%  Similarity=0.571  Sum_probs=32.4

Q ss_pred             HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947           15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD   56 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d   56 (78)
                      .||+.+-.++.+|.|.|.|  |..+.|.+.|||+|. +.|++
T Consensus        10 ~fLn~~Rk~~i~VtIfLvN--G~~L~G~V~sfD~f~-VlL~~   48 (77)
T COG1923          10 PFLNALRKEKIPVTIFLVN--GFKLQGQVESFDNFV-VLLKN   48 (77)
T ss_pred             HHHHHHHhcCCeEEEEEEc--CEEEEEEEEeeeeEE-EEEEc
Confidence            4677777777899999988  899999999999998 44444

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=97.22  E-value=0.00095  Score=45.77  Aligned_cols=41  Identities=20%  Similarity=0.402  Sum_probs=34.2

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD   56 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d   56 (78)
                      -.+|+.+-.++.+|+|.|.+  |.+++|.+.|||.|.=|+-.+
T Consensus        14 D~fLn~~Rk~k~~VtvfL~n--G~rl~G~I~~fD~ftVlL~~~   54 (165)
T PRK14091         14 DIFLNSLRKTKTPVTMFLVK--GVKLQGIITWFDNFSILLRRD   54 (165)
T ss_pred             HHHHHHHHhcCCcEEEEEec--CcEEEEEEEEEcceEEEEEeC
Confidence            45888888999999999987  899999999999998444334

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=96.84  E-value=0.0035  Score=43.00  Aligned_cols=41  Identities=20%  Similarity=0.345  Sum_probs=34.5

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD   56 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d   56 (78)
                      -.+|+.+-.++.+|+|.|.+  |.+++|.+.|||.|.=|.-.+
T Consensus        94 d~fLn~~rk~k~~VtvfL~N--G~~l~G~I~~fD~ftvlL~~~  134 (165)
T PRK14091         94 DVFLSAVRDSGEPVTMFLVN--GVMLQGEIAAFDLFCMLLERD  134 (165)
T ss_pred             HHHHHHHHhcCCcEEEEEec--CcEEEEEEEEEcceEEEEEeC
Confidence            45888888999999999987  899999999999999444334

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

Probab=95.78  E-value=0.028  Score=33.16  Aligned_cols=42  Identities=17%  Similarity=0.183  Sum_probs=31.5

Q ss_pred             HHHHhhcCcceEEEEEEecCCeEEEEEEEEecc---ccceeEeceEEEE
Q 034947           16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDE---YMNLVLDDAEEVH   61 (78)
Q Consensus        16 ~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~---~mNlvL~da~E~~   61 (78)
                      ++..++++.  |.|.+++  |..|+|.+.+++.   =+.++|.-|....
T Consensus         6 l~~~lvG~~--V~V~~~~--G~~yeGif~s~s~~~~~~~vvLk~a~~~~   50 (77)
T PF14438_consen    6 LLTNLVGQT--VEVTTKN--GSVYEGIFHSASPESNEFDVVLKMARKVP   50 (77)
T ss_dssp             HHHTTTTSE--EEEEETT--S-EEEEEEEEE-T---T--EEEEEEEETT
T ss_pred             HHHhCcCCE--EEEEECC--CCEEEEEEEeCCCcccceeEEEEeeeecc
Confidence            566778855  8888876  8899999999999   8999999888763

>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=93.77  E-value=0.41  Score=25.94  Aligned_cols=47  Identities=21%  Similarity=0.192  Sum_probs=32.7

Q ss_pred             hcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEe
Q 034947           21 LQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKE   76 (78)
Q Consensus        21 ~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir   76 (78)
                      +++.  |.+..  + +..+.|+..|+|..=.|+++.....    .....-|+|.+|
T Consensus         2 lG~~--V~v~~--~-~~~~~G~~~gId~~G~L~v~~~~g~----~~~i~sGdv~~r   48 (48)
T PF02237_consen    2 LGQE--VRVET--G-DGEIEGIAEGIDDDGALLVRTEDGS----IRTISSGDVSLR   48 (48)
T ss_dssp             TTSE--EEEEE--T-SCEEEEEEEEEETTSEEEEEETTEE----EEEESSSEEEEE
T ss_pred             CCCE--EEEEE--C-CeEEEEEEEEECCCCEEEEEECCCC----EEEEEEEEEEeC
Confidence            4554  65555  3 5678999999999999998764431    234556777765

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=93.40  E-value=0.31  Score=30.57  Aligned_cols=55  Identities=18%  Similarity=0.323  Sum_probs=40.1

Q ss_pred             HhhcCcceEEEEEEecCCeEEEEEEEEecc-ccceeEeceEEEEecCC--------eeeeeeEEEEec
Q 034947           19 RFLQSKARIQIWLFEQKDLRIEGRIIGFDE-YMNLVLDDAEEVHIKKN--------TRKPLGFFSKET   77 (78)
Q Consensus        19 ~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~-~mNlvL~da~E~~~~~~--------~~~~lG~ilir~   77 (78)
                      .|++++    |.|..+.+.+|+|+|...|. --.|.|.++.-+-.++.        ....+..|+.||
T Consensus         5 ~~IGs~----ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~   68 (96)
T PF12701_consen    5 PYIGSK----ISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRG   68 (96)
T ss_dssp             CCTTCE----EEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEET
T ss_pred             cccCCE----EEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEc
Confidence            478877    66666779999999999998 56799999887632221        123567777776

>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=91.44  E-value=1.5  Score=26.44  Aligned_cols=56  Identities=16%  Similarity=0.297  Sum_probs=39.5

Q ss_pred             HhhcCcceEEEEEEecCCeEEEEEEEEeccccc-eeEeceEEEEecCC---------eeeeeeEEEEecC
Q 034947           19 RFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMN-LVLDDAEEVHIKKN---------TRKPLGFFSKETT   78 (78)
Q Consensus        19 ~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mN-lvL~da~E~~~~~~---------~~~~lG~ilir~~   78 (78)
                      .+++++    |.|..+.+.+|+|+|-.+|..=. +.|.|+..+-.++.         ....+..|+.||+
T Consensus         3 ~~IG~~----isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgs   68 (74)
T cd01736           3 PYIGSK----ISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGS   68 (74)
T ss_pred             cccCce----EEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCC
Confidence            478877    66666779999999999988764 66888877633221         1234677777774

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.

>PRK14633 hypothetical protein; Provisional

Probab=91.32  E-value=0.74  Score=30.73  Aligned_cols=50  Identities=12%  Similarity=0.213  Sum_probs=34.0

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccccceeEe
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      ||+-..++...|-+| .+++++.  |.|.++.  ++.+++.|+|.++|+- ++.|+
T Consensus        75 SSPGldRpL~~~~~f-~r~~G~~--v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~  126 (150)
T PRK14633         75 SSPGMNRQIFNIIQA-QALVGFN--VKAVTLAPVGSQTKFKGVLERVEGN-NVILN  126 (150)
T ss_pred             eCCCCCCCCCCHHHH-HHhCCCe--EEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence            555444555555555 4778876  7777764  4679999999999885 34453

>PRK14634 hypothetical protein; Provisional

Probab=90.34  E-value=1  Score=30.22  Aligned_cols=50  Identities=14%  Similarity=0.263  Sum_probs=34.1

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEec--CCeEEEEEEEEeccccceeEe
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ--KDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~--~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      ||+-..++...|-+|- +++++.  |.|+++..  +.+++.|+|.++|+- ++.|+
T Consensus        81 SSPGldRpL~~~~~f~-r~~G~~--V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l~  132 (155)
T PRK14634         81 SSPGIGDQLSSDRDFQ-TFRGFP--VEVSHRDDDGSEQRLEGLLLERNED-HLQIN  132 (155)
T ss_pred             eCCCCCCcCCCHHHHH-HhCCCe--EEEEEecCCCCeEEEEEEEEEEeCC-EEEEE
Confidence            5654556666666654 677876  88887643  348899999999884 34443

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

Probab=89.98  E-value=1.3  Score=26.41  Aligned_cols=50  Identities=18%  Similarity=0.411  Sum_probs=32.6

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccccceeEe
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      ||+-..++...|-++ .+++++.  |.|+++.  ++.+++.|.|.++|+- +++|.
T Consensus         6 SSPGl~RpL~~~~~~-~r~~G~~--v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l~   57 (83)
T cd01734           6 SSPGAERPLKKEADF-ERAVGKY--VHVKLYQPIDGQKEFEGTLLGVDDD-TVTLE   57 (83)
T ss_pred             cCCCCCCcCCCHHHH-HHhCCCE--EEEEEEcccCCeEEEEEEEEeEeCC-EEEEE
Confidence            555445555666555 4677866  7777763  3347899999999883 34443

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.

>PRK14638 hypothetical protein; Provisional

Probab=89.37  E-value=1.1  Score=29.98  Aligned_cols=48  Identities=21%  Similarity=0.303  Sum_probs=32.4

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEe
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      ||+-..++...|-+|. +++++.  |.|+++  +++++.|+|.++|.- ++.|+
T Consensus        81 SSPGldRpL~~~~~f~-r~~G~~--v~V~~~--~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         81 SSPGLDRPLRGPKDYV-RFTGKL--AKIVTK--DGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             eCCCCCCCCCCHHHHH-HhCCCE--EEEEEC--CCcEEEEEEEEEeCC-EEEEE
Confidence            5554445555665554 678876  777774  479999999999974 34443

>PRK14636 hypothetical protein; Provisional

Probab=88.20  E-value=1.7  Score=29.89  Aligned_cols=50  Identities=20%  Similarity=0.349  Sum_probs=33.6

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccccceeEe
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      ||+-..++...|-+| .+++++.  |.|+++.  ++.+++.|+|.++|+- ++.|.
T Consensus        79 SSPGldRpL~~~~df-~r~~G~~--V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~  130 (176)
T PRK14636         79 SSPGIDRPLTRPKDF-ADWAGHE--ARIALSEPLDGRKQFRGELKGIDGD-TVTIA  130 (176)
T ss_pred             eCCCCCCCCCCHHHH-HHhCCCe--EEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence            565455666666554 5788876  7777763  2347999999999873 35543

>PRK14643 hypothetical protein; Provisional

Probab=88.18  E-value=1.8  Score=29.39  Aligned_cols=49  Identities=14%  Similarity=0.223  Sum_probs=32.9

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccc-ccee
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEY-MNLV   53 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~-mNlv   53 (78)
                      ||+-..++...|-+| .+++++.  |.|+++.  ++.+++.|+|.++|.- ..+.
T Consensus        85 SSPGleRpL~~~~df-~r~~G~~--V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~  136 (164)
T PRK14643         85 SSSGIEKQIRSQEEL-VKALNQW--VYVQLNNEIKKVKEFEGYVTKYNVNTNTFR  136 (164)
T ss_pred             cCCCCCCCCCCHHHH-HHhcCCe--EEEEEecccCCceEEEEEEEEEeCCcEEEE
Confidence            565445555555555 4677876  7777765  3458899999999864 3443

