Citrus Sinensis ID: 035338

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60-------
Protein Sequence
MASTKVQRIMTQPINLIFRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK
Secondary Structure (PSIPRED)
cccccEEEEEEccHHHHHHHHHHHHHHHcEEEEEcEEEEEEccccccccEEEEEEccEEEEEEEccc
Secondary Structure Prediction (SSPRO)
cccccEEEEEccHHHHHHHHHHHcHHHHHHHHHHcHHHEcccccccccccEEEEccccEEEEEEccc
Coil and Loop (DISEMBL)
MASTKVQRIMTQPINLIFRFLQSGFDEYMNLVLDdaeevhikkntrkplgrillkgdnITLMMNTGK
Flexible Loop (DISEMBL)
mastkvqriMTQPINLIFRFLQSGFDEYMNLVLDDAEevhikkntrkplgrillkgdnitlmmntgk
Low Complexity Region (SEG)
MASTKVQRIMTQPINLIFRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK
Disordered region (IsUnstruct)
*******RIMTQPINLIFRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITL******
Disordered Region (DISOPRED)
******Q***TQPINLIFRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNT**
Disordered Region (DISEMBL)
MASTKVQRIMTQPINLIFRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK
Disordered Region (DISPRO)
***TKVQRIMTQPINLIFRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG*
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASTKVQRIMTQPINLIFRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK
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	67	2.2.26 [Sep-21-2011]
Q7ZUG0	92	Small nuclear ribonucleop	yes	no	0.865	0.630	0.594	5e-19
A1XQR9	92	Small nuclear ribonucleop	yes	no	0.955	0.695	0.529	4e-18
P62305	92	Small nuclear ribonucleop	yes	no	0.910	0.663	0.548	7e-18
P62304	92	Small nuclear ribonucleop	yes	no	0.910	0.663	0.548	7e-18
P62303	92	Small nuclear ribonucleop	yes	no	0.910	0.663	0.548	7e-18
A4FUI2	92	Small nuclear ribonucleop	no	no	0.910	0.663	0.548	7e-18
Q9VLV5	94	Probable small nuclear ri	yes	no	0.970	0.691	0.523	2e-17
A8XDT0	90	Probable small nuclear ri	N/A	no	0.925	0.688	0.469	9e-15
Q9XTU6	90	Probable small nuclear ri	yes	no	0.925	0.688	0.457	6e-14
Q9USZ3	84	Small nuclear ribonucleop	yes	no	0.880	0.702	0.481	2e-11

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

 Score = 93.2 bits (230), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 47/79 (59%), Positives = 54/79 (68%), Gaps = 21/79 (26%)

Query: 5  KVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHIKK 43
          KVQ++M QPINLIFR+LQ+                     GFDEYMNLVLDDAEEVH+K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRISVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKT 68

Query: 44 NTRKPLGRILLKGDNITLM 62
            RKPLGRI+LKGDNITL+
Sbjct: 69 KNRKPLGRIMLKGDNITLL 87

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 = 90.1 bits (222), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/85 (52%), Positives = 55/85 (64%), Gaps = 21/85 (24%)

Query: 3  STKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHI 41
          + KVQ++M QPINLIFR+LQ+                     GFDEYMNLVLDDAEE+H 
Sbjct: 7  AQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHS 66

Query: 42 KKNTRKPLGRILLKGDNITLMMNTG 66
          K  +RK LGRI+LKGDNITL+ +  
Sbjct: 67 KTKSRKQLGRIMLKGDNITLLQSVS 91

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 = 89.0 bits (219), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 45/82 (54%), Positives = 54/82 (65%), Gaps = 21/82 (25%)

Query: 5  KVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHIKK 43
          KVQ++M QPINLIFR+LQ+                     GFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query: 44 NTRKPLGRILLKGDNITLMMNT 65
           +RK LGRI+LKGDNITL+ + 
Sbjct: 69 KSRKQLGRIMLKGDNITLLQSV 90

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 = 89.0 bits (219), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 45/82 (54%), Positives = 54/82 (65%), Gaps = 21/82 (25%)

Query: 5  KVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHIKK 43
          KVQ++M QPINLIFR+LQ+                     GFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query: 44 NTRKPLGRILLKGDNITLMMNT 65
           +RK LGRI+LKGDNITL+ + 
Sbjct: 69 KSRKQLGRIMLKGDNITLLQSV 90

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 = 89.0 bits (219), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 45/82 (54%), Positives = 54/82 (65%), Gaps = 21/82 (25%)

Query: 5  KVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHIKK 43
          KVQ++M QPINLIFR+LQ+                     GFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query: 44 NTRKPLGRILLKGDNITLMMNT 65
           +RK LGRI+LKGDNITL+ + 
Sbjct: 69 KSRKQLGRIMLKGDNITLLQSV 90

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 = 89.0 bits (219), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 45/82 (54%), Positives = 54/82 (65%), Gaps = 21/82 (25%)

Query: 5  KVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHIKK 43
          KVQ++M QPINLIFR+LQ+                     GFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query: 44 NTRKPLGRILLKGDNITLMMNT 65
           +RK LGRI+LKGDNITL+ + 
Sbjct: 69 KSRKQLGRIMLKGDNITLLQSV 90

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 = 87.8 bits (216), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 45/86 (52%), Positives = 55/86 (63%), Gaps = 21/86 (24%)

Query: 2  ASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVH 40
           + KVQ++M QPINLIFR+LQ+                     GFDEYMNLVLDDAEEV+
Sbjct: 5  GNPKVQKVMVQPINLIFRYLQNRSRVQVWLYENISLRIEGHIVGFDEYMNLVLDDAEEVY 64

Query: 41 IKKNTRKPLGRILLKGDNITLMMNTG 66
          +K   R+ LGRI+LKGDNITL+ N  
Sbjct: 65 VKTRQRRNLGRIMLKGDNITLIQNVS 90

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 = 79.0 bits (193), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 39/83 (46%), Positives = 53/83 (63%), Gaps = 21/83 (25%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          M+  K+Q++M QP+NLIFR+LQ+                     GFDE+MN+V D+AEEV
Sbjct: 1  MSQRKIQKVMVQPVNLIFRYLQNRTRVQIWLYEDVTHRLEGYIIGFDEFMNVVFDEAEEV 60

Query: 40 HIKKNTRKPLGRILLKGDNITLM 62
          ++K   R  +GRILLKGDNITL+
Sbjct: 61 NMKTKGRNKIGRILLKGDNITLI 83

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 = 76.3 bits (186), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 38/83 (45%), Positives = 53/83 (63%), Gaps = 21/83 (25%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          M++ K+ ++M QP+NLIFR+LQ+                     GFDE+MN+V D+AEEV
Sbjct: 1  MSTRKLNKVMVQPVNLIFRYLQNRTRVQIWLYEDVTHRLEGYIIGFDEFMNVVFDEAEEV 60

Query: 40 HIKKNTRKPLGRILLKGDNITLM 62
          ++K   R  +GRILLKGDNITL+
Sbjct: 61 NMKTKGRNKIGRILLKGDNITLI 83

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 = 67.8 bits (164), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 39/81 (48%), Positives = 48/81 (59%), Gaps = 22/81 (27%)

Query: 3  STKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHI 41
          S +VQ++M  PIN IF+ LQ                      GFDE+MN+VLDDA +V  
Sbjct: 2  SGRVQKVMIPPINFIFKLLQQHTPVSIWLFEQTDIRLQGQIRGFDEFMNIVLDDAVQVDA 61

Query: 42 KKNTRKPLGRILLKGDNITLM 62
          K N R+ LGRILLKGDNITL+
Sbjct: 62 KNNKRE-LGRILLKGDNITLI 81

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	67
15224217	88	putative small nuclear ribonucleoprotein	1.0	0.761	0.738	3e-26
242051601	88	hypothetical protein SORBIDRAFT_03g00195	1.0	0.761	0.715	1e-25
357146132	88	PREDICTED: small nuclear ribonucleoprote	1.0	0.761	0.715	3e-25
313586495	88	small nuclear ribonucleoprotein E [Hevea	1.0	0.761	0.727	3e-25
357145040	88	PREDICTED: small nuclear ribonucleoprote	1.0	0.761	0.704	4e-25
18417572	88	small nuclear ribonucleoprotein E [Arabi	1.0	0.761	0.715	4e-25
225455956	88	PREDICTED: small nuclear ribonucleoprote	1.0	0.761	0.704	7e-25
195606896	88	small nuclear ribonucleoprotein E [Zea m	1.0	0.761	0.693	9e-25
282848216	88	small nuclear ribonucleoprotein polypept	1.0	0.761	0.704	9e-25
115443949	88	Os02g0126700 [Oryza sativa Japonica Grou	1.0	0.761	0.704	1e-24

>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 =  122 bits (305), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 66/88 (75%), Gaps = 21/88 (23%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          MASTKVQRIMTQPINLIFRFLQS                     GFDEYMNLVLD+AEEV
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRITGFDEYMNLVLDEAEEV 60

Query: 40 HIKKNTRKPLGRILLKGDNITLMMNTGK 67
           IKKNTRKPLGRILLKGDNITLMMNTGK
Sbjct: 61 SIKKNTRKPLGRILLKGDNITLMMNTGK 88

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 =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 63/88 (71%), Positives = 66/88 (75%), Gaps = 21/88 (23%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          MASTKVQRIMTQPINLIFRFLQS                     GFDEYMNLVLDDAEE+
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEI 60

Query: 40 HIKKNTRKPLGRILLKGDNITLMMNTGK 67
          ++KKNTRK LGRILLKGDNITLMMNTGK
Sbjct: 61 NVKKNTRKSLGRILLKGDNITLMMNTGK 88

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  119 bits (297), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 63/88 (71%), Positives = 66/88 (75%), Gaps = 21/88 (23%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          MASTKVQRIMTQPINLIFRFLQS                     GFDEYMNLVL+DAEE+
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDMRIEGRIIGFDEYMNLVLEDAEEI 60

Query: 40 HIKKNTRKPLGRILLKGDNITLMMNTGK 67
          +IKKNTRK LGRILLKGDNITLMMNTGK
Sbjct: 61 NIKKNTRKSLGRILLKGDNITLMMNTGK 88

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313586495|gb|ADR71258.1| small nuclear ribonucleoprotein E [Hevea brasiliensis]

 Score =  119 bits (297), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 64/88 (72%), Positives = 65/88 (73%), Gaps = 21/88 (23%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          MASTKVQRIMTQPINLIFRFLQS                     GFDEYMNLVLDDAEEV
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDMRIEGRIIGFDEYMNLVLDDAEEV 60

Query: 40 HIKKNTRKPLGRILLKGDNITLMMNTGK 67
          +IKK TRK LGRILLKGDNITLMMNTGK
Sbjct: 61 NIKKKTRKSLGRILLKGDNITLMMNTGK 88

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 66/88 (75%), Gaps = 21/88 (23%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          MASTKVQRIMTQPINLIFRFLQS                     GFDEYMNLVL+DAEE+
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLEDAEEI 60

Query: 40 HIKKNTRKPLGRILLKGDNITLMMNTGK 67
          ++KKNTRK LGRILLKGDNITLMMNTGK
Sbjct: 61 NVKKNTRKSLGRILLKGDNITLMMNTGK 88

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18417572|ref|NP_567844.1| small nuclear ribonucleoprotein E [Arabidopsis thaliana] gi|297798942|ref|XP_002867355.1| hypothetical protein ARALYDRAFT_913445 [Arabidopsis lyrata subsp. lyrata] gi|21593343|gb|AAM65292.1| small nuclear ribonucleoprotein homolog [Arabidopsis thaliana] gi|51968366|dbj|BAD42875.1| small nuclear ribonucleoprotein homolog [Arabidopsis thaliana] gi|51968768|dbj|BAD43076.1| small nuclear ribonucleoprotein homolog [Arabidopsis thaliana] gi|51971773|dbj|BAD44551.1| small nuclear ribonucleoprotein homolog [Arabidopsis thaliana] gi|88010920|gb|ABD38873.1| At4g30330 [Arabidopsis thaliana] gi|297313191|gb|EFH43614.1| hypothetical protein ARALYDRAFT_913445 [Arabidopsis lyrata subsp. lyrata] gi|332660353|gb|AEE85753.1| small nuclear ribonucleoprotein E [Arabidopsis thaliana]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 63/88 (71%), Positives = 64/88 (72%), Gaps = 21/88 (23%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          MASTKVQRIMTQPINLIFRFLQS                     GFDEYMNLVLD+AEEV
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRITGFDEYMNLVLDEAEEV 60

Query: 40 HIKKNTRKPLGRILLKGDNITLMMNTGK 67
           IKK TRKPLGRILLKGDNITLMMN GK
Sbjct: 61 SIKKKTRKPLGRILLKGDNITLMMNAGK 88

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  117 bits (294), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 66/88 (75%), Gaps = 21/88 (23%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          MA+TKVQRIMTQPINLIFRFLQS                     GFDEYMNLVLDDAEEV
Sbjct: 1  MATTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60

Query: 40 HIKKNTRKPLGRILLKGDNITLMMNTGK 67
          ++KKNT+K LGRILLKGDNITLMMNTGK
Sbjct: 61 NVKKNTKKTLGRILLKGDNITLMMNTGK 88

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  117 bits (293), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 61/88 (69%), Positives = 66/88 (75%), Gaps = 21/88 (23%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          MASTKVQRIMTQPINLIFRFLQS                     GFDEYMNLVL+DAEE+
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLEDAEEI 60

Query: 40 HIKKNTRKPLGRILLKGDNITLMMNTGK 67
          ++KKNTRK LGRILLKGDNITLMMN+GK
Sbjct: 61 NVKKNTRKSLGRILLKGDNITLMMNSGK 88

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  117 bits (293), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 65/88 (73%), Gaps = 21/88 (23%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          MASTKVQRIMTQPINLIFRFLQS                     GFDEYMNLVLDDAEEV
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60

Query: 40 HIKKNTRKPLGRILLKGDNITLMMNTGK 67
          ++KK TRK LGRILLKGDNITLMMN+GK
Sbjct: 61 NVKKKTRKSLGRILLKGDNITLMMNSGK 88

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115443949|ref|NP_001045754.1| Os02g0126700 [Oryza sativa Japonica Group] gi|41053075|dbj|BAD08019.1| putative small nuclear ribonucleoprotein polypeptide E [Oryza sativa Japonica Group] gi|113535285|dbj|BAF07668.1| Os02g0126700 [Oryza sativa Japonica Group] gi|215686543|dbj|BAG88796.1| unnamed protein product [Oryza sativa Japonica Group] gi|218189970|gb|EEC72397.1| hypothetical protein OsI_05681 [Oryza sativa Indica Group] gi|222622094|gb|EEE56226.1| hypothetical protein OsJ_05214 [Oryza sativa Japonica Group]

 Score =  117 bits (292), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 66/88 (75%), Gaps = 21/88 (23%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          MASTKVQRIMTQPINLIFRFLQS                     GFDEYMNLVLD+AEE+
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEI 60

Query: 40 HIKKNTRKPLGRILLKGDNITLMMNTGK 67
          +IKK+TRK LGRILLKGDNITLMMNTGK
Sbjct: 61 NIKKDTRKSLGRILLKGDNITLMMNTGK 88

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

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	67
TAIR|locus:2118781	88	AT4G30330 "AT4G30330" [Arabido	0.671	0.511	0.888	9.4e-27
ZFIN|ZDB-GENE-040426-1112	92	snrpe "small nuclear ribonucle	0.611	0.445	0.804	2.2e-20
UNIPROTKB|E1BHK8	92	SNRPE "Small nuclear ribonucle	0.611	0.445	0.731	2.7e-18
TAIR|locus:2053989	88	AT2G18740 "AT2G18740" [Arabido	0.671	0.511	0.933	9.5e-18
GENEDB_PFALCIPARUM|MAL13P1.253	93	MAL13P1.253 "small nuclear rib	0.597	0.430	0.7	1.8e-17
UNIPROTKB|Q8IDJ7	93	MAL13P1.253 "Small nuclear rib	0.597	0.430	0.7	1.8e-17
WB|WBGene00004919	90	snr-6 [Caenorhabditis elegans	0.582	0.433	0.666	5.2e-16
POMBASE|SPBC11G11.06c	84	sme1 "Sm snRNP core protein Sm	0.567	0.452	0.717	3.9e-14
RGD|2319339	92	LOC100361838 "small nuclear ri	0.910	0.663	0.540	3.4e-13
UNIPROTKB|P62303	92	SNRPE "Small nuclear ribonucle	0.910	0.663	0.540	5.6e-13

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

 Score = 205 (77.2 bits), Expect = 9.4e-27, Sum P(2) = 9.4e-27
 Identities = 40/45 (88%), Positives = 42/45 (93%)

Query:    23 SGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK 67
             +GFDEYMNLVLD+AEEV IKK TRKPLGRILLKGDNITLMMN GK
Sbjct:    44 TGFDEYMNLVLDEAEEVSIKKKTRKPLGRILLKGDNITLMMNAGK 88

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 = 177 (67.4 bits), Expect = 2.2e-20, Sum P(2) = 2.2e-20
 Identities = 33/41 (80%), Positives = 37/41 (90%)

Query:    24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 64
             GFDEYMNLVLDDAEEVH+K   RKPLGRI+LKGDNITL+ +
Sbjct:    49 GFDEYMNLVLDDAEEVHMKTKNRKPLGRIMLKGDNITLLQS 89

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|E1BHK8 SNRPE "Small nuclear ribonucleoprotein E" [Bos taurus (taxid:9913)]

 Score = 157 (60.3 bits), Expect = 2.7e-18, Sum P(2) = 2.7e-18
 Identities = 30/41 (73%), Positives = 35/41 (85%)

Query:    24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 64
             GFDE MNLVLDDAEE+H K  +RK LGRI+LKGDNITL+ +
Sbjct:    49 GFDECMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQS 89

GO:0005681 "spliceosomal complex" evidence=IEA

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

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

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 42/45 (93%), Positives = 44/45 (97%)

Query:    23 SGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK 67
             +GFDEYMNLVLD+AEEV IKKNTRKPLGRILLKGDNITLMMNTGK
Sbjct:    44 TGFDEYMNLVLDEAEEVSIKKNTRKPLGRILLKGDNITLMMNTGK 88

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

GENEDB_PFALCIPARUM|MAL13P1.253 MAL13P1.253 "small nuclear ribonucleoprotein, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 155 (59.6 bits), Expect = 1.8e-17, Sum P(2) = 1.8e-17
 Identities = 28/40 (70%), Positives = 35/40 (87%)

Query:    24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 63
             GFDEYMN+VLD  +E+ +KKNT+K LG+ILLKGD ITL+M
Sbjct:    47 GFDEYMNMVLDQTKEISVKKNTKKELGKILLKGDTITLIM 86

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

GO:0006396 "RNA processing" evidence=ISS

UNIPROTKB|Q8IDJ7 MAL13P1.253 "Small nuclear ribonucleoprotein, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 155 (59.6 bits), Expect = 1.8e-17, Sum P(2) = 1.8e-17
 Identities = 28/40 (70%), Positives = 35/40 (87%)

Query:    24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 63
             GFDEYMN+VLD  +E+ +KKNT+K LG+ILLKGD ITL+M
Sbjct:    47 GFDEYMNMVLDQTKEISVKKNTKKELGKILLKGDTITLIM 86

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

GO:0006396 "RNA processing" evidence=ISS

WB|WBGene00004919 snr-6 [Caenorhabditis elegans (taxid:6239)]

 Score = 138 (53.6 bits), Expect = 5.2e-16, Sum P(2) = 5.2e-16
 Identities = 26/39 (66%), Positives = 33/39 (84%)

Query:    24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
             GFDE+MN+V D+AEEV++K   R  +GRILLKGDNITL+
Sbjct:    45 GFDEFMNVVFDEAEEVNMKTKGRNKIGRILLKGDNITLI 83

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

GO:0000003 "reproduction" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0032940 "secretion by cell" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

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

GO:0006997 "nucleus organization" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

GO:0006915 "apoptotic process" evidence=IMP

GO:0043186 "P granule" evidence=IDA

POMBASE|SPBC11G11.06c sme1 "Sm snRNP core protein Sme1" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 136 (52.9 bits), Expect = 3.9e-14, Sum P(2) = 3.9e-14
 Identities = 28/39 (71%), Positives = 33/39 (84%)

Query:    24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
             GFDE+MN+VLDDA +V  K N R+ LGRILLKGDNITL+
Sbjct:    44 GFDEFMNIVLDDAVQVDAKNNKRE-LGRILLKGDNITLI 81

GO:0000395 "mRNA 5'-splice site recognition" evidence=IC

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005685 "U1 snRNP" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

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

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

RGD|2319339 LOC100361838 "small nuclear ribonucleoprotein E-like" [Rattus norvegicus (taxid:10116)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 33/61 (54%), Positives = 46/61 (75%)

Query:     4 TKVQRIMTQPINLIFRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 63
             +++Q  + + +N+  +    GFDEYMNLVLDDAEE+H K  +RK LGRI+LKGDNITL+ 
Sbjct:    29 SRIQVWLYEQVNIRIKGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQ 88

Query:    64 N 64
             +
Sbjct:    89 S 89

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

GO:0005681 "spliceosomal complex" evidence=IEA

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

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 33/61 (54%), Positives = 45/61 (73%)

Query:     4 TKVQRIMTQPINLIFRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 63
             +++Q  + + +N+       GFDEYMNLVLDDAEE+H K  +RK LGRI+LKGDNITL+ 
Sbjct:    29 SRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQ 88

Query:    64 N 64
             +
Sbjct:    89 S 89

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

---

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)
P62305	RUXE_MOUSE	No assigned EC number	0.5487	0.9104	0.6630	yes	no
P62304	RUXE_HUMAN	No assigned EC number	0.5487	0.9104	0.6630	yes	no
Q9VLV5	RUXE_DROME	No assigned EC number	0.5232	0.9701	0.6914	yes	no
P62303	RUXE_CHICK	No assigned EC number	0.5487	0.9104	0.6630	yes	no
Q7ZUG0	RUXE_DANRE	No assigned EC number	0.5949	0.8656	0.6304	yes	no
A1XQR9	RUXE_PIG	No assigned EC number	0.5294	0.9552	0.6956	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	67
cd01718	79	cd01718, Sm_E, Sm protein E	5e-34
PTZ00138	89	PTZ00138, PTZ00138, small nuclear ribonucleoprotei	3e-27
smart00651	67	smart00651, Sm, snRNP Sm proteins	6e-10
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	7e-10
pfam01423	66	pfam01423, LSM, LSM domain	1e-09
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	1e-08
cd01726	68	cd01726, LSm6, Like-Sm protein 6	3e-07
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	3e-07
cd01732	76	cd01732, LSm5, Like-Sm protein 5	4e-07
cd00600	63	cd00600, Sm_like, Sm and related proteins	1e-06
cd01719	70	cd01719, Sm_G, Sm protein G	2e-06
cd01717	80	cd01717, Sm_B, Sm protein B	7e-06
cd01727	91	cd01727, LSm8, Like-Sm protein 8	3e-04
cd01728	74	cd01728, LSm1, Like-Sm protein 1	5e-04
cd01722	69	cd01722, Sm_F, Sm protein F	6e-04
cd01729	89	cd01729, LSm7, Like-Sm protein 7	0.002
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	0.002

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

 Score =  110 bits (277), Expect = 5e-34
 Identities = 49/79 (62%), Positives = 55/79 (69%), Gaps = 21/79 (26%)

Query: 7  QRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHIKKNT 45
          Q++M QPINLIFR+LQ+                     GFDEYMNLVLDDAEEVH+K NT
Sbjct: 1  QKVMVQPINLIFRYLQNKSRVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNT 60

Query: 46 RKPLGRILLKGDNITLMMN 64
          RKPLGRILLKGDNITL+ N
Sbjct: 61 RKPLGRILLKGDNITLIQN 79

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

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

 Score = 93.6 bits (233), Expect = 3e-27
 Identities = 49/87 (56%), Positives = 54/87 (62%), Gaps = 21/87 (24%)

Query: 1  MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEV 39
          M   K+Q+IMTQPIN IFRF                        GFDEYMN+VLDDAEEV
Sbjct: 3  MTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEV 62