>PRK14639 hypothetical protein; Provisional

Probab=87.78  E-value=1.6  Score=28.80  Aligned_cols=47  Identities=19%  Similarity=0.347  Sum_probs=32.6

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeE
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL   54 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL   54 (78)
                      ||+-..++...|-++ .+++++.  |.|++.  +++++.|+|.++|+- ++.|
T Consensus        69 SSPGl~RpL~~~~~f-~r~~G~~--v~v~l~--~~~~~~G~L~~~~~~-~i~l  115 (140)
T PRK14639         69 SSPGLERKLSKIEHF-AKSIGEL--VKITTN--EKEKFEGKIVSVDDE-NITL  115 (140)
T ss_pred             eCCCCCCcCCCHHHH-HHhCCCE--EEEEEC--CCcEEEEEEEEEeCC-EEEE
Confidence            555445555555554 5788876  777774  479999999999883 4555

>PRK14640 hypothetical protein; Provisional

Probab=87.77  E-value=2  Score=28.66  Aligned_cols=50  Identities=12%  Similarity=0.181  Sum_probs=34.0

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccccceeEe
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      ||+-..++...|-+|. +++++.  |.|+++.  ++.+++.|+|.++|+- ++.|+
T Consensus        78 SSPGl~RpL~~~~~f~-r~~G~~--v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~  129 (152)
T PRK14640         78 SSPGLDRPLFKVAQFE-KYVGQE--AAVTLRMATNNRRKFKGVIKAVQGD-MITLT  129 (152)
T ss_pred             eCCCCCCcCCCHHHHH-HhCCCe--EEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence            5554456666666554 678866  7777753  3568999999999984 34443

>PRK02001 hypothetical protein; Validated

Probab=87.31  E-value=1.8  Score=29.14  Aligned_cols=48  Identities=17%  Similarity=0.311  Sum_probs=33.0

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEe
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      ||+-..++...|-+|- +++++.  |.|++.  +++++.|+|.++|+- +++|+
T Consensus        71 SSPGldRpL~~~~~f~-r~~G~~--v~V~l~--~~~~~~G~L~~~~~~-~i~l~  118 (152)
T PRK02001         71 GSAGLTSPLKVPRQYK-KNIGRE--LEVLTK--NGKKIEGELKSADEN-DITLE  118 (152)
T ss_pred             eCCCCCCcCCCHHHHH-HhCCCE--EEEEEC--CCCEEEEEEEEEeCC-EEEEE
Confidence            5554455566665554 678866  777774  579999999999875 34443

>PRK14632 hypothetical protein; Provisional

Probab=86.46  E-value=2.4  Score=28.91  Aligned_cols=50  Identities=14%  Similarity=0.322  Sum_probs=33.5

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEec-----CCeEEEEEEEEeccccceeEe
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ-----KDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~-----~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      ||+-..++...|-+| .+++++.  |.|+++..     +.+++.|+|.++|+- +++|+
T Consensus        79 SSPGldRpL~~~~~f-~r~iG~~--V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         79 SSPGLERPFFRAEQM-SPYVGRQ--IELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             eCCCCCCcCCCHHHH-HHhCCCE--EEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            555444555555554 4778865  88888762     468999999999873 45554

>PRK14645 hypothetical protein; Provisional

Probab=84.88  E-value=2.7  Score=28.27  Aligned_cols=46  Identities=17%  Similarity=0.198  Sum_probs=30.3

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeE
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL   54 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL   54 (78)
                      ||+-..++...|-+|. +++++.  |.|.  . +++++.|+|.++|+- .+.|
T Consensus        83 SSPGldRpL~~~~df~-r~~G~~--v~v~--~-~~k~~~G~L~~~~d~-~i~l  128 (154)
T PRK14645         83 ESPGPKRPLFTARHFE-RFAGLK--AKVR--G-PGENFTGRIKAVSGD-QVTF  128 (154)
T ss_pred             eCCCCCCCCCCHHHHH-HhCCCE--EEEE--c-CCeEEEEEEEEEeCC-EEEE
Confidence            5554455556665554 677876  5554  3 478999999999884 2444

>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=84.50  E-value=3.3  Score=24.02  Aligned_cols=31  Identities=13%  Similarity=0.246  Sum_probs=24.3

Q ss_pred             EEEEecCCeEEEEEEEEeccccceeEeceEE
Q 034947           29 IWLFEQKDLRIEGRIIGFDEYMNLVLDDAEE   59 (78)
Q Consensus        29 V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E   59 (78)
                      |++++-.|-+++|.+.+||.-.++++=.|.+
T Consensus         9 V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s   39 (61)
T cd01735           9 VSCRTCFEQRLQGEVVAFDYPSKMLILKCPS   39 (61)
T ss_pred             EEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence            6666677889999999999999877554443

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.

>PRK14647 hypothetical protein; Provisional

Probab=83.99  E-value=4  Score=27.39  Aligned_cols=44  Identities=18%  Similarity=0.339  Sum_probs=30.3

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEec-------CCeEEEEEEEEecc
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ-------KDLRIEGRIIGFDE   48 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~-------~~~~~~G~L~gfD~   48 (78)
                      ||+-..++...|-+| .+++++.  |.|.++..       +.+++.|+|.++|+
T Consensus        80 SSPG~~RpL~~~~~f-~r~~G~~--v~V~l~~~~~~~~~~~~~~~~G~L~~~~~  130 (159)
T PRK14647         80 SSPGLDRPLKKEADY-ERYAGRL--VKVRTFELLADEAGNKRKTFLGELEGLAD  130 (159)
T ss_pred             cCCCCCCcCCCHHHH-HHhCCcE--EEEEEeccccccccCCceEEEEEEEeecC
Confidence            555444555555544 5778866  87887642       35899999999987

>PRK14644 hypothetical protein; Provisional

Probab=80.74  E-value=4.1  Score=26.84  Aligned_cols=49  Identities=14%  Similarity=0.117  Sum_probs=32.9

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEec--CCeEEEEEEEEeccccceeEe
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ--KDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~--~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      ||+-..++...+  -+.+++++.  |.|+++..  +.+++.|.|.++|+- ++.|+
T Consensus        67 SSPGldRpL~~~--~f~r~~G~~--v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         67 SSPGFDMDYETD--ELENHIGEI--IDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             ECCCCCCCCCHH--HHHHhCCCe--EEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            555444544442  478889976  77887653  238899999999984 35554

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=80.48  E-value=6.5  Score=26.02  Aligned_cols=44  Identities=18%  Similarity=0.440  Sum_probs=30.0

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEecc
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDE   48 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~   48 (78)
                      ||+-..++...|-+ +.+++++.  |.|+++.  ++++++.|+|.++|+
T Consensus        79 SSPGi~RpL~~~~~-f~r~~G~~--v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         79 SSPGLDRPLKKARD-FRRFIGRE--VKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             eCCCCCCcCCCHHH-HHHhCCCe--EEEEEEcccCCceEEEEEEEEeeC
Confidence            55544444445544 45788876  7777653  467899999999987

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	78
3cw1_E	92	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		2e-25

>pdb|3CW1|E Chain E, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 92

Iteration: 1
 Score =  110 bits (275), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 60/67 (89%)
Query: 5  KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
          KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68
Query: 65 NTRKPLG 71
           +RK LG
Sbjct: 69 KSRKQLG 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	78
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	9e-31
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	2e-19
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	2e-15
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	2e-13
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	5e-11
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	4e-09
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	4e-08
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	4e-08
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	6e-08
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	3e-06
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	7e-06
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	2e-05
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	2e-05
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	3e-05
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	5e-05
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	2e-04
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	3e-04
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	5e-04

>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 =  102 bits (256), Expect = 9e-31
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query: 5  KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
          KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query: 65 NTRKPLG 71
           +RK LG
Sbjct: 69 KSRKQLG 75

>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 = 73.7 bits (181), Expect = 2e-19
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 3  STKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI 62
          S     +   P+ LI + + S     +W+  + +    G ++GFD+Y+N+VL D  E   
Sbjct: 11 SQDPMSMTILPLELIDKCIGSN----LWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDT 66

Query: 63 KKNTRKPLG 71
               +   
Sbjct: 67 VTGVTEKHS 75

>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 = 63.1 bits (154), Expect = 2e-15
 Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          M  P  ++   +     I++ +  ++  ++ G++ G D+YMNL L +A E   ++  R 
Sbjct: 3  MVLPNQMVKSMVGK--IIRVEMKGEE-NQLVGKLEGVDDYMNLYLTNAMECKGEEKVRS 58

>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 = 59.6 bits (144), Expect = 2e-13
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 4/71 (5%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
            S +    +  P+ LI + + ++    I++  + D    G + GFDEY+N+VLDD +E 
Sbjct: 17 GGSNQKGGNIILPLALIDKCIGNR----IYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEY 72

Query: 61 HIKKNTRKPLG 71
            K +     G
Sbjct: 73 GFKADEEDISG 83

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

 Score = 51.9 bits (125), Expect = 5e-11
 Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 4/57 (7%)

Query: 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          +P+++I R L     + + L  +K     GR+IG+D ++N+VL DAE +   +  ++
Sbjct: 4  RPLDVIHRSLDK--DVLVIL--KKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKR 56

>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 = 47.3 bits (113), Expect = 4e-09
 Identities = 13/60 (21%), Positives = 27/60 (45%)

Query: 9  IMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
           M        + L       + +  + +  + G +  +D++MNLVL D+EE+    + +K
Sbjct: 2  AMNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKK 61

>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 = 44.6 bits (106), Expect = 4e-08
 Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 4/57 (7%)

Query: 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          +P++++ R L+S   +++    +      G + G+D +MNLVL DAEE+   +  RK
Sbjct: 4  RPLDVLNRSLKSPVIVRL----KGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRK 56

>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 = 44.6 bits (106), Expect = 4e-08
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 1  MASTKVQRIMTQ-PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEE 59
          +     QR+  Q P++ +   L S   I++    + D    G +  FD +MNLVL+DAEE
Sbjct: 3  VIDVSSQRVNVQRPLDALGNSLNSPVIIKL----KGDREFRGVLKSFDLHMNLVLNDAEE 58

Query: 60 VHIKKNTRK 68
          +   + TR+
Sbjct: 59 LEDGEVTRR 67

>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 = 44.4 bits (105), Expect = 6e-08
 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          M+ P+N    FL       + +  +  +  +G ++  D YMN+ L + EE      +  
Sbjct: 1  MSLPLNPK-PFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGH 58

>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 = 40.1 bits (94), Expect = 3e-06
 Identities = 13/69 (18%), Positives = 30/69 (43%), Gaps = 6/69 (8%)