Query: 40 HIKKNTRKPLGRILLKGDNITLMMNTG 66
          + KKNTRK LGRILLKGDNITL+M   
Sbjct: 63 YTKKNTRKDLGRILLKGDNITLIMAAK 89

Length = 89

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

 Score = 49.0 bits (118), Expect = 6e-10
 Identities = 16/39 (41%), Positives = 26/39 (66%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
          GFD++MNLVL+D EE       ++ LG + ++G+NI  +
Sbjct: 27 GFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYI 65

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

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

 Score = 48.7 bits (117), Expect = 7e-10
 Identities = 17/38 (44%), Positives = 30/38 (78%), Gaps = 1/38 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITL 61
          GFD+++NLVL++AEE+ I+  + + LG +L++GDN+  
Sbjct: 30 GFDQHLNLVLENAEEI-IEGESVRKLGTVLVRGDNVVF 66

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|201787 pfam01423, LSM, LSM domain

 Score = 48.3 bits (116), Expect = 1e-09
 Identities = 20/40 (50%), Positives = 27/40 (67%), Gaps = 1/40 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 63
          GFD++MNLVLDD EE        K LG +L++G+NI L+ 
Sbjct: 27 GFDQFMNLVLDDVEETIKDGKVNK-LGLVLIRGNNIVLIS 65

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|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional

 Score = 46.1 bits (110), Expect = 1e-08
 Identities = 20/42 (47%), Positives = 31/42 (73%), Gaps = 1/42 (2%)

Query: 18 FRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNI 59
          FR    G+D +MNLVLD+AEE+   +  RK LG+++++GDN+
Sbjct: 27 FRGELQGYDIHMNLVLDNAEEIQDGEVVRK-LGKVVIRGDNV 67

Length = 72

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

 Score = 42.1 bits (100), Expect = 3e-07
 Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 1/34 (2%)

Query: 26 DEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNI 59
          D YMNLVL+D EE    +   K  G   ++G+N+
Sbjct: 32 DGYMNLVLEDTEEYVDGQLVAK-YGDAFIRGNNV 64

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

 Score = 42.3 bits (100), Expect = 3e-07
 Identities = 23/42 (54%), Positives = 30/42 (71%), Gaps = 3/42 (7%)

Query: 24 GFDEYMNLVLDDAEEVHIK---KNTRKPLGRILLKGDNITLM 62
          GFD+YMNLVLDD EE+      KN R+  G +L++GDNI L+
Sbjct: 36 GFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLI 77

Length = 79

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

 Score = 42.2 bits (100), Expect = 4e-07
 Identities = 19/41 (46%), Positives = 27/41 (65%), Gaps = 2/41 (4%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRK--PLGRILLKGDNITLM 62
          GFD+Y+N+VL+D  E  I    RK   L +ILL G+NI ++
Sbjct: 32 GFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNIAML 72

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

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

 Score = 40.7 bits (96), Expect = 1e-06
 Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 63
           FD+YMNLVLDD  E       R  LG +L++G NI  + 
Sbjct: 25 AFDKYMNLVLDDVVETGRDGKVRV-LGLVLIRGSNIVSIR 63

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

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

 Score = 40.2 bits (95), Expect = 2e-06
 Identities = 16/39 (41%), Positives = 28/39 (71%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
          GFD +MNLVLDDA E  +    + P+G ++++G++I ++
Sbjct: 29 GFDPFMNLVLDDAVEE-VGDGEKTPIGMVVIRGNSIIMI 66

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

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

 Score = 39.1 bits (92), Expect = 7e-06
 Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 10/45 (22%)

Query: 25 FDEYMNLVLDDAEEVHIKKNTRKP----------LGRILLKGDNI 59
          FD++MNLVL D EE    K  +K           LG +LL+G+N+
Sbjct: 30 FDKHMNLVLSDCEEFRKIKPKKKKKGEEREEKRVLGLVLLRGENV 74

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|212474 cd01727, LSm8, Like-Sm protein 8

 Score = 35.2 bits (82), Expect = 3e-04
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 3/42 (7%)

Query: 24 GFDEYMNLVLDDAEEVHIKK---NTRKPLGRILLKGDNITLM 62
          GFD+  NL+L +  E            PLG  LL+GDN+ ++
Sbjct: 28 GFDQTTNLILSNCHERVYSSDEGVEEVPLGLYLLRGDNVAVI 69

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

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

 Score = 34.0 bits (79), Expect = 5e-04
 Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 3/45 (6%)

Query: 20 FLQSGFDEYMNLVLDDAEEVHI--KKNTRKPLGRILLKGDNITLM 62
           L+S FD++ NLVL+D  E  I   +    P G  +++G+N+ L+
Sbjct: 28 ILRS-FDQFANLVLEDTVERIIVGNQYGDIPRGLFIIRGENVVLL 71

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

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

 Score = 33.7 bits (78), Expect = 6e-04
 Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 2/40 (5%)

Query: 20 FLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNI 59
           L S  D YMNL L + EE  I       LG +L++ +N+
Sbjct: 27 TLVS-VDSYMNLQLANTEEY-IDGKFTGNLGEVLIRCNNV 64

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|212476 cd01729, LSm7, Like-Sm protein 7

 Score = 33.3 bits (77), Expect = 0.002
 Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 9/46 (19%)

Query: 24 GFDEYMNLVLDDAEE--------VHIKKNTRKPLGRILLKGDNITL 61
          G+D+ +NLVLDD  E          +   TR  LG ++ +G ++ L
Sbjct: 31 GYDQLLNLVLDDTVEYLRDPEDPYKLTDETRS-LGLVVCRGTSVVL 75

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

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

 Score = 32.5 bits (74), Expect = 0.002
 Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
            D+YMNL L D  E  + +   + LG ++L+G+NI L+
Sbjct: 30 AVDDYMNLHLTDTMEC-VGEEKVRSLGTVVLRGNNILLI 67

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	67
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.8
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.8
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.79
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.78
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.77
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.77
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.77
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.75
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.75
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.74
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.73
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.73
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.73
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.72
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	99.71
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.71
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.69
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.65
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.65
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.64
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.64
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.62
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.61
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.56
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.51
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.5
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.48
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.33
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	99.31
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	99.24
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	99.11
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.07
KOG3168	177	consensus U1 snRNP component [Transcription]	99.06
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	98.8
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	98.7
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	98.47
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	98.02
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.74
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	97.44

>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=9.6e-20  Score=106.92  Aligned_cols=62  Identities=24%  Similarity=0.473  Sum_probs=55.3

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecC-------ceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK-------NTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~-------~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      +|.+++++++.|.+++++.      |||+||||+|+||+|+....       .+.+.+|.++|||+||++|++.+
T Consensus         6 ~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           6 DLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             hHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            5899999999999999887      99999999999999996432       25788999999999999999876

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

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

Probab=99.80  E-value=1.4e-19  Score=104.28  Aligned_cols=62  Identities=29%  Similarity=0.598  Sum_probs=56.7

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcCC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK   67 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~~   67 (67)
                      .|++++++++.|.+++++.      |||+|||++|+||+|+. .+.+.+.+|.++|||+||++|++.|+
T Consensus         4 ~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~-~~~~~~~lg~v~IRG~~I~~i~~~~~   71 (72)
T cd01719           4 ELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVN-SGGEKNNIGMVVIRGNSIVMLEALER   71 (72)
T ss_pred             hhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEc-cCCceeEeceEEECCCEEEEEEcccc
Confidence            5889999999999999877      99999999999999985 56678899999999999999999874

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.

>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=99.80  E-value=2e-19  Score=104.69  Aligned_cols=60  Identities=30%  Similarity=0.593  Sum_probs=53.6

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEec--CceeeecCeEEEeCCcEEEEEEc
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK--KNTRKPLGRILLKGDNITLMMNT   65 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~--~~~~~~~g~~~iRG~nV~~i~~~   65 (67)
                      |++++++++.|.+++++.      |||+|||++|+||+|++.+  +++.+.+|.++||||||++|+|.
T Consensus         8 L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~   75 (76)
T cd01732           8 IDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG   75 (76)
T ss_pred             HHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence            688899999999999987      9999999999999999632  34678899999999999999985

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=99.79  E-value=3.8e-19  Score=102.13  Aligned_cols=59  Identities=29%  Similarity=0.572  Sum_probs=53.3

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      -|++++++++.|.+++++.      |||+|||++|+||+|.. +++..+.+|.++|||+||++|+|
T Consensus         8 ~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~~V~~i~~   72 (72)
T PRK00737          8 VLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ-DGEVVRKLGKVVIRGDNVVYVSP   72 (72)
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEc-CCCeEeEcCcEEEeCCEEEEEcC
Confidence            4789999999999999877      99999999999999984 66677899999999999999974

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

Probab=99.78  E-value=6.2e-19  Score=101.64  Aligned_cols=64  Identities=25%  Similarity=0.409  Sum_probs=56.5

Q ss_pred             CChhhhhccccCcEEEEEccccc------cccceecEEEccEEEEEec---CceeeecCeEEEeCCcEEEEEEcC
Q 035338            1 MASTKVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK---KNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         1 ms~~~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~---~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      ||.  |++++++++.|++++++.      |||+|||++|+||+|+...   +.+++.+|.+++||+||++|++.|
T Consensus         1 ~~~--L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d   73 (74)
T cd01727           1 SST--LEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID   73 (74)
T ss_pred             Chh--HHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence            455  999999999999999887      9999999999999998642   335778999999999999999876

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.77  E-value=1.2e-19  Score=108.58  Aligned_cols=43  Identities=81%  Similarity=1.158  Sum_probs=38.3

Q ss_pred             cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338           24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus        24 ~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |||+|||++|+||+|+..++++.+.+|.++||||||++|++.+
T Consensus        47 gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~~~   89 (89)
T PTZ00138         47 GFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAAK   89 (89)
T ss_pred             EEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEcCC
Confidence            9999999999999998644567889999999999999998763

>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=99.77  E-value=1.5e-18  Score=98.44  Aligned_cols=59  Identities=27%  Similarity=0.563  Sum_probs=53.2

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      -|++++++++.|.+++++.      +||+|||++|+||+|++ .+.+++.+|.++|||+||++|+|
T Consensus         4 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           4 VLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEID-DGEPVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             HHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEe-cCCeEeEcCcEEEeCCEEEEEcC
Confidence            3788999999999999877      99999999999999985 55578899999999999999975

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.

>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=99.77  E-value=1.4e-18  Score=101.91  Aligned_cols=59  Identities=19%  Similarity=0.414  Sum_probs=51.5

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecC------------ceeeecCeEEEeCCcEEEEEE
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK------------NTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~------------~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      |++.+++++.|.+++++.      |||+||||+|+||+|++...            ..++.+|.++|||+||++|++
T Consensus         6 l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~~   82 (82)
T cd01730           6 IRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVSP   82 (82)
T ss_pred             HHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEECC
Confidence            577799999999999988      99999999999999997421            247789999999999999874

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.

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

Probab=99.75  E-value=1e-18  Score=101.24  Aligned_cols=62  Identities=23%  Similarity=0.512  Sum_probs=56.4

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcCC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK   67 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~~   67 (67)
                      +|.|||.+++.+.+++.+.      |||.|||+||+|++|.. ..+.+..+|.++|||++|+++++.++
T Consensus         8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~-~~~~~~~ig~~vIrgnsiv~~eaL~~   75 (77)
T KOG1780|consen    8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPN-GDGDKNNIGMVVIRGNSIVMVEALER   75 (77)
T ss_pred             hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeec-CcCCcceeeeEEEeccEEEEEeeccc
Confidence            7999999999999999888      99999999999999985 44568889999999999999998764

>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=99.75  E-value=4e-18  Score=99.20  Aligned_cols=60  Identities=32%  Similarity=0.538  Sum_probs=53.4

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEec---------CceeeecCeEEEeCCcEEEEEE
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK---------KNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~---------~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      +|.+++++++.|.+++++.      |||+|||++|+||+|++..         +.+++.+|.++|||++|++|+.
T Consensus         4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            6999999999999999988      9999999999999998642         2356889999999999999974

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.

>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=99.74  E-value=5.5e-18  Score=99.44  Aligned_cols=60  Identities=62%  Similarity=0.928  Sum_probs=48.5

Q ss_pred             hhhccccC--cEEEEEc--cccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338            5 KVQRIMTQ--PINLIFR--FLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         5 ~l~~~m~~--pi~v~~~--~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      .+.+++..  |+.|.++  +++.      |||+|||++|+||+|+...+++.+.+|.++||||||++|+|
T Consensus        10 ~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p   79 (79)
T cd01718          10 LIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN   79 (79)
T ss_pred             HHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence            46777877  5666555  4444      99999999999999996435677889999999999999975

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.

>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=99.73  E-value=9.4e-18  Score=95.04  Aligned_cols=57  Identities=21%  Similarity=0.454  Sum_probs=51.9

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEE
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM   63 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~   63 (67)
                      |++++++++.|.+++++.      +||+|||++|+||+|.. .+++++.+|.++|||++|++|+
T Consensus         5 L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~-~~~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           5 LKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYV-NGQLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             HHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEe-CCceeeEeCCEEEECCEEEEEC
Confidence            688999999999999877      99999999999999974 6667889999999999999985

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.

>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=99.73  E-value=9.6e-18  Score=99.87  Aligned_cols=60  Identities=20%  Similarity=0.448  Sum_probs=50.5

Q ss_pred             hhccc--cCcEEEEEccccc------cccceecEEEccEEEEEecC------------ceeeecCeEEEeCCcEEEEEEc
Q 035338            6 VQRIM--TQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK------------NTRKPLGRILLKGDNITLMMNT   65 (67)
Q Consensus         6 l~~~m--~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~------------~~~~~~g~~~iRG~nV~~i~~~   65 (67)
                      |++.+  ++|+.|.+++.+.      |||+|||++|+||+|++...            .+++.+|.+||||+||++|++.
T Consensus         7 L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~Is~~   86 (87)
T cd01720           7 LTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVILVLRN   86 (87)
T ss_pred             HHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEEEecC
Confidence            45565  7899999999888      99999999999999986431            2366789999999999999874

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.

>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=99.73  E-value=1.2e-17  Score=96.85  Aligned_cols=60  Identities=23%  Similarity=0.406  Sum_probs=53.3

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecC--ceeeecCeEEEeCCcEEEEEE
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK--NTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~--~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      .|.+++++++.|.+++++.      |||+|||++|+||.|+...+  ..++.+|.+++||+||++|++
T Consensus         6 ~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728           6 SLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             HHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence            6899999999999999888      99999999999999986443  246789999999999999986

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.

>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=99.72  E-value=1.6e-17  Score=94.43  Aligned_cols=58  Identities=22%  Similarity=0.438  Sum_probs=52.1

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEE
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM   63 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~   63 (67)
                      -|++++++++.|.+++++.      +||+|||++|+||+|+. .+.+...+|.++|||+||.+|+
T Consensus         5 ~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~-~~~~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           5 FLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI-DGKSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             HHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEe-CCccccCcCcEEEECCEEEEEC
Confidence            4788999999999999877      99999999999999984 6667788999999999999984

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.

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

Probab=99.71  E-value=4.6e-19  Score=104.41  Aligned_cols=66  Identities=76%  Similarity=1.167  Sum_probs=57.9

Q ss_pred             CChhhhhccccCcEEEEEccccc---------------------cccceecEEEccEEEEEecCceeeecCeEEEeCCcE
Q 035338            1 MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNI   59 (67)
Q Consensus         1 ms~~~l~~~m~~pi~v~~~~~~~---------------------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV   59 (67)
                      ||..++++.|.+|++++++..+.                     |||+|||+||+||+|...+....+++|.+++.|+||
T Consensus         1 ms~~kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnI   80 (88)
T KOG1774|consen    1 MSREKVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNI   80 (88)
T ss_pred             CCcccccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcE
Confidence            78888999999999999977654                     999999999999999976655566999999999999


Q ss_pred             EEEEEcC
Q 035338           60 TLMMNTG   66 (67)
Q Consensus        60 ~~i~~~~   66 (67)
                      .+|...+
T Consensus        81 tli~~~~   87 (88)
T KOG1774|consen   81 TLIQSAG   87 (88)
T ss_pred             EEEeecC
Confidence            9998765

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

Probab=99.71  E-value=3.3e-17  Score=91.74  Aligned_cols=61  Identities=25%  Similarity=0.499  Sum_probs=54.5

Q ss_pred             hhhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338            4 TKVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         4 ~~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      +.|++++++|+.|.++++..      +||+|||++|+||.|....+.+.+.+|.++|||++|.+|.+
T Consensus         1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred             ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence            35899999999999999877      99999999999999996333388999999999999999975

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

>smart00651 Sm snRNP Sm proteins

Probab=99.69  E-value=1e-16  Score=89.58  Aligned_cols=60  Identities=27%  Similarity=0.576  Sum_probs=53.6

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      .|++++++++.|.+++++.      +||+|||++|+||+|+..++.+.+.+|.++|||++|.+|++
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence            3788999999999999877      99999999999999996443688999999999999999874

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

>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=99.65  E-value=3.9e-16  Score=90.40  Aligned_cols=61  Identities=11%  Similarity=0.216  Sum_probs=52.8

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |++..+++|.|.++++..      +||+|||++|+||+|...+++.....+.++|||++|.+|...+
T Consensus         6 L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~   72 (76)
T cd01723           6 LKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPD   72 (76)
T ss_pred             HHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCH
Confidence            578899999999999877      9999999999999998544555567899999999999998764

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.

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

Probab=99.65  E-value=4.3e-16  Score=90.47  Aligned_cols=60  Identities=35%  Similarity=0.658  Sum_probs=50.8

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEe-cCce-eeecC-eEEEeCCcEEEEEE
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHI-KKNT-RKPLG-RILLKGDNITLMMN   64 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~-~~~~-~~~~g-~~~iRG~nV~~i~~   64 (67)
                      -|++++++++.|.+++++.      |||+|||++|+||+|+.. ++.. .+.++ .++|||+||++|.+
T Consensus        11 ~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958          11 FLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             HHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence            4788999999999999877      999999999999999963 3433 35555 99999999999864

>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=99.64  E-value=8.2e-16  Score=87.90  Aligned_cols=60  Identities=12%  Similarity=0.233  Sum_probs=52.2

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |++..++++.|.++++..      +||+|||++|+||.+.. .+++...+|.++|||+||.+|...|
T Consensus         5 L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~-~~g~~~~~~~v~IRG~nI~~v~lPd   70 (70)
T cd01721           5 LHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTA-RDGRVSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             HhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEEC-CCCcEeEcCcEEEeCCEEEEEEeCC
Confidence            678889999999999866      99999999999999874 3445677899999999999998765

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.

>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=99.64  E-value=8.6e-16  Score=89.19  Aligned_cols=61  Identities=16%  Similarity=0.283  Sum_probs=54.6

Q ss_pred             hhhhccccCcEEEEEccccc------cccceecEEEccEEEEEec-----CceeeecCeEEEeCCcEEEEEE
Q 035338            4 TKVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK-----KNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         4 ~~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~-----~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      .+|++++++++.|.+++++.      +||+|||++|+||.|+...     +.+.+.+|+++|||++|++|+.
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence            36899999999999999988      9999999999999999743     2578899999999999999873

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.

>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=99.62  E-value=1.9e-15  Score=90.30  Aligned_cols=60  Identities=18%  Similarity=0.334  Sum_probs=53.7

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |+++.+++|.|.++++..      ++|+|||++|+||+++. +++....+|.++|||+||.+|...+
T Consensus         6 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~-~~~~~~~~~~v~IRG~nI~yi~lPd   71 (90)
T cd01724           6 LMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTL-KGRNPVPLDTLSIRGNNIRYFILPD   71 (90)
T ss_pred             HHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEc-CCCceeEcceEEEeCCEEEEEEcCC
Confidence            578899999999999866      99999999999999984 5667788999999999999998765

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=99.61  E-value=2.8e-15  Score=82.65  Aligned_cols=57  Identities=35%  Similarity=0.669  Sum_probs=51.2

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEE
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM   63 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~   63 (67)
                      |++++++++.|.+++++.      +||+|||++|+||.|.. ...+.+.+|.++|||++|.+|.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~-~~~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETI-KEGKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEe-cCCcEEECCeEEEECCEEEEEC
Confidence            578899999999998877      99999999999999986 4467889999999999999874

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.

>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=99.56  E-value=1.4e-14  Score=84.49  Aligned_cols=58  Identities=17%  Similarity=0.336  Sum_probs=50.4

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      |+...+++|.|.++++..      ++|+|||++|+||++.. .++....+|.++|||+||.+|..
T Consensus        14 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~-~~~~~~~~~~v~IRG~nI~yI~l   77 (78)
T cd01733          14 LQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIID-RNGKQVQVEEIMVTGRNIRYVHI   77 (78)
T ss_pred             HHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEc-CCCceeECCcEEEECCEEEEEEc
Confidence            577889999999998866      99999999999999874 45566689999999999999975

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.

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

Probab=99.51  E-value=1.1e-14  Score=84.30  Aligned_cols=60  Identities=28%  Similarity=0.488  Sum_probs=54.9

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |+.+.++|+.|.++++.+      +.|.|||+.|.+|+|+ +++.....+|.++||+|||.+|...+
T Consensus        13 L~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~-idG~~~g~lGEilIRCNNvlyi~gv~   78 (79)
T KOG3482|consen   13 LNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEY-IDGVSTGNLGEILIRCNNVLYIRGVP   78 (79)
T ss_pred             HhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhh-hcccccccceeEEEEeccEEEEecCC
Confidence            678899999999999977      9999999999999999 48888899999999999999997654

>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=99.50  E-value=7.6e-14  Score=81.78  Aligned_cols=61  Identities=11%  Similarity=0.241  Sum_probs=50.2

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecC-ceeeecCeEEEeCCcEEEEEEcC
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK-NTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~-~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |+++.+++|.|.++++..      ++|+|||++|+||++...++ .....++.++|||++|.+|...+
T Consensus         6 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~   73 (81)
T cd01725           6 FKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPA   73 (81)
T ss_pred             HHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeCh
Confidence            578889999999998766      99999999999998874222 23456689999999999998764

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.

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

Probab=99.48  E-value=5.3e-15  Score=85.60  Aligned_cols=61  Identities=18%  Similarity=0.388  Sum_probs=55.4

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      =|++++++|+.|++.++..      +.|.|||+.|+.++|+ .++..++.+|.+||||+||.+|+...
T Consensus        10 fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~-~ngql~n~ygdaFirGnnVlyIs~~~   76 (77)
T KOG1783|consen   10 FLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEY-VNGQLKNKYGDAFIRGNNVLYISTQK   76 (77)
T ss_pred             HHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHH-hcCcccccccceeeccccEEEEEecc
Confidence            4788999999999988755      9999999999999999 58889999999999999999998753

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

Probab=99.33  E-value=7e-14  Score=84.95  Aligned_cols=62  Identities=24%  Similarity=0.466  Sum_probs=55.4

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEec-------CceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK-------KNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~-------~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      +|.+|.++.|.|.+.++++      |||+.|||||+|++|+.-+       +.+.|++|.+++||..+++|++.|
T Consensus        21 DLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~d   95 (108)
T KOG1781|consen   21 DLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPAD   95 (108)
T ss_pred             hHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCc
Confidence            5899999999999999988      9999999999999998533       235699999999999999999875

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

Probab=99.31  E-value=1.1e-12  Score=78.78  Aligned_cols=62  Identities=23%  Similarity=0.418  Sum_probs=55.8

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEec---CceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK---KNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~---~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      -|..||++.+.|++.+++-      |||+..||+|+|+-|++.+   +.+...+|..+|||+||.+|.+.|
T Consensus         4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iD   74 (96)
T KOG1784|consen    4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEID   74 (96)
T ss_pred             hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecc
Confidence            3899999999999999877      9999999999999999754   456788999999999999999875

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

Probab=99.24  E-value=3.7e-12  Score=75.50  Aligned_cols=56  Identities=27%  Similarity=0.503  Sum_probs=46.7