Query: 3  STKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI 62
          ++ + +        +   +  +  +++    +    I G +  FD+++NL+L+DAEE  I
Sbjct: 2  ASDISKCFATLGATLQDSIGKQVLVKL----RDSHEIRGILRSFDQHVNLLLEDAEE--I 55

Query: 63 KKNTRKPLG 71
                  G
Sbjct: 56 IDGNVYKRG 64

>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 = 39.4 bits (92), Expect = 7e-06
 Identities = 15/49 (30%), Positives = 30/49 (61%), Gaps = 4/49 (8%)

Query: 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          +P++L+   L     +++    + D  + GR+  +DE++N+VL DAEE+
Sbjct: 9  EPLDLVRLSLDEIVYVKL----RGDRELNGRLHAYDEHLNMVLGDAEEI 53

>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 = 37.7 bits (88), Expect = 2e-05
 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 2/43 (4%)

Query: 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          ++ I L     +  +G +   D YMNL L+  EE    K T  
Sbjct: 16 KVLIRL--SSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNV 56

>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 = 37.7 bits (88), Expect = 2e-05
 Identities = 10/30 (33%), Positives = 17/30 (56%)

Query: 39 IEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          ++G + GFD +MNLV+D+  E+        
Sbjct: 27 VQGILRGFDPFMNLVIDECVEMATSGQQNN 56

>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 = 39.2 bits (91), Expect = 2e-05
 Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 14/60 (23%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLR-IEGRIIGFDEYMNLVLDDAEE 59
          M   K  + M Q I+          R++  L   +D R   G    FD++MNL+L D +E
Sbjct: 1  MTVGKSSK-MLQHIDY---------RMRCIL---QDGRIFIGTFKAFDKHMNLILCDCDE 47

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

 Score = 38.0 bits (88), Expect = 3e-05
 Identities = 12/48 (25%), Positives = 29/48 (60%), Gaps = 2/48 (4%)

Query: 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          P++++ + +++  ++ I     K L   GR+  FD + N+VL++ +E+
Sbjct: 28 PLSVLTQSVKNNTQVLINCRNNKKLL--GRVKAFDRHCNMVLENVKEM 73

>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 = 37.0 bits (86), Expect = 5e-05
 Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 4/56 (7%)

Query: 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          P++L+   L  +  I++    +    + G +  FD + N+VL DA E   + N  +
Sbjct: 11 PLDLLKLNLDERVYIKL----RGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEE 62

>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 = 35.2 bits (81), Expect = 2e-04
 Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)

Query: 36 DLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLG 71
               G ++  D Y NL L++AEE  +   +   LG
Sbjct: 42 STEYRGTLVSTDNYFNLQLNEAEEF-VAGVSHGTLG 76

>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 = 35.1 bits (81), Expect = 3e-04
 Identities = 14/71 (19%), Positives = 22/71 (30%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          M S+      +Q   L    L +     I +  +      G +   D YMNL L +    
Sbjct: 1  MGSSHHHHHHSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRT 60

Query: 61 HIKKNTRKPLG 71
              +    L 
Sbjct: 61 MPDGDKFFRLP 71

>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 = 34.9 bits (80), Expect = 5e-04
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 4/67 (5%)

Query: 2  ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVH 61
          +S   +R   + I  + R+   + +           +I G + GFD+ MNLVLDD EE  
Sbjct: 13 SSQPTERPRKESILDLSRYQDQRIQATF----TGGRQITGILKGFDQLMNLVLDDVEEQL 68

Query: 62 IKKNTRK 68
                K
Sbjct: 69 RNPEDGK 75

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	78
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.93
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.9
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.9
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.89
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.87
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.86
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.86
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.86
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
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.85
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.85
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.84
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.84
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.84
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.83
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.83
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.82
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.8
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.8
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.8
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.76
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.74
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.65
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	98.02
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	97.99
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	97.95
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	97.94
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	97.9
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	97.88
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	97.87
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	97.84
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	95.97
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	95.87
1ycy_A	71	Conserved hypothetical protein; structural genomic	94.09
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	87.73
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	83.99

>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=99.93  E-value=1.4e-26  Score=143.58  Aligned_cols=75  Identities=64%  Similarity=1.064  Sum_probs=64.4

Q ss_pred             cccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947            4 TKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus         4 ~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ++.||.|..|+++|.++++++.+|.+|++.++|+++.|+|.|||+||||+|+||+|+..+++..+.+|.++|||.
T Consensus         8 ~~~~~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~   82 (92)
T 3s6n_E            8 QKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGD   82 (92)
T ss_dssp             ------CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGG
T ss_pred             CccceeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCC
Confidence            467889999999999999999888888888889999999999999999999999999766778889999999994

>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=99.90  E-value=1.1e-23  Score=127.16  Aligned_cols=71  Identities=23%  Similarity=0.295  Sum_probs=57.6

Q ss_pred             CCccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947            1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus         1 ms~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ||+. .++....|+.+|.++++++  |.|+|++  |+++.|+|.|||+|||++|+||+|+  +++..+.+|.++|||.
T Consensus         1 m~~~-~~~~~~~P~~~L~~~~~~~--V~V~l~~--g~~~~G~L~~~D~~mNlvL~d~~e~--~~~~~~~lg~v~iRG~   71 (81)
T 1i8f_A            1 MASD-ISKCFATLGATLQDSIGKQ--VLVKLRD--SHEIRGILRSFDQHVNLLLEDAEEI--IDGNVYKRGTMVVRGE   71 (81)
T ss_dssp             ----------CCHHHHHHTTTTSE--EEEEEGG--GEEEEEEEEEECTTCCEEEEEEEEE--ETTEEEEEEEEEECGG
T ss_pred             CCcc-cCccccchHHHHHHHCCCe--EEEEEcC--CcEEEEEEEEEcCCCeeEEccEEEE--cCCcccCCCEEEECCC
Confidence            7875 6888899999999999965  9999976  8999999999999999999999999  5677899999999994

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

Probab=99.90  E-value=1.8e-23  Score=130.11  Aligned_cols=69  Identities=20%  Similarity=0.373  Sum_probs=57.0

Q ss_pred             cceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947            6 VQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus         6 ~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      +++.+..|+++|.++++++  |.|.+++  |++|.|+|.|||+||||+|+||+|+..+++..+.+|.++|||.
T Consensus        14 ~~~~~~~Pl~lL~~~l~k~--V~V~Lk~--gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG~   82 (94)
T 4emk_A           14 PMSMTILPLELIDKCIGSN--LWVIMKS--EREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGN   82 (94)
T ss_dssp             ------CHHHHHHHTTTSE--EEEEESS--SEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECST
T ss_pred             CccccccCHHHHHHHcCCe--EEEEECC--CcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcCC
Confidence            5677899999999999976  7777754  9999999999999999999999999646677899999999995

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

Probab=99.89  E-value=3.3e-23  Score=125.60  Aligned_cols=71  Identities=30%  Similarity=0.375  Sum_probs=60.5

Q ss_pred             CCccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947            1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus         1 ms~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ||++  .+....|+++|.++++++  |.|+|++  |+++.|+|.|||+|||++|+||+|++ .++..+.+|.++|||.
T Consensus         6 ms~~--~~~~~~P~~~L~~~~~~~--V~V~Lk~--g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~IRG~   76 (83)
T 1mgq_A            6 VSSQ--RVNVQRPLDALGNSLNSP--VIIKLKG--DREFRGVLKSFDLHMNLVLNDAEELE-DGEVTRRLGTVLIRGD   76 (83)
T ss_dssp             ------CCCTTCTTHHHHHTTTSE--EEEEETT--TEEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGG
T ss_pred             cccc--cccCcChHHHHHHhCCCE--EEEEEcC--CcEEEEEEEEECCCceeEEccEEEEe-cCCcccCCCEEEECCC
Confidence            7864  566789999999999975  9999966  99999999999999999999999996 5677889999999994

>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=99.87  E-value=4.6e-22  Score=118.77  Aligned_cols=65  Identities=23%  Similarity=0.386  Sum_probs=58.7

Q ss_pred             eecChHHHHHHhhcCcceEEEEEEecCC-eEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947            9 IMTQPINLIFRFLQSKARIQIWLFEQKD-LRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus         9 ~~~~Pl~~L~~~~~k~~~V~V~lk~~~~-~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      .|..|+++|.++++++  |+|++++  | +++.|+|.|||+|||++|+||+|++ +++..+.+|.++|||.
T Consensus         2 ~m~~P~~~L~~~~~~~--v~V~lk~--g~~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~   67 (77)
T 1ljo_A            2 AMVLPNQMVKSMVGKI--IRVEMKG--EENQLVGKLEGVDDYMNLYLTNAMECK-GEEKVRSLGEIVLRGN   67 (77)
T ss_dssp             CCCCHHHHHHHTTTSE--EEEEETT--CSSEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGG
T ss_pred             CccchHHHHHHHCCCE--EEEEEeC--CCEEEEEEEEEECCcceEEEeeEEEEe-cCCcEeECCeEEEeCC
Confidence            3679999999999976  8888865  8 9999999999999999999999996 6677889999999994

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

Probab=99.86  E-value=4.5e-22  Score=121.61  Aligned_cols=63  Identities=19%  Similarity=0.250  Sum_probs=57.3

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..|+++|.++++++  |+|+|++  |+++.|+|.|||+|||++|+||+|+. +++..+.+|.++|||.
T Consensus         5 ~~P~~~L~~~~~k~--V~V~Lk~--g~~~~G~L~~~D~~mNlvL~d~~e~~-~g~~~~~lg~v~IRG~   67 (86)
T 3s6n_F            5 LNPKPFLNGLTGKP--VMVKLKW--GMEYKGYLVSVDGYMNMQLANTEEYI-DGALSGHLGEVLIRCN   67 (86)
T ss_dssp             CCHHHHHHHHTTSE--EEEEETT--SCEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEESSEEECGG
T ss_pred             cCcHHHHHHhCCCe--EEEEEcC--CeEEEEEEEEEcCceEEEEeeEEEEc-CCceeeEccEEEEeCC
Confidence            57999999999976  9899866  89999999999999999999999984 7777889999999994

>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=99.86  E-value=3.8e-22  Score=123.69  Aligned_cols=70  Identities=19%  Similarity=0.249  Sum_probs=52.4