Q ss_pred             ccCcEEEEEccccc------cccceecEEEccEEEEEec------------CceeeecCeEEEeCCcEEEEEEc
Q 035338           10 MTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK------------KNTRKPLGRILLKGDNITLMMNT   65 (67)
Q Consensus        10 m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~------------~~~~~~~g~~~iRG~nV~~i~~~   65 (67)
                      ..-.+.|++++.++      +||+|+|++|.||+|+...            ...++.+.++|+||++|++|+|.
T Consensus        14 LdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvspp   87 (91)
T KOG3460|consen   14 LDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVSPP   87 (91)
T ss_pred             ccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEcCc
Confidence            35668888888766      9999999999999998642            13478889999999999999985

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

Probab=99.11  E-value=1.7e-11  Score=76.88  Aligned_cols=62  Identities=23%  Similarity=0.415  Sum_probs=54.6

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCc--eeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKN--TRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~--~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .+.++..+++-|++++++.      +||+|-|++|++|.|++.-+.  ...+.|..+|||.||+++...|
T Consensus        13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid   82 (129)
T KOG1782|consen   13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEID   82 (129)
T ss_pred             HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCC
Confidence            5788899999999999988      999999999999999976443  4667799999999999998765

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

Probab=99.07  E-value=6.4e-11  Score=69.28  Aligned_cols=60  Identities=33%  Similarity=0.623  Sum_probs=51.8

Q ss_pred             hccccCcEEEEEccccc------cccceecEEEccEEEEEec--CceeeecCeEEEeCCcEEEEEEcC
Q 035338            7 QRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK--KNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         7 ~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~--~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      -|-+++++-+++++.++      |||.|.|++|+|++||-..  +....+.+.+++.||||.+..|..
T Consensus        13 DkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG   80 (84)
T KOG1775|consen   13 DKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG   80 (84)
T ss_pred             HHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence            46688999999999877      9999999999999999654  346778899999999999988764

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=99.06  E-value=1.9e-11  Score=80.19  Aligned_cols=62  Identities=32%  Similarity=0.494  Sum_probs=52.3

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEec---------CceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK---------KNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~---------~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      ++-..++-.+++++++++.      +||.|||++|.||+|+-..         +++++.+|+|++||.||++.+.-+
T Consensus         8 kml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg   84 (177)
T KOG3168|consen    8 KMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG   84 (177)
T ss_pred             HHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence            5666778888899988877      9999999999999998531         468999999999999999987644

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

Probab=98.80  E-value=7.6e-09  Score=65.19  Aligned_cols=60  Identities=13%  Similarity=0.197  Sum_probs=52.2

Q ss_pred             hccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            7 QRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         7 ~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .-.-+.|+.|.++.+..      .+|.+|||.|.+++++..++.+...+..|+|||++|.++...|
T Consensus         8 ~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d   73 (134)
T KOG3293|consen    8 KTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPD   73 (134)
T ss_pred             HhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccH
Confidence            34457899999988765      9999999999999999877888888999999999999987654

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

Probab=98.70  E-value=3.7e-08  Score=60.89  Aligned_cols=56  Identities=18%  Similarity=0.335  Sum_probs=47.7

Q ss_pred             ccCcEEEEEccccc-----------------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338           10 MTQPINLIFRFLQS-----------------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus        10 m~~pi~v~~~~~~~-----------------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      ++.||++++.+..+                 ..|++||+.|+|.+-+. .......+..+||||+.|.++...|
T Consensus         3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~-~dg~vs~le~V~IRGS~IRFlvlPd   75 (119)
T KOG3172|consen    3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTA-RDGRVSQLEQVFIRGSKIRFLVLPD   75 (119)
T ss_pred             cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEc-cCCcceeeeeEEEecCeEEEEECch
Confidence            47899999988766                 89999999999998884 5567888999999999999987654

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

Probab=98.47  E-value=4.4e-08  Score=60.61  Aligned_cols=57  Identities=19%  Similarity=0.472  Sum_probs=43.2

Q ss_pred             ccccCcEEEEEccccc--------cccceecEEEccEEEEEec------C------ceeeecCeEEEeCCcEEEEEE
Q 035338            8 RIMTQPINLIFRFLQS--------GFDEYMNLVLDDAEEVHIK------K------NTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         8 ~~m~~pi~v~~~~~~~--------~~D~~mNlvL~da~e~~~~------~------~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      .-+..-..+++.|...        +||-|.|++|+++.|.+..      +      ...+.+|.+||||++|+.+..
T Consensus        31 ~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~r  107 (114)
T KOG3459|consen   31 ASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVLR  107 (114)
T ss_pred             HHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEEe
Confidence            3344455666666544        9999999999999998742      1      136789999999999998764

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

Probab=98.02  E-value=2.2e-05  Score=47.16  Aligned_cols=58  Identities=16%  Similarity=0.251  Sum_probs=43.9

Q ss_pred             hccccCcEEEEEccccc------cccceecEEEccEEEEEecC-ceeeecCeEEEeCCcEEEEEE
Q 035338            7 QRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK-NTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         7 ~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~-~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      +.++++.+.|.+++...      +.|+|+|+-|+|..-...+. .--..+..|||||+.|.++..
T Consensus         8 kslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l   72 (96)
T KOG3448|consen    8 KSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL   72 (96)
T ss_pred             HHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEe
Confidence            45788999999988654      99999999999987764211 122334579999999999865

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

Probab=97.74  E-value=8.9e-06  Score=46.31  Aligned_cols=29  Identities=24%  Similarity=0.481  Sum_probs=23.5

Q ss_pred             CcEEEEEccccc----------cccceecEEEccEEEEE
Q 035338           12 QPINLIFRFLQS----------GFDEYMNLVLDDAEEVH   40 (67)
Q Consensus        12 ~pi~v~~~~~~~----------~~D~~mNlvL~da~e~~   40 (67)
                      .+|.|.++....          +||+|||++|.|+.|.+
T Consensus         9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y   47 (66)
T cd01739           9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETY   47 (66)
T ss_pred             cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhh
Confidence            566776665433          99999999999999987

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.

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

Probab=97.44  E-value=0.00052  Score=42.45  Aligned_cols=59  Identities=15%  Similarity=0.256  Sum_probs=47.6

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |+++..-.+.|-++.+..      +.|.+||..|.++.-.. ++ +........+||+||-++...|
T Consensus         7 L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~-~~-~pv~l~~lsirgnniRy~~lpD   71 (109)
T KOG3428|consen    7 LKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTV-KG-EPVRLDTLSIRGNNIRYYILPD   71 (109)
T ss_pred             HHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEec-CC-CceeEEEEEeecceEEEEEccC
Confidence            456666778888888755      99999999999987763 55 6677889999999999987654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	67
3cw1_E	92	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		6e-19
1i81_A	83	Crystal Structure Of A Heptameric Lsm Protein From		5e-05
1loj_A	87	Crystal Structure Of A Methanobacterial Sm-Like Arc		5e-05
1jbm_A	86	Heptameric Crystal Structure Of Mth649, An Sm-Like		5e-05
1jri_A	85	The Crystal Structure Of An Sm-Like Archaeal Protei		6e-05
1th7_A	81	Crystal Structure Of An Archaeal Sm Protein From Su		4e-04

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

Iteration: 1
 Score = 89.0 bits (219), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 45/82 (54%), Positives = 54/82 (65%), Gaps = 21/82 (25%)
Query: 5  KVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHIKK 43
          KVQ++M QPINLIFR+LQ+                     GFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68
Query: 44 NTRKPLGRILLKGDNITLMMNT 65
           +RK LGRI+LKGDNITL+ + 
Sbjct: 69 KSRKQLGRIMLKGDNITLLQSV 90

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 32/45 (71%), Gaps = 1/45 (2%)
Query: 18 FRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
          FR +   FD +MNLVL+DAEE+   + TR+ LG +L++GDNI  +
Sbjct: 38 FRGVLKSFDLHMNLVLNDAEELEDGEVTRR-LGTVLIRGDNIVYI 81

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 31/43 (72%), Gaps = 1/43 (2%)
Query: 18 FRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNIT 60
          FR +   FD +MNLVL+DAEE+   + TR+ LG +L++GDNI 
Sbjct: 36 FRGVLKSFDLHMNLVLNDAEELEDGEVTRR-LGTVLIRGDNIV 77

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 31/43 (72%), Gaps = 1/43 (2%)
Query: 18 FRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNIT 60
          FR +   FD +MNLVL+DAEE+   + TR+ LG +L++GDNI 
Sbjct: 36 FRGVLKSFDLHMNLVLNDAEELEDGEVTRR-LGTVLIRGDNIV 77

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 31/43 (72%), Gaps = 1/43 (2%)
Query: 18 FRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNIT 60
          FR +   FD +MNLVL+DAEE+   + TR+ LG +L++GDNI 
Sbjct: 36 FRGVLKSFDLHMNLVLNDAEELEDGEVTRR-LGTVLIRGDNIV 77

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 18 FRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
           R +   +D++MNLVL D+EE+     + K LG I+++GDN+ L+
Sbjct: 32 VRGMLRSYDQHMNLVLSDSEEIQ-SDGSGKKLGTIVIRGDNVILI 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	67
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	8e-23
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	4e-18
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	5e-14
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	3e-11
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	2e-10
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	3e-10
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	2e-09
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	2e-09
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	2e-08
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	3e-08
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	3e-07
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	3e-07
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	1e-06
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	2e-06
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	2e-06
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-06
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	1e-05
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	2e-05
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	1e-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 = 81.8 bits (202), Expect = 8e-23
 Identities = 45/81 (55%), Positives = 54/81 (66%), Gaps = 21/81 (25%)

Query: 5  KVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHIKK 43
          KVQ++M QPINLIFR+LQ+                     GFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query: 44 NTRKPLGRILLKGDNITLMMN 64
           +RK LGRI+LKGDNITL+ +
Sbjct: 69 KSRKQLGRIMLKGDNITLLQS 89

>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 = 70.3 bits (172), Expect = 4e-18
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 17/82 (20%)

Query: 3  STKVQRIMTQPINLIFRFLQS-----------------GFDEYMNLVLDDAEEVHIKKNT 45
          S     +   P+ LI + + S                 GFD+Y+N+VL D  E       
Sbjct: 11 SQDPMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGV 70

Query: 46 RKPLGRILLKGDNITLMMNTGK 67
           +    +LL G+ + +++  GK
Sbjct: 71 TEKHSEMLLNGNGMCMLIPGGK 92

>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 = 59.2 bits (144), Expect = 5e-14
 Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 19/71 (26%)

Query: 10 MTQPINLIFRFLQS------------------GFDEYMNLVLDDAEEVHIKKNTRKPLGR 51
          M  P  ++   +                    G D+YMNL L +A E   ++  R  LG 
Sbjct: 3  MVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRS-LGE 61

Query: 52 ILLKGDNITLM 62
          I+L+G+N+ L+
Sbjct: 62 IVLRGNNVVLI 72

>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 = 53.1 bits (127), Expect = 3e-11
 Identities = 23/98 (23%), Positives = 39/98 (39%), Gaps = 31/98 (31%)

Query: 1   MASTKVQRIMTQPINLIFRFLQS-----------------GFDEYMNLVLDDAEEVH--- 40
             S +    +  P+ LI + + +                 GFDEY+N+VLDD +E     
Sbjct: 17  GGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKA 76

Query: 41  -----------IKKNTRKPLGRILLKGDNITLMMNTGK 67
                      +K+     L  ILL G+N+ +++  G 
Sbjct: 77  DEEDISGGNKKLKRVMVNRLETILLSGNNVAMLVPGGD 114

>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 = 50.4 bits (121), Expect = 2e-10
 Identities = 17/39 (43%), Positives = 29/39 (74%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
           +D++MNLVL D+EE+    + +K LG I+++GDN+ L+
Sbjct: 38 SYDQHMNLVLSDSEEIQSDGSGKK-LGTIVIRGDNVILI 75

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

 Score = 49.2 bits (118), Expect = 3e-10
 Identities = 13/39 (33%), Positives = 27/39 (69%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
          G+D ++N+VL DAE +   +  ++  G+I+++GDN+  +
Sbjct: 33 GYDIHLNVVLADAEMIQDGEVVKR-YGKIVIRGDNVLAI 70

>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 = 47.7 bits (114), Expect = 2e-09
 Identities = 16/39 (41%), Positives = 27/39 (69%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
          G+D +MNLVL DAEE+   +  RK +G ++++GD +  +
Sbjct: 33 GYDIHMNLVLLDAEEIQNGEVVRK-VGSVVIRGDTVVFV 70