Q ss_pred             cccceeecChHHHHHHhhcCcceEEEEEEecCC-eEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947            4 TKVQRIMTQPINLIFRFLQSKARIQIWLFEQKD-LRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus         4 ~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~-~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..+......|+.+|.++++++  |+|+|++  | +++.|+|.|||+|||++|+||+|++ +++..+.+|.++|||.
T Consensus        13 ~~~~~~~~~P~~~L~~~i~k~--V~V~Lk~--g~~~~~G~L~~~D~~MNlvL~d~~E~~-~~~~~~~lg~v~IRG~   83 (93)
T 1n9r_A           13 DISAMQPVNPKPFLKGLVNHR--VGVKLKF--NSTEYRGTLVSTDNYFNLQLNEAEEFV-AGVSHGTLGEIFIRCN   83 (93)
T ss_dssp             -------------CGGGTTSE--EEEEESS--TTEEEEEEEEECCTTTCEEEEEEEEEE-TTEEEEECCSEEECGG
T ss_pred             cccccccCChHHHHHHhCCCE--EEEEEcC--CCEEEEEEEEEEccccEEEEeeEEEEc-CCCeEeEcCEEEEcCC
Confidence            334566789999999999965  9999976  7 9999999999999999999999995 7777889999999994

>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=99.86  E-value=1e-21  Score=116.92  Aligned_cols=63  Identities=22%  Similarity=0.312  Sum_probs=57.0

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..|+++|.++++++  |.|+|++  |+++.|+|.|||+|||++|+||+|+. +++..+.+|.++|||.
T Consensus         3 ~~P~~~L~~~~~k~--V~V~Lk~--g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~   65 (75)
T 4emk_B            3 SSPNEFLNKVIGKK--VLIRLSS--GVDYKGILSCLDGYMNLALERTEEYV-NGKKTNVYGDAFIRGN   65 (75)
T ss_dssp             SHHHHHHHHTTTSE--EEEECTT--SCEEEEEEEEECTTCEEEEEEEEEEE-TTEEEEEEEEEEEEGG
T ss_pred             CchHHHHHHhCCCe--EEEEEcC--CcEEEEEEEEEcCcceEEEccEEEEe-cCCcccEecEEEEcCC
Confidence            47999999999975  8888865  89999999999999999999999994 7777889999999994

>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=2.2e-21  Score=116.85  Aligned_cols=64  Identities=23%  Similarity=0.358  Sum_probs=57.5

Q ss_pred             ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ...|+++|.++++++  |.|+|++  |+++.|+|.|||+|||++|+||+|++ .++..+.+|.++|||.
T Consensus         7 ~~~P~~~L~~~~~~~--V~V~l~~--g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~   70 (81)
T 1th7_A            7 AETAHKVLAESLNNL--VLVKLKG--NKEVRGMLRSYDQHMNLVLSDSEEIQ-SDGSGKKLGTIVIRGD   70 (81)
T ss_dssp             CHHHHHHHHHHTTSE--EEEEETT--TEEEEEEEEEECTTCCEEEEEEEEEC-SSSCEEEEEEEEECGG
T ss_pred             ccchHHHHHHhCCCe--EEEEEcC--CcEEEEEEEEEcCCCCEEEccEEEEe-cCCceeECCEEEECCC
Confidence            368999999999975  8888865  89999999999999999999999996 5567889999999994

>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=1.6e-21  Score=121.13  Aligned_cols=67  Identities=22%  Similarity=0.292  Sum_probs=59.0

Q ss_pred             eeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec------CCeeeeeeEEEEecC
Q 034947            8 RIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK------KNTRKPLGFFSKETT   78 (78)
Q Consensus         8 ~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~------~~~~~~lG~ilir~~   78 (78)
                      .-|..|+.+|.++++++  |.|.|++  ||++.|+|.|||+||||||+||+|++.+      ++..+.+|.++|||.
T Consensus         6 ~~~~~p~~~L~~~i~k~--V~V~Lk~--gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~   78 (96)
T 3bw1_A            6 HHMETPLDLLKLNLDER--VYIKLRG--ARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGD   78 (96)
T ss_dssp             CCCCCHHHHHGGGTTSE--EEEEEGG--GCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGG
T ss_pred             hhhhhHHHHHHHHCCCe--EEEEECC--CcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCC
Confidence            34789999999999976  8888866  8999999999999999999999999754      345788999999994

>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=3e-21  Score=114.62  Aligned_cols=63  Identities=29%  Similarity=0.503  Sum_probs=56.9

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..|+++|.++++++  |.|++++  |+++.|+|.|||+|||++|+||+|++ .+...+.+|.++|||.
T Consensus         3 ~~P~~~L~~~~~~~--V~V~l~~--g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~   65 (75)
T 1h64_1            3 ERPLDVIHRSLDKD--VLVILKK--GFEFRGRLIGYDIHLNVVLADAEMIQ-DGEVVKRYGKIVIRGD   65 (75)
T ss_dssp             CCHHHHHHTTTTSE--EEEEETT--SEEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGG
T ss_pred             chHHHHHHHHCCCE--EEEEECC--CCEEEEEEEEEeCCCCeEEeeEEEEe-eCCceeECCEEEECCC
Confidence            47999999999975  8888865  99999999999999999999999996 5677889999999994

>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=99.85  E-value=1e-21  Score=126.44  Aligned_cols=68  Identities=28%  Similarity=0.444  Sum_probs=56.5

Q ss_pred             ceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec---------CCe-----eeeeeE
Q 034947            7 QRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK---------KNT-----RKPLGF   72 (78)
Q Consensus         7 ~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~---------~~~-----~~~lG~   72 (78)
                      .+.+..|+++|.++++++  |.|.|  ++|+++.|+|.|||+||||||+||+|++.+         ++.     .+.+|.
T Consensus        23 ~~~~~~Pl~lL~~~l~k~--V~V~L--k~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~   98 (121)
T 2fwk_A           23 GGNIILPLALIDKCIGNR--IYVVM--KGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLET   98 (121)
T ss_dssp             -CCCCCHHHHHHHTBTSB--CEEEE--TTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSE
T ss_pred             cccccCcHHHHHHHcCCe--EEEEE--CCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcce
Confidence            446789999999999976  76776  559999999999999999999999999743         323     688999


Q ss_pred             EEEecC
Q 034947           73 FSKETT   78 (78)
Q Consensus        73 ilir~~   78 (78)
                      ++|||.
T Consensus        99 v~IRG~  104 (121)
T 2fwk_A           99 ILLSGN  104 (121)
T ss_dssp             EEECGG
T ss_pred             EEECCC
Confidence            999994

>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=3.7e-21  Score=114.58  Aligned_cols=63  Identities=29%  Similarity=0.428  Sum_probs=57.0

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..|+++|.++++++  |.|+|++  |+++.|+|.|||+|||++|+||+|++ .+...+.+|.++|||.
T Consensus         3 ~~P~~~L~~~~~~~--V~V~L~~--g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~   65 (77)
T 1i4k_A            3 PRPLDVLNRSLKSP--VIVRLKG--GREFRGTLDGYDIHMNLVLLDAEEIQ-NGEVVRKVGSVVIRGD   65 (77)
T ss_dssp             CCHHHHHHTTTTSE--EEEEETT--SCEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGG
T ss_pred             ccHHHHHHHhCCCE--EEEEEcC--CCEEEEEEEEEcCCCCeEEeeEEEEe-cCCcEeECCEEEECCC
Confidence            47999999999965  9999966  89999999999999999999999996 5667889999999994

>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=6e-21  Score=118.14  Aligned_cols=65  Identities=28%  Similarity=0.434  Sum_probs=55.1

Q ss_pred             ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec----C--------CeeeeeeEEEEec
Q 034947           10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK----K--------NTRKPLGFFSKET   77 (78)
Q Consensus        10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~----~--------~~~~~lG~ilir~   77 (78)
                      ...|+++|+.+++++  |.|+|+  +|++|.|+|.|||+||||+|+||+|++.+    +        +..+.+|.++|||
T Consensus         7 ~~~Pl~lL~~~~~~~--V~V~l~--~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG   82 (93)
T 4emg_A            7 VAEPLDLVRLSLDEI--VYVKLR--GDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRG   82 (93)
T ss_dssp             --CTTHHHHTTTTSE--EEEEET--TTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECG
T ss_pred             cCCCHHHHHHhCCCE--EEEEEC--CCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECC
Confidence            579999999999975  888885  49999999999999999999999999752    2        3578999999999


Q ss_pred             C
Q 034947           78 T   78 (78)
Q Consensus        78 ~   78 (78)
                      .
T Consensus        83 ~   83 (93)
T 4emg_A           83 D   83 (93)
T ss_dssp             G
T ss_pred             C
Confidence            4

>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=99.84  E-value=1e-20  Score=112.83  Aligned_cols=63  Identities=11%  Similarity=0.073  Sum_probs=56.4

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..|+++|+++++++  |+|+|++  |++++|+|.|||+|||++|+||+|+. .++....+|.++|||.
T Consensus         4 ~~P~~~L~~~~g~~--V~VeLk~--g~~~~G~L~~~D~~MNl~L~~~~e~~-~~~~~~~lg~v~IRG~   66 (75)
T 1d3b_A            4 GVPIKVLHEAEGHI--VTCETNT--GEVYRGKLIEAEDNMNCQMSNITVTY-RDGRVAQLEQVYIRGC   66 (75)
T ss_dssp             CCHHHHHHHTTTSE--EEEEETT--SCEEEEEEEEECTTCCEEEEEEEEEC-TTSCEEEEEEEEECGG
T ss_pred             cCHHHHHHHhCCCE--EEEEECC--CcEEEEEEEEEccceeEEEEeEEEEC-CCCcEEEcCeEEEeCC
Confidence            57999999999975  9899865  89999999999999999999999995 4445889999999994

>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=99.83  E-value=5.8e-21  Score=120.81  Aligned_cols=65  Identities=18%  Similarity=0.136  Sum_probs=48.2

Q ss_pred             ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      .-.|+.+|.++++++  |+|+|++  |++|.|+|.|||+||||+|+||+|+..+++..+.+|.++|||.
T Consensus        14 ~~~p~~lL~~~igk~--V~V~Lk~--G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG~   78 (105)
T 4emh_A           14 PMLPLTLLNATQGRP--ILVELKN--GETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGN   78 (105)
T ss_dssp             ------------CCE--EEEEETT--SCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECGG
T ss_pred             CCcHHHHHHHhCCCE--EEEEECC--CCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeCC
Confidence            468999999999976  9999966  8999999999999999999999999767777889999999994

>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=99.83  E-value=6.7e-21  Score=121.74  Aligned_cols=69  Identities=32%  Similarity=0.415  Sum_probs=46.0

Q ss_pred             cceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC------CeeeeeeEEEEecC
Q 034947            6 VQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK------NTRKPLGFFSKETT   78 (78)
Q Consensus         6 ~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~------~~~~~lG~ilir~~   78 (78)
                      +.++...|+..|.++++++  |.|.|+  +||+|.|+|.|||+||||||+||+|++.+.      ...+.+|.++|||.
T Consensus        17 ~~~~kke~i~~L~~~l~k~--V~V~L~--dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~   91 (113)
T 4emk_C           17 TERPRKESILDLSRYQDQR--IQATFT--GGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGT   91 (113)
T ss_dssp             ---------------CCSE--EEEEET--TSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTT
T ss_pred             ccCCccchHHHHHHHcCCc--EEEEEe--CCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCC
Confidence            4556678999999999976  888875  599999999999999999999999997542      46889999999995

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

Probab=99.82  E-value=1.4e-20  Score=120.55  Aligned_cols=68  Identities=18%  Similarity=0.321  Sum_probs=53.7

Q ss_pred             eecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC-------------CeeeeeeEEEE
Q 034947            9 IMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK-------------NTRKPLGFFSK   75 (78)
Q Consensus         9 ~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~-------------~~~~~lG~ili   75 (78)
                      .+..|+++|.+++++.++|.|+|++  |++|.|+|.|||+||||||+||+|++...             +..+.+|.++|
T Consensus        24 ~~~~Pl~lL~~~~~~~k~V~V~Lk~--gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~I  101 (118)
T 1b34_B           24 FNTGPLSVLTQSVKNNTQVLINCRN--NKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFL  101 (118)
T ss_dssp             --CCHHHHHHHHHHHTCEEEEEETT--SCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEE
T ss_pred             cccChHHHHHHHhcCCcEEEEEECC--CcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEE
Confidence            3679999999999633469999965  89999999999999999999999996321             12457999999


Q ss_pred             ecC
Q 034947           76 ETT   78 (78)
Q Consensus        76 r~~   78 (78)
                      ||.
T Consensus       102 RG~  104 (118)
T 1b34_B          102 RGD  104 (118)
T ss_dssp             CGG
T ss_pred             cCC
Confidence            994

>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=99.80  E-value=3.7e-20  Score=110.49  Aligned_cols=61  Identities=23%  Similarity=0.441  Sum_probs=43.3

Q ss_pred             hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      |.++|.++++++  |.|.|++  |+++.|+|.|||+|||++|+||+|+. .+++.+.+|.++|||.
T Consensus         5 ~~~~L~~~~~k~--V~V~Lk~--gr~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~v~iRG~   65 (76)
T 3s6n_G            5 HPPELKKFMDKK--LSLKLNG--GRHVQGILRGFDPFMNLVIDECVEMA-TSGQQNNIGMVVIRGN   65 (76)
T ss_dssp             ---------CCE--EEEEETT--TEEEEEEEEEECTTCCEEEEEEEECC-CC----CBSSEEECSS
T ss_pred             chHHHHHhCCCe--EEEEECC--CcEEEEEEEEECCcceEEEeceEEEc-cCCcEeEcCEEEECCC
Confidence            667899999976  8888865  99999999999999999999999995 4456789999999995

>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=99.80  E-value=2.3e-20  Score=114.23  Aligned_cols=63  Identities=19%  Similarity=0.337  Sum_probs=52.2

Q ss_pred             ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEe---------cCCeeeeeeEEEEecC
Q 034947           12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI---------KKNTRKPLGFFSKETT   78 (78)
Q Consensus        12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~---------~~~~~~~lG~ilir~~   78 (78)
                      .|..+|.++++++  |.|.+++  |+++.|+|.|||+||||+|+||+|++.         ++...+.+|.++|||.
T Consensus         4 ~~~~~L~~~~~k~--V~V~l~~--gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~   75 (91)
T 1d3b_B            4 GKSSKMLQHIDYR--MRCILQD--GRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGE   75 (91)
T ss_dssp             ---CCCGGGTTSE--EEEEETT--CCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGG
T ss_pred             ChhHHHHHHcCCc--EEEEECC--CeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCC
Confidence            5778899999976  8888854  999999999999999999999999852         2356789999999994

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

Probab=99.80  E-value=1.3e-19  Score=116.33  Aligned_cols=62  Identities=19%  Similarity=0.267  Sum_probs=55.9

Q ss_pred             ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      .|+.+|.++++++  |+|+|++  |++|.|+|.|||+||||+|+||+|+. .+.....+|.++|||.
T Consensus         2 ~p~~~L~~~~gk~--V~V~Lk~--g~~~~G~L~~~D~~MNlvL~d~~e~~-~~~~~~~lg~v~IRG~   63 (119)
T 1b34_A            2 KLVRFLMKLSHET--VTIELKN--GTQVHGTITGVDVSMNTHLKAVKMTL-KNREPVQLETLSIRGN   63 (119)
T ss_dssp             CHHHHHHTCTTCE--EEEEETT--CCEEEEEEEEECTTCCEEEEEEEEEC-TTSCCEEEEEEEECGG
T ss_pred             ChHHHHHHhCCCE--EEEEEcC--CCEEEEEEEEEcccceEEeccEEEec-CCCceeEcceEEEcCC
Confidence            6999999999965  9999965  89999999999999999999999995 5556789999999994

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

Probab=99.76  E-value=1.2e-18  Score=122.73  Aligned_cols=64  Identities=19%  Similarity=0.332  Sum_probs=55.7

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEe---------cCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI---------KKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~---------~~~~~~~lG~ilir~~   78 (78)
                      +++...|.++++|+  |.|+|++  ||+|+|+|+|||+||||||+||+|++.         +.++.+.+|+++|||.
T Consensus         3 v~k~~kL~klIdKr--V~V~Lkd--GRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGd   75 (231)
T 3pgw_B            3 VGKSSKMLQHIDYR--MRCILQD--GRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGE   75 (231)
T ss_pred             cCchHHHHHhcCCe--EEEEECC--CcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCC
Confidence            46778999999987  8888855  999999999999999999999999963         1357899999999995

>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=99.74  E-value=3.6e-18  Score=110.96  Aligned_cols=63  Identities=11%  Similarity=0.049  Sum_probs=56.1

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..|+++|.+++++.  |+|.|++  |++|.|+|.+||.|||++|+||+|+..++ ....+|.++|||.
T Consensus         4 ~~P~~~L~~~~gk~--V~VeLkn--G~~~~G~L~~~D~~MNi~L~dv~e~~~~g-~~~~l~~v~IRGn   66 (126)
T 2y9a_D            4 GVPIKVLHEAEGHI--VTCETNT--GEVYRGKLIEAEDNMNCQMSNITVTYRDG-RVAQLEQVYIRGS   66 (126)
T ss_dssp             CCSHHHHHSCSSCE--EEEEESS--CCEEEEEEEEECTTSCEEEEEEEEECTTS-CCEEEEEEEECGG
T ss_pred             ccHHHHHHHhCCCE--EEEEECC--CcEEEEEEEEEcCceEEEEeeEEEEcCCC-cEeecccEEEeCC
Confidence            57999999999975  9999976  89999999999999999999999995344 4789999999984

>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=99.65  E-value=8e-17  Score=105.04  Aligned_cols=56  Identities=16%  Similarity=0.178  Sum_probs=49.5

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      .++|.++++++  |+|+|++  |+++.|+|.|||+||||+|+||+|+.     ...+|.++|||.
T Consensus         2 ~~~L~~~igk~--V~V~Lk~--G~~~~G~L~~~D~~MNlvL~d~~E~~-----~~~lg~v~IRG~   57 (130)
T 1m5q_A            2 VAELNNLLGRE--VQVVLSN--GEVYKGVLHAVDNQLNIVLANASNKA-----GEKFNRVFIMYR   57 (130)
T ss_dssp             HHHHHHTTTSE--EEEEETT--SCEEEEEEEEECTTCCEEEEEEECTT-----CCEEEEEEECGG
T ss_pred             hhHHHHhCCCe--EEEEECC--CcEEEEEEEEEcccceeEEeeEEEEc-----CCEeceEEEeCC
Confidence            36899999975  9999966  89999999999999999999999972     368999999994

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

Probab=98.02  E-value=1.7e-05  Score=48.33  Aligned_cols=42  Identities=14%  Similarity=0.225  Sum_probs=36.1

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEec-cccceeEece
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFD-EYMNLVLDDA   57 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD-~~mNlvL~da   57 (78)
                      ..|+ -|.++++|+  |.|.+.  +|+.|.|.|.+|| .-.|++|.||
T Consensus         7 ~~p~-el~~li~Ke--V~V~l~--dg~~y~G~l~tvDp~s~sIvL~n~   49 (86)
T 1y96_A            7 KGPL-EWQDYIYKE--VRVTAS--EKNEYKGWVLTTDPVSANIVLVNF   49 (86)
T ss_dssp             SCHH-HHHHTTTCE--EEEEET--TTEEEEEEEEEECTTTCCEEEEEE
T ss_pred             CCHH-HHHhhcCCE--EEEEEc--CCCEEEEEEEEECCCceEEEEeec
Confidence            3566 678899987  777775  4999999999999 9999999998

>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=97.99  E-value=1.1e-05  Score=48.85  Aligned_cols=40  Identities=18%  Similarity=0.550  Sum_probs=34.0

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD   56 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d   56 (78)
                      -.+|+.+-.++.+|+|.|.+  |..++|.+.|||+|+ +.|++
T Consensus         9 d~fLn~lrk~~~~Vtv~L~N--G~~l~G~I~~fD~ft-VlL~~   48 (82)
T 1u1s_A            9 DPYLNTLRKERVPVSIYLVN--GIKLQGQIESFDQFV-ILLKN   48 (82)
T ss_dssp             HHHHHHHHHTTCCEEEEETT--SCEEEEEEEEECSSE-EEEES
T ss_pred             HHHHHHHHHcCCcEEEEEeC--CcEEEEEEEEEcceE-EEEec
Confidence            45788888888999999976  899999999999999 55553

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

Probab=97.95  E-value=4.5e-06  Score=49.29  Aligned_cols=37  Identities=11%  Similarity=0.340  Sum_probs=31.2

Q ss_pred             HHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEe
Q 034947           16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus        16 ~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      +|+..-.++.+|+|.|.+  |..++|.+.|||+|+ +.|+
T Consensus        17 fLn~~r~~~~~Vtv~L~N--G~~l~G~I~~fD~ft-Vll~   53 (71)
T 2qtx_A           17 FEYARRLNGKKVKIFLRN--GEVLDAEVTGVSNYE-IMVK   53 (71)
T ss_dssp             CCGGGGGTTCEEEEEETT--SCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHHcCCcEEEEEeC--CeEEEEEEEEEcceE-EEEE
Confidence            667777888899999976  899999999999999 4444

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

Probab=97.94  E-value=1.5e-05  Score=47.85  Aligned_cols=41  Identities=17%  Similarity=0.493  Sum_probs=34.8

Q ss_pred             ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEe
Q 034947           12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus        12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      .--.+|+.+..++.+|+|.|.+  |..++|.+.+||.|+ +.|+
T Consensus         8 lQd~fLn~lrk~k~~VtI~Lvn--G~~L~G~I~~fD~f~-VlL~   48 (79)
T 3sb2_A            8 LQDPFLNALRKEHVPVSIYLVN--GIKLQGHVESFDQYV-VLLR   48 (79)
T ss_dssp             THHHHHHHHHHTTCCEEEEETT--SCEEEEEEEEECSSE-EEEE
T ss_pred             hHHHHHHHHHhcCCeEEEEEeC--CCEEEEEEEEECCcE-EEEE
Confidence            3346899999999999999977  899999999999999 4454