>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 = 47.7 bits (114), Expect = 2e-09
 Identities = 20/39 (51%), Positives = 29/39 (74%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
           FD +MNLVL+DAEE+   + TR+ LG +L++GDNI  +
Sbjct: 44 SFDLHMNLVLNDAEELEDGEVTRR-LGTVLIRGDNIVYI 81

>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 = 45.1 bits (107), Expect = 2e-08
 Identities = 13/39 (33%), Positives = 25/39 (64%), Gaps = 2/39 (5%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
           FD+++NL+L+DAEE  I        G ++++G+N+  +
Sbjct: 40 SFDQHVNLLLEDAEE--IIDGNVYKRGTMVVRGENVLFI 76

>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 = 44.2 bits (105), Expect = 3e-08
 Identities = 12/39 (30%), Positives = 25/39 (64%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
          GFD +MNLV+D+  E+         +G ++++G++I ++
Sbjct: 33 GFDPFMNLVIDECVEMATSGQQN-NIGMVVIRGNSIIML 70

>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 = 41.9 bits (99), Expect = 3e-07
 Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
            D YMNL L+  EE  +        G   ++G+N+  +
Sbjct: 33 CLDGYMNLALERTEEY-VNGKKTNVYGDAFIRGNNVLYV 70

>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 = 42.4 bits (100), Expect = 3e-07
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 6/45 (13%)

Query: 24 GFDEYMNLVLDDAEEVHI------KKNTRKPLGRILLKGDNITLM 62
           FD + N+VL DA E            + +    + ++GD +TL+
Sbjct: 39 AFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLI 83

>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 = 40.6 bits (95), Expect = 1e-06
 Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
            D Y NL L++AEE  +   +   LG I ++ +N+  +
Sbjct: 51 STDNYFNLQLNEAEEF-VAGVSHGTLGEIFIRCNNVLYI 88

>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C Length = 113

 Score = 40.7 bits (95), Expect = 2e-06
 Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 6/45 (13%)

Query: 24 GFDEYMNLVLDDAEEVHIKKN------TRKPLGRILLKGDNITLM 62
          GFD+ MNLVLDD EE              + LG ++++G  + L+
Sbjct: 52 GFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLI 96

>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 = 40.1 bits (94), Expect = 2e-06
 Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 15 NLIFRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
           + ++      D YMN+ L + EE +I       LG +L++ +N+  +
Sbjct: 26 GMEYKGYLVSVDGYMNMQLANTEE-YIDGALSGHLGEVLIRCNNVLYI 72

>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 = 40.8 bits (95), Expect = 5e-06
 Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 9/44 (20%)

Query: 25 FDEYMNLVLDDAEE---VHIKKNTRKP------LGRILLKGDNI 59
          FD++MNL+L D +E   +  K + +        LG +LL+G+N+
Sbjct: 34 FDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENL 77

>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Length = 93

 Score = 38.3 bits (89), Expect = 1e-05
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 12/51 (23%)

Query: 24 GFDEYMNLVLDDAEEV------------HIKKNTRKPLGRILLKGDNITLM 62
           +DE++N+VL DAEE+               K  RK    + ++GD++ L+
Sbjct: 38 AYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVILI 88

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

 Score = 37.9 bits (88), Expect = 2e-05
 Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 9/48 (18%)

Query: 24 GFDEYMNLVLDDAEEVHI---------KKNTRKPLGRILLKGDNITLM 62
           FD++MNL+L D +E            ++  ++ LG +LL+G+N+  M
Sbjct: 33 AFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSM 80

>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 = 35.9 bits (83), Expect = 1e-04
 Identities = 10/36 (27%), Positives = 15/36 (41%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNI 59
            D YMNL L +        +    L    ++G+NI
Sbjct: 45 NCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNI 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	67
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.81
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.8
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.8
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.8
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.79
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.79
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.78
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.77
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.77
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.76
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.76
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.76
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.76
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.76
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.75
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.75
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.74
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.73
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.72
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.72
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.71
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.67
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.64
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.59
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	96.53

>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=99.81  E-value=2.4e-20  Score=107.02  Aligned_cols=66  Identities=23%  Similarity=0.545  Sum_probs=46.4

Q ss_pred             CChh---hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcCC
Q 035338            1 MAST---KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK   67 (67)
Q Consensus         1 ms~~---~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~~   67 (67)
                      ||..   .|++++++++.|.+++++.      |||+|||++|+||+|+. .+++.+.+|.++|||+||++|++.|.
T Consensus         1 ms~~~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            1 MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMA-TSGQQNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             -------------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECC-CC----CBSSEEECSSSEEEEEC---
T ss_pred             CCCcchHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEc-cCCcEeEcCEEEECCCeEEEEEeccC
Confidence            5553   7999999999999999877      99999999999999985 55578899999999999999999874

>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=99.80  E-value=6.7e-20  Score=109.48  Aligned_cols=63  Identities=24%  Similarity=0.519  Sum_probs=56.5

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcCC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK   67 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~~   67 (67)
                      =|.++++++|.|.+++++.      |||+||||+|+||+|+..++++.+.+|.++|||+||++|++.++
T Consensus        24 lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG~nI~~i~p~~~   92 (94)
T 4emk_A           24 LIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGNGMCMLIPGGK   92 (94)
T ss_dssp             HHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECSTTEEEEEECC-
T ss_pred             HHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcCCEEEEEEeCCC
Confidence            3688999999999999877      99999999999999996456778999999999999999998764

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

Probab=99.80  E-value=8.3e-20  Score=104.14  Aligned_cols=61  Identities=28%  Similarity=0.484  Sum_probs=56.0

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .|++++++++.|.+++++.      |||+|||++|+||+|++ .+.+.+.+|.++|||+||++|++.+
T Consensus         8 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 1h64_1            8 VIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQ-DGEVVKRYGKIVIRGDNVLAISPTE   74 (75)
T ss_dssp             HHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGGGEEEEEEC-
T ss_pred             HHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEe-eCCceeECCEEEECCCEEEEEEeCC
Confidence            6889999999999999877      99999999999999996 6678899999999999999999876

>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=99.80  E-value=4.5e-20  Score=105.53  Aligned_cols=65  Identities=20%  Similarity=0.358  Sum_probs=58.0

Q ss_pred             CChh---hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            1 MAST---KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         1 ms~~---~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      ||..   .|++++++++.|.+++++.      |||+|||++|+||+|+. ++++.+.+|.++|||+||++|++.|
T Consensus         1 m~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 4emk_B            1 MDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYV-NGKKTNVYGDAFIRGNNVLYVSALD   74 (75)
T ss_dssp             CCSHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEE-TTEEEEEEEEEEEEGGGSSEEEEC-
T ss_pred             CCCchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEe-cCCcccEecEEEEcCCeEEEEEecC
Confidence            5653   6889999999999999877      99999999999999985 6777899999999999999999976

>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=99.79  E-value=2.1e-19  Score=102.76  Aligned_cols=61  Identities=26%  Similarity=0.498  Sum_probs=56.4

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .|++++++++.|.+++++.      +||+|||++|+||+|++ .+.+.+.+|.++|||+||++|.+.+
T Consensus         8 ~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~~I~~i~~~d   74 (77)
T 1i4k_A            8 VLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQ-NGEVVRKVGSVVIRGDTVVFVSPAP   74 (77)
T ss_dssp             HHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGGGEEEEEECC
T ss_pred             HHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEe-cCCcEeECCEEEECCCEEEEEEeCC
Confidence            6889999999999999877      99999999999999996 5668889999999999999999876

>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=99.79  E-value=2.5e-19  Score=106.83  Aligned_cols=62  Identities=21%  Similarity=0.386  Sum_probs=56.1

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEec------CceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK------KNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~------~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .|++++++++.|.+++++.      |||+||||+|+||+|++..      +...+.+|.++|||+||++|++.+
T Consensus        14 ~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d   87 (96)
T 3bw1_A           14 LLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPS   87 (96)
T ss_dssp             HHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC
T ss_pred             HHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecC
Confidence            6899999999999999888      9999999999999999753      345788999999999999999876

>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=99.78  E-value=2.8e-19  Score=102.44  Aligned_cols=61  Identities=30%  Similarity=0.518  Sum_probs=55.9

Q ss_pred             hhhccccCcEEEEEccc-cc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFL-QS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~-~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .|.+++++++.|.++++ +.      |||+|||++|+||+|++ ++++.+.+|.++|||+||++|++.|
T Consensus         9 ~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~nI~~i~~~d   76 (77)
T 1ljo_A            9 MVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECK-GEEKVRSLGEIVLRGNNVVLIQPQE   76 (77)
T ss_dssp             HHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGGGEEEEEEC-
T ss_pred             HHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEe-cCCcEeECCeEEEeCCeEEEEEeCC
Confidence            58899999999999999 66      99999999999999996 6778899999999999999999876

>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=99.77  E-value=5.1e-19  Score=102.31  Aligned_cols=61  Identities=28%  Similarity=0.495  Sum_probs=55.7

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .|++++++++.|.+++++.      +||+|||++|+||+|++ .+++.+.+|.++|||+||++|.+.+
T Consensus        13 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~~I~~i~~~~   79 (81)
T 1th7_A           13 VLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQ-SDGSGKKLGTIVIRGDNVILISPLQ   79 (81)
T ss_dssp             HHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEC-SSSCEEEEEEEEECGGGEEEEEEC-
T ss_pred             HHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEe-cCCceeECCEEEECCCEEEEEEecC
Confidence            6889999999999999877      99999999999999995 5667899999999999999999875

>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=99.77  E-value=5.9e-19  Score=103.72  Aligned_cols=62  Identities=29%  Similarity=0.493  Sum_probs=55.3

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEe---------cCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHI---------KKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~---------~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .|.+++++++.|.+++++.      |||+|||++|+||+|++.         .+.+.+.+|.++|||+||++|++.+
T Consensus         8 ~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~~~~   84 (91)
T 1d3b_B            8 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEG   84 (91)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEEE
T ss_pred             HHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEEcCC
Confidence            7999999999999999887      999999999999999752         2346889999999999999998764

>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=99.76  E-value=8.5e-19  Score=101.46  Aligned_cols=60  Identities=23%  Similarity=0.426  Sum_probs=55.4

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .|.+++++++.|.+++++.      +||+|||++|+||+|+  ++++.+.+|.++|||+||++|++.+
T Consensus        15 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~--~~~~~~~lg~v~iRG~~I~~i~~~d   80 (81)
T 1i8f_A           15 TLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI--IDGNVYKRGTMVVRGENVLFISPVP   80 (81)
T ss_dssp             HHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE--ETTEEEEEEEEEECGGGEEEEEECC
T ss_pred             HHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE--cCCcccCCCEEEECCCEEEEEEeCC
Confidence            5789999999999999877      9999999999999998  5678899999999999999999876

>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=99.76  E-value=3e-19  Score=106.22  Aligned_cols=61  Identities=52%  Similarity=0.824  Sum_probs=51.0

Q ss_pred             hhccccCcEEEEE----ccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            6 VQRIMTQPINLIF----RFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         6 l~~~m~~pi~v~~----~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |.+++++++.|.+    ++++.      |||+|||++|+||+|+..++++.+.+|.++|||+||++|++.+
T Consensus        21 L~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~nV~~i~~~~   91 (92)
T 3s6n_E           21 IFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSVS   91 (92)
T ss_dssp             HHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGGGEEEEEEC-
T ss_pred             HHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCCEEEEEEeCC
Confidence            4566667777776    77666      9999999999999999655677889999999999999999876

>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=99.76  E-value=7.4e-19  Score=107.77  Aligned_cols=62  Identities=32%  Similarity=0.498  Sum_probs=50.8

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecC------ceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK------NTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~------~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .|.++++++|.|.+++++.      |||+||||||+||+|++...      .+.+.+|.++|||+||++|++.|
T Consensus        27 ~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d  100 (113)
T 4emk_C           27 DLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMD  100 (113)
T ss_dssp             -----CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC
T ss_pred             HHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecC
Confidence            5899999999999999887      99999999999999996432      46889999999999999999876