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

Probab=97.90  E-value=1.8e-05  Score=49.73  Aligned_cols=41  Identities=17%  Similarity=0.548  Sum_probs=35.1

Q ss_pred             hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947           13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD   56 (78)
Q Consensus        13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d   56 (78)
                      =-.+|+.+..++.+|+|.|.+  |..++|.+.+||.|+ +.|++
T Consensus        10 Qd~fLn~lrk~k~~VtI~LvN--G~~L~G~I~~fD~f~-VlL~~   50 (104)
T 2y90_A           10 QDPFLNALRRERVPVSIYLVN--GIKLQGQIESFDQFV-ILLKN   50 (104)
T ss_dssp             HHHHHHHHHHTTCCEEEEETT--SCEEEEEEEEECSSE-EEEES
T ss_pred             HHHHHHHHHhcCCcEEEEEeC--CCEEEEEEEEECCcE-EEEEC
Confidence            346899999999999999976  899999999999999 55554

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

Probab=97.88  E-value=1.5e-05  Score=47.22  Aligned_cols=40  Identities=18%  Similarity=0.563  Sum_probs=34.3

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD   56 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d   56 (78)
                      -.+|+.+..++.+|+|.|.+  |..++|.+.+||.|+ +.|++
T Consensus        11 d~~L~~lrk~k~~Vti~L~n--G~~l~G~I~~fD~f~-vlL~~   50 (74)
T 2ylb_A           11 DPFLNALRRERVPVSIYLVN--GIKLQGQIESFDQFV-ILLKN   50 (74)
T ss_dssp             HHHHHHHHHHTCCEEEEETT--SCEEEEEEEEECSSE-EEEES
T ss_pred             HHHHHHHHhcCCcEEEEEeC--CCEEEEEEEEECCcE-EEEEC
Confidence            46888888888899999976  899999999999999 55554

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

Probab=97.87  E-value=1.6e-05  Score=47.63  Aligned_cols=39  Identities=15%  Similarity=0.571  Sum_probs=32.7

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEe
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      -.+|+.+-.++.+|+|.|.+  |..++|.+.|||+|+ +.|+
T Consensus        13 d~fLn~lrk~~~~Vtv~L~n--G~~l~G~I~~fD~f~-VlL~   51 (78)
T 3ahu_A           13 DQFLNQIRKENTYVTVFLLN--GFQLRGQVKGFDNFT-VLLE   51 (78)
T ss_dssp             HHHHHHHHHHTCCEEEEETT--SCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHHHHcCCcEEEEEeC--CeEEEEEEEEEcceE-EEEE
Confidence            35788888778899999976  899999999999999 4444

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

Probab=97.84  E-value=1.9e-05  Score=47.15  Aligned_cols=39  Identities=15%  Similarity=0.493  Sum_probs=33.1

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEe
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      -.+|+.+..++.+|+|.|.+  |..++|.+.+||.|+ +.|+
T Consensus         9 d~fLn~lrk~k~~VtI~L~n--G~~l~G~I~~fD~f~-VlL~   47 (77)
T 1kq1_A            9 DKALENFKANQTEVTVFFLN--GFQMKGVIEEYDKYV-VSLN   47 (77)
T ss_dssp             HHHHHHHHHHTCEEEEEETT--SCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHHHhcCCeEEEEEeC--CCEEEEEEEEECCcE-EEEE
Confidence            35888888888899999976  899999999999999 4444

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

Probab=95.97  E-value=0.011  Score=34.49  Aligned_cols=43  Identities=21%  Similarity=0.197  Sum_probs=35.7

Q ss_pred             cCh-HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947           11 TQP-INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD   56 (78)
Q Consensus        11 ~~P-l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d   56 (78)
                      ..| ...|..++..+.+|.|.|.+  |..++|.+.-+|.|+ +.|.+
T Consensus         7 ~lPsvR~lQ~~ik~k~~V~I~L~t--G~~l~G~i~WQD~~c-l~L~~   50 (70)
T 3hfo_A            7 GLPSVRQVQLLIKDQTPVEIKLLT--GDSLFGTIRWQDTDG-LGLVD   50 (70)
T ss_dssp             SCHHHHHHHHHHHHTCEEEEEETT--SCEEEEEEEEECSSE-EEEEC
T ss_pred             CCCcHHHHHHHHhhCceEEEEecC--CCEEEEEEEEeCCCE-EEEEc
Confidence            345 78999999999898888865  889999999999999 55554

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

Probab=95.87  E-value=0.026  Score=33.07  Aligned_cols=41  Identities=22%  Similarity=0.331  Sum_probs=34.9

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEece
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA   57 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da   57 (78)
                      ...|..++..+.+|.|+|.+  |..++|.+.-+|.|+ +.|.+.
T Consensus        13 vR~lQ~~Ik~k~~V~I~L~t--Gd~l~G~i~WQD~~c-l~L~~~   53 (72)
T 3hfn_A           13 IRQLQNLIKQAAPVEIKLVT--GDAITGRVLWQDPTC-VCIADE   53 (72)
T ss_dssp             HHHHHHHHSSCCEEEEEETT--SCEEEEEEEEECSSE-EEEEC-
T ss_pred             HHHHHHHHhhCceEEEEecC--CCEEEEEEEEECCCE-EEEEcC
Confidence            78999999999898888855  889999999999999 666554

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

Probab=94.09  E-value=0.19  Score=28.96  Aligned_cols=42  Identities=21%  Similarity=0.387  Sum_probs=31.1

Q ss_pred             HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEE
Q 034947           15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVH   61 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~   61 (78)
                      ..|.++-+++  |-|.+  ++...|.|+|.-||+-. +.|.|++.+.
T Consensus         9 ktL~~WKg~r--vAv~v--g~ehSFtGiledFDeEv-iLL~dV~D~~   50 (71)
T 1ycy_A            9 KVLKEWKGHK--VAVSV--GGDHSFTGTLEDFDEEV-ILLKDVVDVI   50 (71)
T ss_dssp             HHHHHHTTSE--EEEEE--C----CEEEEEEECSSE-EEEEEEEETT
T ss_pred             HHHHHhCCcE--EEEEe--cCcceeeeehhhcCcce-eehhhHHHHh
Confidence            4677888876  66666  77889999999999998 8899999873

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

Probab=87.73  E-value=2.8  Score=25.19  Aligned_cols=55  Identities=22%  Similarity=0.298  Sum_probs=39.3

Q ss_pred             hhcCcceEEEEEEecCCeEEEEEEEEecccc-ceeEeceEEEEecCC--------eeeeeeEEEEecC
Q 034947           20 FLQSKARIQIWLFEQKDLRIEGRIIGFDEYM-NLVLDDAEEVHIKKN--------TRKPLGFFSKETT   78 (78)
Q Consensus        20 ~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~m-NlvL~da~E~~~~~~--------~~~~lG~ilir~~   78 (78)
                      |++++    |.|..+.+.+|+|+|...|.-= -+.|.++.-+-.++.        ....+.-|+.||.
T Consensus        11 yIGs~----iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgs   74 (88)
T 2vxe_A           11 ELGSK----ISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGS   74 (88)
T ss_dssp             CTTCE----EEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETT
T ss_pred             ccCCe----EEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccC
Confidence            78877    6777788999999999998764 588999887733322        1234566777763

>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=83.99  E-value=1.4  Score=28.81  Aligned_cols=50  Identities=20%  Similarity=0.346  Sum_probs=31.9

Q ss_pred             CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccccceeEe
Q 034947            2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD   55 (78)
Q Consensus         2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~mNlvL~   55 (78)
                      ||+-..++...|-+| .+++++.  |.|+++.  ++.+++.|+|.++|+-. ++|+
T Consensus        85 SSPGldRpL~~~~df-~r~~G~~--V~V~l~~~~~g~k~~~G~L~~~~~~~-v~l~  136 (164)
T 1ib8_A           85 TSPGLERPLKTKDAV-AGAVGKY--IHVGLYQAIDKQKVFEGTLLAFEEDE-LTME  136 (164)
T ss_dssp             ECCSSSSCCSSHHHH-HHHCSEE--EEEECSSCSSSCSEEEEEEEEEETTE-EEEE
T ss_pred             eCCCCCCCCCCHHHH-HHhCCcE--EEEEEecccCCceEEEEEEEEEeCCE-EEEE
Confidence            455444555555554 4778865  7676642  34589999999998653 4443

---

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	78
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	5e-13
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-10
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	5e-09
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	5e-08
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	1e-07
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-07
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	2e-06
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	1e-05
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	1e-05
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-05
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	4e-05
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	0.003

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

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

 Score = 56.4 bits (136), Expect = 5e-13
 Identities = 13/68 (19%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPL 70
          T P++++ + +++  ++ I    + + ++ GR+  FD + N+VL++ +E+  +       
Sbjct: 1  TGPLSVLTQSVKNNTQVLINC--RNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 58

Query: 71 GFFSKETT 78
             SK   
Sbjct: 59 KKKSKPVN 66

>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 = 49.7 bits (119), Expect = 1e-10
 Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 3/59 (5%)

Query: 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          M  P  ++   +    R+++   + ++ ++ G++ G D+YMNL L +A E   ++  R 
Sbjct: 3  MVLPNQMVKSMVGKIIRVEM---KGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRS 58

>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 = 46.0 bits (109), Expect = 5e-09
 Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 4/56 (7%)

Query: 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKN 65
          +  P+ LI + + +    +I++  + D    G + GFDEY+N+VLDD +E   K +
Sbjct: 3  IILPLALIDKCIGN----RIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKAD 54

>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 = 43.2 bits (102), Expect = 5e-08
 Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 4/57 (7%)

Query: 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          +P+++I R L     + +    +K     GR+IG+D ++N+VL DAE +   +  ++
Sbjct: 2  RPLDVIHRSLDKDVLVIL----KKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKR 54

>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 = 42.4 bits (100), Expect = 1e-07
 Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 4/56 (7%)

Query: 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          P++++ R L+S   +++    +      G + G+D +MNLVL DAEE+   +  RK
Sbjct: 4  PLDVLNRSLKSPVIVRL----KGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRK 55

>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 = 41.6 bits (98), Expect = 2e-07
 Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 4/59 (6%)

Query: 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          + +P++ +   L S   I++    + D    G +  FD +MNLVL+DAEE+   + TR+
Sbjct: 4  VQRPLDALGNSLNSPVIIKL----KGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRR 58

>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 = 39.0 bits (91), Expect = 2e-06
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 6/50 (12%)

Query: 17 IFRFLQSKARIQIWLFEQKDLR-IEGRIIGFDEYMNLVLDDAEEVHIKKN 65
          + + +  + R  +     +D R   G    FD++MNL+L D +E    K 
Sbjct: 3  MLQHIDYRMRCIL-----QDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP 47