>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=99.76  E-value=1.1e-18  Score=103.81  Aligned_cols=61  Identities=21%  Similarity=0.421  Sum_probs=55.6

Q ss_pred             hhhccccCcEEEEEccc-cc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFL-QS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~-~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      -|+++++++|.|.++++ +.      |||+|||++|+||+|++ ++++.+.+|.++|||+||++|.+.+
T Consensus        25 ~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~-~~~~~~~lg~v~IRG~nI~~I~~~~   92 (93)
T 1n9r_A           25 FLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV-AGVSHGTLGEIFIRCNNVLYIRELP   92 (93)
T ss_dssp             -CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEE-TTEEEEECCSEEECGGGEEEEEECC
T ss_pred             HHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEc-CCCeEeEcCEEEEcCCeEEEEEeCC
Confidence            47889999999999999 66      99999999999999995 6778899999999999999999875

>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=99.76  E-value=1.1e-18  Score=102.32  Aligned_cols=61  Identities=20%  Similarity=0.380  Sum_probs=55.9

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      -|+++++++|.|.+++++.      |||+|||++|+||+|+. ++++.+.+|.++|||+||++|.+.+
T Consensus        10 ~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~-~g~~~~~lg~v~IRG~nI~~i~~~d   76 (86)
T 3s6n_F           10 FLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYI-DGALSGHLGEVLIRCNNVLYIRGVE   76 (86)
T ss_dssp             HHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEESSEEECGGGEEEEEECC
T ss_pred             HHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEc-CCceeeEccEEEEeCCeEEEEEeCC
Confidence            5789999999999999877      99999999999999984 6667889999999999999999876

>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=99.75  E-value=1.6e-18  Score=100.72  Aligned_cols=59  Identities=32%  Similarity=0.553  Sum_probs=54.2

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      .|++++++++.|.+++++.      +||+|||++|+||+|++ .+++.+.+|.++|||+||++|+|
T Consensus        19 ~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           19 ALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE-DGEVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             HHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGGGEEEEEC
T ss_pred             HHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEe-cCCcccCCCEEEECCCEEEEEEC
Confidence            5789999999999999877      99999999999999996 66788999999999999999975

>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=99.75  E-value=2.3e-18  Score=98.68  Aligned_cols=61  Identities=8%  Similarity=0.117  Sum_probs=54.8

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      =|++++++++.|.++++..      |||+|||++|+||+|+. ++++.+.+|.++|||+||.+|...|
T Consensus         9 ~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~-~~~~~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            9 VLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY-RDGRVAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             HHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC-TTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             HHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEEC-CCCcEEEcCeEEEeCCEEEEEEcCC
Confidence            3688999999999999877      99999999999999985 5557889999999999999998865

>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=99.74  E-value=2e-18  Score=104.78  Aligned_cols=61  Identities=20%  Similarity=0.279  Sum_probs=49.8

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |+++++++|.|.+++++.      |||+||||+|+||+|+..++++.+.+|.++|||+||++|.+.+
T Consensus        21 L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG~nI~~I~~pd   87 (105)
T 4emh_A           21 LNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNIKYLRIQD   87 (105)
T ss_dssp             -----CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECGGGEEEEEC--
T ss_pred             HHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeCCeEEEEecCH
Confidence            788999999999999877      9999999999999998645667889999999999999999865

>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=99.73  E-value=2.5e-18  Score=106.13  Aligned_cols=62  Identities=32%  Similarity=0.625  Sum_probs=52.9

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEec---------Cce-----eeecCeEEEeCCcEEEEEEc
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK---------KNT-----RKPLGRILLKGDNITLMMNT   65 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~---------~~~-----~~~~g~~~iRG~nV~~i~~~   65 (67)
                      |.++++++|.|.+++++.      |||+||||+|+||+|++.+         +..     .+.+|.++|||+||++|.+.
T Consensus        33 L~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~nVv~I~~~  112 (121)
T 2fwk_A           33 IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAMLVPG  112 (121)
T ss_dssp             HHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEEEEESS
T ss_pred             HHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCEEEEEEec
Confidence            478999999999999877      9999999999999999742         223     68899999999999999986


Q ss_pred             CC
Q 035338           66 GK   67 (67)
Q Consensus        66 ~~   67 (67)
                      ++
T Consensus       113 ~~  114 (121)
T 2fwk_A          113 GD  114 (121)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

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

Probab=99.72  E-value=6.9e-18  Score=100.23  Aligned_cols=60  Identities=27%  Similarity=0.440  Sum_probs=51.9

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEec----C--------ceeeecCeEEEeCCcEEEEEEc
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK----K--------NTRKPLGRILLKGDNITLMMNT   65 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~----~--------~~~~~~g~~~iRG~nV~~i~~~   65 (67)
                      |+..+++++.|.+++++.      |||+||||+|+||+|++..    +        .+++.+|.++|||+||++|++.
T Consensus        14 L~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nVv~I~p~   91 (93)
T 4emg_A           14 VRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVILIAPP   91 (93)
T ss_dssp             HHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGEEEEECC
T ss_pred             HHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeEEEEEec
Confidence            456689999999999877      9999999999999999742    2        2578999999999999999985

>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=99.72  E-value=1.1e-17  Score=113.01  Aligned_cols=62  Identities=29%  Similarity=0.493  Sum_probs=55.6

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEe---------cCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHI---------KKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~---------~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      +|+++++++|.|.+++.+.      +||+||||||+||+|++.         .+++++.+|+++|||+||++|+..+
T Consensus         8 kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isve~   84 (231)
T 3pgw_B            8 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEG   84 (231)
T ss_pred             HHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEecC
Confidence            8999999999999999888      999999999999999963         1347899999999999999998654

>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=99.71  E-value=1.1e-17  Score=103.02  Aligned_cols=61  Identities=16%  Similarity=0.256  Sum_probs=55.2

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      -|+++++++|.|.+++...      +||+||||+|+||+|+. .+.+...+|.++|||+||++|.+.|
T Consensus         6 ~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~-~~~~~~~lg~v~IRG~nI~~I~~pd   72 (119)
T 1b34_A            6 FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTL-KNREPVQLETLSIRGNNIRYFILPD   72 (119)
T ss_dssp             HHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEEC-TTSCCEEEEEEEECGGGEEEEECCT
T ss_pred             HHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEec-CCCceeEcceEEEcCCeEEEEEecc
Confidence            4789999999999999877      99999999999999995 5567789999999999999999876

>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=99.67  E-value=3.7e-17  Score=100.44  Aligned_cols=62  Identities=18%  Similarity=0.400  Sum_probs=50.1

Q ss_pred             hhccc--cCcEEEEEccccc------cccceecEEEccEEEEEecC-------------ceeeecCeEEEeCCcEEEEEE
Q 035338            6 VQRIM--TQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK-------------NTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         6 l~~~m--~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~-------------~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      |.+++  +++|.|.+++++.      |||+||||+|+||+|++...             .+.+.+|.++|||+||++|++
T Consensus        32 L~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~nVv~I~~  111 (118)
T 1b34_B           32 LTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLR  111 (118)
T ss_dssp             HHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEEEEEE
T ss_pred             HHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCCEEEEEEe
Confidence            56777  4999999999877      99999999999999986321             125579999999999999998


Q ss_pred             cCC
Q 035338           65 TGK   67 (67)
Q Consensus        65 ~~~   67 (67)
                      .++
T Consensus       112 ~~~  114 (118)
T 1b34_B          112 NPL  114 (118)
T ss_dssp             CCC
T ss_pred             Cch
Confidence            764

>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=99.64  E-value=1.9e-16  Score=98.67  Aligned_cols=61  Identities=8%  Similarity=0.138  Sum_probs=54.6

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      -|+++++++|.|.+++...      +||+|||++|+||+|+. ..++...++.+||||+||.+|++.|
T Consensus         9 ~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~-~~g~~~~l~~v~IRGnnI~~I~lpd   75 (126)
T 2y9a_D            9 VLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY-RDGRVAQLEQVYIRGSKIRFLILPD   75 (126)
T ss_dssp             HHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEEC-TTSCCEEEEEEEECGGGEEEEECCS
T ss_pred             HHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEc-CCCcEeecccEEEeCCEEEEEEccc
Confidence            5789999999999999877      99999999999999985 4446889999999999999999765

>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=99.59  E-value=6.9e-16  Score=96.58  Aligned_cols=57  Identities=14%  Similarity=0.289  Sum_probs=51.5

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .|++++++++.|.+++++.      |||+|||++|+||+|+.     .+.+|.++|||+||++|.+.+
T Consensus         4 ~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~-----~~~lg~v~IRG~nI~~I~~~d   66 (130)
T 1m5q_A            4 ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA-----GEKFNRVFIMYRYIVHIDSTE   66 (130)
T ss_dssp             HHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT-----CCEEEEEEECGGGEEEEEECC
T ss_pred             HHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc-----CCEeceEEEeCCeEEEEEcCC
Confidence            4789999999999999877      99999999999999972     267899999999999999876

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

Probab=96.53  E-value=0.0027  Score=36.96  Aligned_cols=56  Identities=11%  Similarity=0.060  Sum_probs=45.4

Q ss_pred             hhhhccccCcEEEEEccccc------ccc-ceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            4 TKVQRIMTQPINLIFRFLQS------GFD-EYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         4 ~~l~~~m~~pi~v~~~~~~~------~~D-~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      -+|+.+++|.+.|.+.+++.      +|| .-.|++|.+|.    .+   ..+..++|-|.-|.-|...+
T Consensus        10 ~el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~----~~---~~~~~~iI~G~aI~eI~v~~   72 (86)
T 1y96_A           10 LEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFL----ED---GSMSVTGIMGHAVQTVETMN   72 (86)
T ss_dssp             HHHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEEC----TT---SCEEEEEECGGGEEEEEEEE
T ss_pred             HHHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeecc----cC---CeEEEEEEecceEEEEEEec
Confidence            47899999999999999876      999 99999999981    12   23357899999998887543

---

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	67
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-08
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	4e-08
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	6e-08
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	7e-08
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	9e-08
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-07
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	2e-07
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	2e-07
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	2e-07
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	4e-07
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	7e-06
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	0.001

>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 = 44.3 bits (105), Expect = 1e-08
 Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 19/71 (26%)

Query: 10 MTQPINLIFRFLQS------------------GFDEYMNLVLDDAEEVHIKKNTRKPLGR 51
          M  P  ++   +                    G D+YMNL L +A E   ++  R  LG 
Sbjct: 3  MVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRS-LGE 61

Query: 52 ILLKGDNITLM 62
          I+L+G+N+ L+
Sbjct: 62 IVLRGNNVVLI 72

>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 = 43.3 bits (102), Expect = 4e-08
 Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 9/48 (18%)

Query: 24 GFDEYMNLVLDDAEEV---------HIKKNTRKPLGRILLKGDNITLM 62
           FD++MNL+L D +E            ++  ++ LG +LL+G+N+  M
Sbjct: 27 AFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSM 74

>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 = 42.4 bits (100), Expect = 6e-08
 Identities = 13/39 (33%), Positives = 25/39 (64%), Gaps = 2/39 (5%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
           FD+++NL+L+DAEE  I        G ++++G+N+  +
Sbjct: 31 SFDQHVNLLLEDAEE--IIDGNVYKRGTMVVRGENVLFI 67

>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 = 7e-08
 Identities = 16/39 (41%), Positives = 27/39 (69%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
          G+D +MNLVL DAEE+   +  RK +G ++++GD +  +
Sbjct: 32 GYDIHMNLVLLDAEEIQNGEVVRK-VGSVVIRGDTVVFV 69

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

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

 Score = 42.0 bits (99), Expect = 9e-08
 Identities = 13/39 (33%), Positives = 27/39 (69%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
          G+D ++N+VL DAE +   +  ++  G+I+++GDN+  +
Sbjct: 31 GYDIHLNVVLADAEMIQDGEVVKR-YGKIVIRGDNVLAI 68

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

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

 Score = 41.2 bits (97), Expect = 2e-07
 Identities = 20/39 (51%), Positives = 29/39 (74%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
           FD +MNLVL+DAEE+   + TR+ LG +L++GDNI  +
Sbjct: 35 SFDLHMNLVLNDAEELEDGEVTRR-LGTVLIRGDNIVYI 72