>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 = 37.4 bits (87), Expect = 1e-05
 Identities = 11/30 (36%), Positives = 20/30 (66%)

Query: 39 IEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          + G +  +D++MNLVL D+EE+    + +K
Sbjct: 30 VRGMLRSYDQHMNLVLSDSEEIQSDGSGKK 59

>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 = 36.6 bits (85), Expect = 1e-05
 Identities = 9/33 (27%), Positives = 14/33 (42%)

Query: 36 DLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
               G ++  D Y NL L++AEE     +   
Sbjct: 17 STEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGT 49

>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 = 36.2 bits (84), Expect = 2e-05
 Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 2/33 (6%)

Query: 39 IEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLG 71
          I G +  FD+++NL+L+DAEE  I        G
Sbjct: 25 IRGILRSFDQHVNLLLEDAEE--IIDGNVYKRG 55

>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 = 35.9 bits (83), Expect = 4e-05
 Identities = 6/56 (10%), Positives = 17/56 (30%), Gaps = 4/56 (7%)

Query: 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRK 68
          PI ++          +            G++I  ++ MN  + +    +      +
Sbjct: 3  PIKVLHEAEGHIVTCET----NTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ 54

>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 = 31.6 bits (72), Expect = 0.003
 Identities = 7/26 (26%), Positives = 13/26 (50%)

Query: 39 IEGRIIGFDEYMNLVLDDAEEVHIKK 64
           +G +   D  +N+VL +A     +K
Sbjct: 23 YKGVLHAVDNQLNIVLANASNKAGEK 48

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	78
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.86
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.85
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.85
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.85
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.83
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.82
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.81
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.79
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.78
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.77
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.75
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.65
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.49
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	97.97
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	97.64
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	94.03
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	93.8
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	92.26
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	87.35

>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=99.86  E-value=4.5e-22  Score=117.67  Aligned_cols=66  Identities=23%  Similarity=0.386  Sum_probs=58.9

Q ss_pred             eecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947            9 IMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus         9 ~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      .|..|+++|+++++++  |.|+|++ +++++.|+|.|||+|||++|+||+|+. ++...+.+|.++|||.
T Consensus         2 ~~~~P~~~L~~~~~~~--V~V~lk~-~~~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~~g~~~IRG~   67 (75)
T d1ljoa_           2 AMVLPNQMVKSMVGKI--IRVEMKG-EENQLVGKLEGVDDYMNLYLTNAMECK-GEEKVRSLGEIVLRGN   67 (75)
T ss_dssp             CCCCHHHHHHHTTTSE--EEEEETT-CSSEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGG
T ss_pred             CccccHHHHHHhcCCE--EEEEEEC-CCEEEEEEEEEEcCCCcEEEeEEEEEc-CCCcEeEcceEEEeCC
Confidence            4789999999999976  9999974 358999999999999999999999995 6677889999999995

>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=99.85  E-value=1e-21  Score=114.48  Aligned_cols=63  Identities=29%  Similarity=0.503  Sum_probs=57.0

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..|+++|.++++++  |.|.+++  |+.+.|+|.+||+||||+|+||+|+. +++..+.+|.++|||.
T Consensus         1 ~~Pl~~L~~~~~~~--V~V~lk~--g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~l~~~~IRG~   63 (71)
T d1h641_           1 ERPLDVIHRSLDKD--VLVILKK--GFEFRGRLIGYDIHLNVVLADAEMIQ-DGEVVKRYGKIVIRGD   63 (71)
T ss_dssp             CCHHHHHHTTTTSE--EEEEETT--SEEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGG
T ss_pred             CCchHHHHHhCCCE--EEEEEcC--CCEEEEEEEEECCCCCeEEeeEEEEe-cCCcEeEcCcEEEECC
Confidence            37999999999976  8888865  89999999999999999999999995 6677889999999994

>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=99.85  E-value=1.1e-21  Score=114.75  Aligned_cols=63  Identities=29%  Similarity=0.428  Sum_probs=57.2

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..|+++|.++++++  |.|.+++  |+++.|+|.|||+|||++|+||+|+. .++..+.+|.++|||.
T Consensus         2 ~~Pl~~L~~~~~~~--V~V~lk~--g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~~g~~~IRG~   64 (72)
T d1i4k1_           2 PRPLDVLNRSLKSP--VIVRLKG--GREFRGTLDGYDIHMNLVLLDAEEIQ-NGEVVRKVGSVVIRGD   64 (72)
T ss_dssp             CCHHHHHHTTTTSE--EEEEEGG--GCEEEEEEEEECTTCCEEEEEEEEES-SSSEEEEEEEEEECGG
T ss_pred             CChHHHHHHhCCCE--EEEEECC--CCEEEEEEEEEcCCCCeEEeeEEEEe-cCCeEeEcceEEEeCC
Confidence            46999999999975  9999976  89999999999999999999999994 6677889999999994

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

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

Probab=99.85  E-value=1.6e-21  Score=114.64  Aligned_cols=64  Identities=31%  Similarity=0.407  Sum_probs=57.9

Q ss_pred             ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      +..|+++|+++++++  |.|++++  |+.|.|+|.+||+|||++|+||+|+. +++..+.+|.++|||.
T Consensus         4 ~~~Pl~~L~~~~~k~--V~V~lk~--g~~~~G~L~~~D~~mNl~L~~~~e~~-~~~~~~~~~~~~IRG~   67 (74)
T d1mgqa_           4 VQRPLDALGNSLNSP--VIIKLKG--DREFRGVLKSFDLHMNLVLNDAEELE-DGEVTRRLGTVLIRGD   67 (74)
T ss_dssp             TTCTTHHHHHTTTSE--EEEEETT--TEEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGG
T ss_pred             ccCcHHHHHHhCCCe--EEEEECC--CCEEEEEEEEECCCCCeEEeeEEEEe-CCCeEeEcceEEEeCC
Confidence            567999999999975  9999966  99999999999999999999999995 6677889999999994

>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=99.83  E-value=3.1e-21  Score=118.09  Aligned_cols=66  Identities=18%  Similarity=0.336  Sum_probs=53.7

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC-------------CeeeeeeEEEEec
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK-------------NTRKPLGFFSKET   77 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~-------------~~~~~lG~ilir~   77 (78)
                      +.|+++|.+++..+++|.|++++  ++.+.|+|.|||+||||||+||+|++...             ...+.+|.+||||
T Consensus         1 tGPl~~l~~~~~~~~rV~V~lr~--~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRG   78 (93)
T d1b34b_           1 TGPLSVLTQSVKNNTQVLINCRN--NKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRG   78 (93)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEETT--SCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECG
T ss_pred             CCcHHHHHHHHhCCcEEEEEECC--CCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeC
Confidence            47999999999655679999965  89999999999999999999999986431             1357899999999


Q ss_pred             C
Q 034947           78 T   78 (78)
Q Consensus        78 ~   78 (78)
                      .
T Consensus        79 d   79 (93)
T d1b34b_          79 D   79 (93)
T ss_dssp             G
T ss_pred             C
Confidence            3

>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=99.82  E-value=3.3e-21  Score=117.21  Aligned_cols=66  Identities=29%  Similarity=0.436  Sum_probs=56.3

Q ss_pred             eecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec--------------CCeeeeeeEEE
Q 034947            9 IMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK--------------KNTRKPLGFFS   74 (78)
Q Consensus         9 ~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~--------------~~~~~~lG~il   74 (78)
                      .|..|+++|+++++++  |.|.+++  |++|.|+|.|||+||||+|+||+|++..              .+..+.+|.+|
T Consensus         2 ~~~~Pl~~L~~~l~k~--V~V~l~~--gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~   77 (92)
T d2fwka1           2 NIILPLALIDKCIGNR--IYVVMKG--DKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETIL   77 (92)
T ss_dssp             CCCCHHHHHHHTBTSB--CEEEETT--TEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEE
T ss_pred             CccChHHHHHHHcCCE--EEEEEcC--CCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEE
Confidence            4789999999999976  8888855  9999999999999999999999998542              12457899999


Q ss_pred             EecC
Q 034947           75 KETT   78 (78)
Q Consensus        75 ir~~   78 (78)
                      |||.
T Consensus        78 iRG~   81 (92)
T d2fwka1          78 LSGN   81 (92)
T ss_dssp             ECGG
T ss_pred             EeCC
Confidence            9993

>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=99.81  E-value=6.4e-20  Score=108.19  Aligned_cols=63  Identities=24%  Similarity=0.367  Sum_probs=55.9

Q ss_pred             cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      ..|.++|.++++++  |.|.+++  |+.+.|+|.|||+|||++|+||+|+. .+.+.+.+|.++|||.
T Consensus         6 ~~~~~~L~~~~~~~--V~V~lk~--g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~~~~v~iRG~   68 (76)
T d1th7a1           6 ETAHKVLAESLNNL--VLVKLKG--NKEVRGMLRSYDQHMNLVLSDSEEIQ-SDGSGKKLGTIVIRGD   68 (76)
T ss_dssp             HHHHHHHHHHTTSE--EEEEETT--TEEEEEEEEEECTTCCEEEEEEEEEC-SSSCEEEEEEEEECGG
T ss_pred             ccHHHHHHHhCCCE--EEEEECC--CCEEEEEEEEECCCCCEEEeEEEEEe-cCCcccCcceEEEECC
Confidence            45999999999976  8888865  99999999999999999999999995 5566778999999994

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.1e-19  Score=105.10  Aligned_cols=62  Identities=11%  Similarity=0.080  Sum_probs=55.2

Q ss_pred             ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      .|+.+|.++.++.  |+|+||+  |+.+.|+|.+||.|||++|+||+|+. .+.....+|.++|||.
T Consensus         2 ~Pl~~L~~~~g~~--V~VeLkn--g~~~~G~L~~~D~~mNi~L~~~~~~~-~~~~~~~~~~v~IRG~   63 (72)
T d1d3ba_           2 VPIKVLHEAEGHI--VTCETNT--GEVYRGKLIEAEDNMNCQMSNITVTY-RDGRVAQLEQVYIRGC   63 (72)
T ss_dssp             CHHHHHHHTTTSE--EEEEETT--SCEEEEEEEEECTTCCEEEEEEEEEC-TTSCEEEEEEEEECGG
T ss_pred             CchHHHHhcCCCE--EEEEECC--CeEEEEEEEEEcCCeeEEEEEEEEEc-CCCcEeEcCeEEEECC
Confidence            5999999999965  9999976  88999999999999999999999985 5556678999999994

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

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

Probab=99.78  E-value=3.5e-19  Score=104.00  Aligned_cols=60  Identities=22%  Similarity=0.251  Sum_probs=52.6

Q ss_pred             hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      +-.+|+++++++  |.|+|++  |+++.|+|.+||+|||++|+||+|+. ++ ..+.+|.++|||.
T Consensus         3 ~~~~L~~~~~k~--V~V~Lk~--g~~~~G~L~~~D~~mNivL~~~~e~~-~~-~~~~~g~v~iRG~   62 (71)
T d1i8fa_           3 LGATLQDSIGKQ--VLVKLRD--SHEIRGILRSFDQHVNLLLEDAEEII-DG-NVYKRGTMVVRGE   62 (71)
T ss_dssp             HHHHHHTTTTSE--EEEEEGG--GEEEEEEEEEECTTCCEEEEEEEEEE-TT-EEEEEEEEEECGG
T ss_pred             HhHHHHHhCCCE--EEEEECC--CCEEEEEEEEECCCcceEEccEEEEE-CC-CEEEcceEEEeCC
Confidence            457899999976  9999976  89999999999999999999999985 43 5678999999994

>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=99.77  E-value=1.4e-19  Score=105.08  Aligned_cols=58  Identities=21%  Similarity=0.336  Sum_probs=50.6

Q ss_pred             HHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           17 IFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        17 L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      |.++++++  |.|+||+ ++++|+|+|.+||+|||++|+||+|. .+++....+|.++|||.
T Consensus         1 L~~~~~~~--V~V~Lk~-~~~~~~G~L~~~D~~mNlvL~~~~e~-~~~~~~~~lg~~~IRG~   58 (68)
T d1n9ra_           1 LKGLVNHR--VGVKLKF-NSTEYRGTLVSTDNYFNLQLNEAEEF-VAGVSHGTLGEIFIRCN   58 (68)
T ss_dssp             CGGGTTSE--EEEEESS-TTEEEEEEEEECCTTTCEEEEEEEEE-ETTEEEEECCSEEECGG
T ss_pred             ChhHCCCE--EEEEEEc-CCEEEEEEEEEECCcCceEEeeEEEE-ecCCcccCcCeEEEECC
Confidence            45688865  9999984 36899999999999999999999998 47777889999999994

>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=99.75  E-value=5.6e-19  Score=105.16  Aligned_cols=58  Identities=22%  Similarity=0.391  Sum_probs=48.3

Q ss_pred             HHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec---------CCeeeeeeEEEEecC
Q 034947           17 IFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK---------KNTRKPLGFFSKETT   78 (78)
Q Consensus        17 L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~---------~~~~~~lG~ilir~~   78 (78)
                      |.++++++  |.|.+  .+||.+.|+|.|||+||||||+||+|++..         .+..+.+|.++|||.
T Consensus         3 L~~~l~~r--v~V~l--~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~   69 (81)
T d1d3bb_           3 MLQHIDYR--MRCIL--QDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGE   69 (81)
T ss_dssp             CGGGTTSE--EEEEE--TTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGG
T ss_pred             hHHHCCCE--EEEEE--cCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCC
Confidence            45789976  77777  459999999999999999999999998531         124688999999994

>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=99.65  E-value=1.7e-16  Score=94.35  Aligned_cols=60  Identities=20%  Similarity=0.281  Sum_probs=52.7

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      +.||.++.++.  |+|.||+  |..+.|+|.++|.|||++|+||++.. .+.....+|.++|||.
T Consensus         3 v~fL~~~~g~~--V~VeLkn--g~~~~G~L~~~D~~MNl~L~~~~~~~-~~~~~~~~~~v~IRG~   62 (80)
T d1b34a_           3 VRFLMKLSHET--VTIELKN--GTQVHGTITGVDVSMNTHLKAVKMTL-KNREPVQLETLSIRGN   62 (80)
T ss_dssp             HHHHHTCTTCE--EEEEETT--CCEEEEEEEEECTTCCEEEEEEEEEC-TTSCCEEEEEEEECGG
T ss_pred             HHHHHHcCCCE--EEEEECC--CCEEEEEEEEEcCCcEEEEEEEEEEc-CCCCEEEcccEEEcCC
Confidence            46899999965  9999976  89999999999999999999999985 5555678999999994

>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=99.49  E-value=1.4e-14  Score=92.71  Aligned_cols=56  Identities=16%  Similarity=0.178  Sum_probs=48.3

Q ss_pred             HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947           14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT   78 (78)
Q Consensus        14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~   78 (78)
                      +..|.++++++  |.|.|++  |+.+.|+|.+||+|||++|+||++.  +++   +++.++|||.
T Consensus         2 ~~~L~~~~gk~--V~VeLkn--g~~~~G~L~~~D~~mNivL~da~~~--~~~---k~~~v~IRG~   57 (127)
T d1m5q1_           2 VAELNNLLGRE--VQVVLSN--GEVYKGVLHAVDNQLNIVLANASNK--AGE---KFNRVFIMYR   57 (127)
T ss_dssp             HHHHHTTTTSE--EEEEETT--SCEEEEEEEEECTTCCEEEEEEEET--TCC---EEEEEEECGG
T ss_pred             hhHHHHhCCCE--EEEEECC--CCEEEEEEEEECCCceEEEeEEEEC--CCC---cccEEEEeCC
Confidence            46799999965  9999976  8999999999999999999999986  222   5899999994

>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=97.97  E-value=6.1e-06  Score=46.69  Aligned_cols=39  Identities=18%  Similarity=0.596  Sum_probs=33.4

Q ss_pred             HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947           15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD   56 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d   56 (78)
                      .+|+.+..++.+|+|.|.+  |.+++|.+.|||+|. +.|++
T Consensus         5 ~fLn~~rk~~~~VtifL~n--Gvkl~G~I~~fD~ft-vLL~~   43 (66)
T d1u1sa1           5 PYLNTLRKERVPVSIYLVN--GIKLQGQIESFDQFV-ILLKN   43 (66)
T ss_dssp             HHHHHHHHTTCCEEEEETT--SCEEEEEEEEECSSE-EEEES
T ss_pred             HHHHHHHHcCCcEEEEEEc--CcEEEEEEEEEcceE-EEEEC
Confidence            4788888888999999977  899999999999997 45543

>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=97.64  E-value=3.5e-05  Score=42.72  Aligned_cols=42  Identities=12%  Similarity=0.414  Sum_probs=34.2

Q ss_pred             HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceE
Q 034947           15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAE   58 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~   58 (78)
                      .+|+.+-.++.+|+|.|.+  |.+++|.+.|||.|.=+.-.+..
T Consensus         5 ~fln~lr~~~~~VtifL~n--Gvkl~G~I~~fD~ftvlL~~~~~   46 (60)
T d1kq1a_           5 KALENFKANQTEVTVFFLN--GFQMKGVIEEYDKYVVSLNSQGK   46 (60)
T ss_dssp             HHHHHHHHHTCEEEEEETT--SCEEEEEEEEECSSEEEEEETTE
T ss_pred             HHHHHHHHcCCcEEEEEEC--CcEEEEEEEEEcceEEEEEeCCc
Confidence            4778888888999999977  99999999999999955444433

>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=94.03  E-value=0.11  Score=26.32  Aligned_cols=47  Identities=21%  Similarity=0.162  Sum_probs=32.9

Q ss_pred             hhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEe
Q 034947           20 FLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKE   76 (78)
Q Consensus        20 ~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir   76 (78)
                      |++++  |.|.  . .+.++.|+-.|+|+.=.|+|+....     .+.-.-|+|-||
T Consensus         1 f~gk~--V~v~--~-g~~~i~G~a~gId~~G~Lll~t~~g-----~~~~~sGEVSlR   47 (47)
T d1biaa2           1 FINRP--VKLI--I-GDKEIFGISRGIDKQGALLLEQDGI-----IKPWMGGEISLR   47 (47)
T ss_dssp             TTTSE--EEEE--E-TTEEEEEEEEEECTTSCEEEEETTE-----EEEESSCEEEEC
T ss_pred             CCCCE--EEEE--E-CCeEEEEEEeeECCCCcEEEEECCC-----EEEEEEEEEEeC
Confidence            46765  5553  3 3588999999999999999974332     234556777665

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

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

Probab=93.80  E-value=0.12  Score=28.15  Aligned_cols=42  Identities=21%  Similarity=0.387  Sum_probs=30.6

Q ss_pred             HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEE
Q 034947           15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVH   61 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~   61 (78)
                      ..|.++-+++  |-|.+  ++...|.|+|.-||+-. +.|.|++.+.
T Consensus         5 ktL~~WKg~k--vAv~v--gsehSFtGiledFDeEv-iLL~dV~D~~   46 (66)
T d1ycya1           5 KVLKEWKGHK--VAVSV--GGDHSFTGTLEDFDEEV-ILLKDVVDVI   46 (66)
T ss_dssp             HHHHHHTTSE--EEEEE--C----CEEEEEEECSSE-EEEEEEEETT
T ss_pred             HHHHHhCCcE--EEEEe--cCcceeEEEhhhcCcce-EeehhhHHHh
Confidence            3567777766  66666  67889999999999998 8899999873

>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=92.26  E-value=0.31  Score=27.54  Aligned_cols=55  Identities=16%  Similarity=0.304  Sum_probs=40.2

Q ss_pred             hhcCcceEEEEEEecCCeEEEEEEEEeccccc-eeEeceEEEEecCC--------eeeeeeEEEEecC
Q 034947           20 FLQSKARIQIWLFEQKDLRIEGRIIGFDEYMN-LVLDDAEEVHIKKN--------TRKPLGFFSKETT   78 (78)
Q Consensus        20 ~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mN-lvL~da~E~~~~~~--------~~~~lG~ilir~~   78 (78)
                      |++++    |.|..+.+.+|+|+|...|..=+ +.|+|+.-+-.++.        ....++.|+.||.
T Consensus         2 yIGs~----IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgs   65 (80)
T d2vxfa1           2 YIGSK----ISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGS   65 (80)
T ss_dssp             STTSE----EEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETT
T ss_pred             ccCCE----EEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCc
Confidence            56776    77777889999999999997764 78999887732321        2345677887774

>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=87.35  E-value=0.23  Score=26.88  Aligned_cols=37  Identities=22%  Similarity=0.413  Sum_probs=26.4

Q ss_pred             HHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccccceeE
Q 034947           15 NLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVL   54 (78)
Q Consensus        15 ~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~mNlvL   54 (78)
                      .-+.+++++.  |.|.|+.  ++-+.+.|.|.++|+-. +.|
T Consensus         7 ~~f~r~~G~~--v~v~l~~p~~g~k~f~G~L~~~~~~~-i~l   45 (74)
T d1ib8a1           7 DAVAGAVGKY--IHVGLYQAIDKQKVFEGTLLAFEEDE-LTM   45 (74)
T ss_dssp             HHHHHHCSEE--EEEECSSCSSSCSEEEEEEEEEETTE-EEE
T ss_pred             HHHHHhCCCE--EEEEEecccCCceEEEEEEEeecCCe-EEE
Confidence            3456788966  7777653  34578999999999864 444