>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 = 41.2 bits (97), Expect = 2e-07
 Identities = 17/39 (43%), Positives = 29/39 (74%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
           +D++MNLVL D+EE+    + +K LG I+++GDN+ L+
Sbjct: 36 SYDQHMNLVLSDSEEIQSDGSGKK-LGTIVIRGDNVILI 73

>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 = 41.2 bits (97), Expect = 2e-07
 Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 1/39 (2%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
            D Y NL L++AEE  +   +   LG I ++ +N+  +
Sbjct: 26 STDNYFNLQLNEAEEF-VAGVSHGTLGEIFIRCNNVLYI 63

>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 = 41.8 bits (98), Expect = 2e-07
 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 31/89 (34%)

Query: 10 MTQPINLIFRFLQS-----------------GFDEYMNLVLDDAEEV------------- 39
          +  P+ LI + + +                 GFDEY+N+VLDD +E              
Sbjct: 3  IILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGN 62

Query: 40 -HIKKNTRKPLGRILLKGDNITLMMNTGK 67
            +K+     L  ILL G+N+ +++  G 
Sbjct: 63 KKLKRVMVNRLETILLSGNNVAMLVPGGD 91

>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 = 41.0 bits (96), Expect = 4e-07
 Identities = 12/83 (14%), Positives = 35/83 (42%), Gaps = 32/83 (38%)

Query: 11 TQPINLIFRFLQS-------------------GFDEYMNLVLDDAEEVHIKK-------- 43
          T P++++ + +++                    FD + N+VL++ +E+  +         
Sbjct: 1  TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKK 60

Query: 44 -----NTRKPLGRILLKGDNITL 61
               N  + + ++ L+GD++ +
Sbjct: 61 KSKPVNKDRYISKMFLRGDSVIV 83

>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 = 37.1 bits (86), Expect = 7e-06
 Identities = 6/49 (12%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 15 NLIFRFLQSGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 63
            ++R      ++ MN  + +    +      + L ++ ++G  I  ++
Sbjct: 22 GEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ-LEQVYIRGCKIRFLI 69

>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 = 32.4 bits (74), Expect = 0.001
 Identities = 8/39 (20%), Positives = 15/39 (38%), Gaps = 5/39 (12%)

Query: 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM 62
            D  +N+VL +A     +K       R+ +    I  +
Sbjct: 29 AVDNQLNIVLANASNKAGEK-----FNRVFIMYRYIVHI 62

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	67
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.77
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.77
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.76
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.76
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.75
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.75
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.75
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.75
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.74
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.69
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.66
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.59
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.41

>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=99.77  E-value=3e-19  Score=100.28  Aligned_cols=60  Identities=23%  Similarity=0.426  Sum_probs=54.5

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .|+++++++|.|.+++++.      +||+|||++|+||+|+.  .++.+++|.++|||+||++|++.+
T Consensus         6 ~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~--~~~~~~~g~v~iRG~~I~~I~~~P   71 (71)
T d1i8fa_           6 TLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII--DGNVYKRGTMVVRGENVLFISPVP   71 (71)
T ss_dssp             HHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEE--TTEEEEEEEEEECGGGEEEEEECC
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEE--CCCEEEcceEEEeCCeEEEEeCCC
Confidence            5899999999999999877      99999999999999985  346788999999999999999864

>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=99.77  E-value=2.9e-19  Score=100.30  Aligned_cols=60  Identities=27%  Similarity=0.515  Sum_probs=54.7

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEc
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNT   65 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~   65 (67)
                      -|++++++++.|.+++++.      +||+|||++|+||+|+. .++.++.+|.++|||++|++|+++
T Consensus         7 ~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~~g~~~IRG~~I~~Ispa   72 (72)
T d1i4k1_           7 VLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQ-NGEVVRKVGSVVIRGDTVVFVSPA   72 (72)
T ss_dssp             HHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEES-SSSEEEEEEEEEECGGGEEEEECC
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEe-cCCeEeEcceEEEeCCeEEEEEcC
Confidence            4789999999999999877      99999999999999984 667888999999999999999864

>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=99.76  E-value=5.5e-19  Score=98.55  Aligned_cols=60  Identities=20%  Similarity=0.396  Sum_probs=53.0

Q ss_pred             hhccccCcEEEEEc-cccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            6 VQRIMTQPINLIFR-FLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         6 l~~~m~~pi~v~~~-~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |++++++++.|.++ ++..      +||+|||++|+||+|+. +++..+.+|.++|||+||.+|.+.+
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~~~IRG~nI~~I~~~p   67 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV-AGVSHGTLGEIFIRCNNVLYIRELP   67 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEE-TTEEEEECCSEEECGGGEEEEEECC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEe-cCCcccCcCeEEEECCEEEEEEeCC
Confidence            67899999999998 4443      99999999999999984 7778889999999999999998654

>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=99.76  E-value=5.4e-19  Score=98.78  Aligned_cols=59  Identities=29%  Similarity=0.514  Sum_probs=54.5

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEc
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNT   65 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~   65 (67)
                      |++++++++.|.+++++.      +||+|||++|+||+|+. ++++.+.+|.++|||++|++|+|.
T Consensus         7 L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~l~~~~IRG~~I~~Isp~   71 (71)
T d1h641_           7 IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQ-DGEVVKRYGKIVIRGDNVLAISPT   71 (71)
T ss_dssp             HHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGGGEEEEEEC
T ss_pred             HHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEe-cCCcEeEcCcEEEECCeEEEEeCC
Confidence            789999999999999877      99999999999999985 677889999999999999999984

>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=99.75  E-value=4.6e-19  Score=103.33  Aligned_cols=63  Identities=32%  Similarity=0.595  Sum_probs=54.3

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEec--------------CceeeecCeEEEeCCcEEEEEE
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK--------------KNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~--------------~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      -|++++++++.|.+++++.      +||+|||++|+||+|++..              ....+.+|.+||||+||++|+|
T Consensus         9 ~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~Vv~I~p   88 (92)
T d2fwka1           9 LIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAMLVP   88 (92)
T ss_dssp             HHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEEEEES
T ss_pred             HHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEEEEEEe
Confidence            3788999999999999877      9999999999999998642              1245689999999999999998


Q ss_pred             cCC
Q 035338           65 TGK   67 (67)
Q Consensus        65 ~~~   67 (67)
                      ..|
T Consensus        89 ~~~   91 (92)
T d2fwka1          89 GGD   91 (92)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

>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=99.75  E-value=1.2e-18  Score=98.59  Aligned_cols=60  Identities=28%  Similarity=0.509  Sum_probs=55.0

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEc
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNT   65 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~   65 (67)
                      -|++++++++.|.+++++.      +||+|||++|+||+|+. .+++++.+|.++|||++|++|++.
T Consensus        11 ~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~~~~v~iRG~~I~~I~~~   76 (76)
T d1th7a1          11 VLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQ-SDGSGKKLGTIVIRGDNVILISPL   76 (76)
T ss_dssp             HHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEC-SSSCEEEEEEEEECGGGEEEEEEC
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEe-cCCcccCcceEEEECCEEEEEEeC
Confidence            5788999999999999877      99999999999999985 666888999999999999999984

>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=99.75  E-value=1.3e-18  Score=98.63  Aligned_cols=60  Identities=30%  Similarity=0.531  Sum_probs=53.7

Q ss_pred             hhhhccccCcEEEEEccc-cc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338            4 TKVQRIMTQPINLIFRFL-QS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         4 ~~l~~~m~~pi~v~~~~~-~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      ..|++++++++.|.+++. +.      +||+|||++|+||+|+. ++++.+.+|.++|||+||.+|+|
T Consensus         8 ~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           8 QMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECK-GEEKVRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             HHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGGGEEEEEE
T ss_pred             HHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEc-CCCcEeEcceEEEeCCEEEEEEC
Confidence            368899999999999854 44      99999999999999985 67788999999999999999987

>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=99.75  E-value=1e-18  Score=98.48  Aligned_cols=59  Identities=32%  Similarity=0.553  Sum_probs=54.2

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      -|++++++++.|.+++++.      +||+|||++|+||+|+. ++++++.+|.++|||++|++|+|
T Consensus        10 ~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~-~~~~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_          10 ALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE-DGEVTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             HHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEE-TTEEEEEEEEEEECGGGEEEEEC
T ss_pred             HHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEe-CCCeEeEcceEEEeCCEEEEEeC
Confidence            3789999999999999877      99999999999999985 67788999999999999999986

>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=99.74  E-value=1.2e-18  Score=99.73  Aligned_cols=61  Identities=28%  Similarity=0.447  Sum_probs=53.6

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEec---------CceeeecCeEEEeCCcEEEEEEc
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK---------KNTRKPLGRILLKGDNITLMMNT   65 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~---------~~~~~~~g~~~iRG~nV~~i~~~   65 (67)
                      +|.+++++++.|.+++++.      |||+||||+|+||+|++..         ..+.+.+|.++|||+||++|+..
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEcc
Confidence            4899999999999999887      9999999999999998631         13568899999999999999863

>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=99.69  E-value=9.8e-18  Score=98.25  Aligned_cols=61  Identities=18%  Similarity=0.418  Sum_probs=48.9

Q ss_pred             hhccc--cCcEEEEEccccc------cccceecEEEccEEEEEecC-------------ceeeecCeEEEeCCcEEEEEE
Q 035338            6 VQRIM--TQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK-------------NTRKPLGRILLKGDNITLMMN   64 (67)
Q Consensus         6 l~~~m--~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~-------------~~~~~~g~~~iRG~nV~~i~~   64 (67)
                      |.+.+  +++|.|.+++.+.      |||+||||+|+||+|++...             .+.+.+|.++|||+||++|..
T Consensus         7 l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnVv~I~~   86 (93)
T d1b34b_           7 LTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLR   86 (93)
T ss_dssp             HHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEEEEEE
T ss_pred             HHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEEEEEEc
Confidence            55666  7899999999877      99999999999999986421             235789999999999999987


Q ss_pred             cC
Q 035338           65 TG   66 (67)
Q Consensus        65 ~~   66 (67)
                      .+
T Consensus        87 ~p   88 (93)
T d1b34b_          87 NP   88 (93)
T ss_dssp             CC
T ss_pred             Ch
Confidence            54

>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=99.66  E-value=7.7e-17  Score=90.34  Aligned_cols=60  Identities=8%  Similarity=0.129  Sum_probs=53.8

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |++..++++.|.++++..      +||.|||++|+||+++. .+++...++.++|||++|.+|...|
T Consensus         7 L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~-~~~~~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           7 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY-RDGRVAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             HHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC-TTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             HHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEc-CCCcEeEcCeEEEECCEEEEEEcCC
Confidence            577889999999999877      99999999999999984 5567788999999999999998865

>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=99.59  E-value=9.2e-16  Score=87.53  Aligned_cols=60  Identities=17%  Similarity=0.278  Sum_probs=54.0

Q ss_pred             hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      |++..++++.|.++++..      ++|.|||++|+||+++. ++++...++.++|||++|.+|...|
T Consensus         6 L~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~-~~~~~~~~~~v~IRG~~Ir~i~lPd   71 (80)
T d1b34a_           6 LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTL-KNREPVQLETLSIRGNNIRYFILPD   71 (80)
T ss_dssp             HHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEEC-TTSCCEEEEEEEECGGGEEEEECCT
T ss_pred             HHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEc-CCCCEEEcccEEEcCCEEEEEECCC
Confidence            678899999999999877      99999999999999984 5567788999999999999999866

>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=99.41  E-value=8e-14  Score=85.57  Aligned_cols=57  Identities=14%  Similarity=0.289  Sum_probs=49.7

Q ss_pred             hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338            5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG   66 (67)
Q Consensus         5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~   66 (67)
                      .|++++++++.|.++++..      +||+|||++|+||++.  .++   .++.++|||++|.+|...+
T Consensus         4 ~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~--~~~---k~~~v~IRG~~I~~I~~~e   66 (127)
T d1m5q1_           4 ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK--AGE---KFNRVFIMYRYIVHIDSTE   66 (127)
T ss_dssp             HHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEET--TCC---EEEEEEECGGGEEEEEECS
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEEC--CCC---cccEEEEeCCeEEEEEcch
Confidence            3899999999999999877      9999999999999885  232   4678999999999998765