Psyllid ID: psy488

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80------
Protein Sequence
MDVDRTSSRSDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDIEI
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEEEccEEEEEEEEEcccccEEEEcccccccccccccEEEEcccEEEEEc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEcEEEEEEEEEccccHHHEEHHccccccccccHHHEEEcccEEEEEc
Coil and Loop (DISEMBL)
mdvdrtssrsDEEIAAEMREKFLKAMsslsgqpctinmFERTVVTaefqgtnsdlTEFYVRNlktpigtfhehallrvddivdiei
Flexible Loop (DISEMBL)
mdvdrtssrsdeeIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEfqgtnsdlTEFYVRNLKTpigtfhehallrvddivdiei
Low Complexity Region (SEG)
MDVDRTSSRSDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDIEI
Disordered region (IsUnstruct)
*******************************QPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDI**
Disordered Region (DISOPRED)
*****************MREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDIEI
Disordered Region (DISEMBL)
*************IAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDIEI
Disordered Region (DISPRO)
**************AAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDIEI
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDVDRTSSRSDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDIEI
Positional Conservation
no confident homologs detected

---

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	86	2.2.26 [Sep-21-2011]
Q9CWY4	129	Gem-associated protein 7	yes	N/A	0.825	0.550	0.388	8e-09
Q17QA0	125	Gem-associated protein 7	yes	N/A	0.825	0.568	0.361	3e-08
Q9H840	131	Gem-associated protein 7	yes	N/A	0.930	0.610	0.365	7e-07

>sp|Q9CWY4|GEMI7_MOUSE Gem-associated protein 7 OS=Mus musculus GN=Gemin7 PE=2 SV=1

 Score = 58.9 bits (141), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 11  DEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTF 70
           ++   A +RE++L+++ ++ G P +  + E   VTA+F  T+ D+  FYV  L+TPIG  
Sbjct: 53  EQRARATLRERYLRSLLAMVGHPVSFTLHEGVHVTAQFGATDLDVANFYVSQLQTPIGVQ 112

Query: 71  HEHALLRVDDIV 82
            E ALLR  DI+
Sbjct: 113 AE-ALLRCSDII 123

The SMN complex plays an essential role in spliceosomal snRNP assembly in the cytoplasm and is required for pre-mRNA splicing in the nucleus.
Mus musculus (taxid: 10090)

>sp|Q17QA0|GEMI7_BOVIN Gem-associated protein 7 OS=Bos taurus GN=GEMIN7 PE=2 SV=1

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 11  DEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTF 70
           +++  A +RE++L+++ ++ G+P    + E   V A F  T+ D+  FYV  L+TPIG  
Sbjct: 49  EQQARASLRERYLRSLLAMVGRPVCFTLHEGVQVIAHFGATDLDVANFYVSQLQTPIG-I 107

Query: 71  HEHALLRVDDIV 82
              ALLR  DI+
Sbjct: 108 QAEALLRCSDII 119

The SMN complex plays an essential role in spliceosomal snRNP assembly in the cytoplasm and is required for pre-mRNA splicing in the nucleus.

Bos taurus (taxid: 9913)

>sp|Q9H840|GEMI7_HUMAN Gem-associated protein 7 OS=Homo sapiens GN=GEMIN7 PE=1 SV=1

 Score = 52.8 bits (125), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 47/82 (57%), Gaps = 2/82 (2%)

Query: 2   DVDRTSSRSDEEIA-AEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYV 60
            + + S  S E+ A A +RE++L+++ ++ G   +  + E   V A F  T+ D+  FYV
Sbjct: 45  PIAQESLESQEQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYV 104

Query: 61  RNLKTPIGTFHEHALLRVDDIV 82
             L+TPIG   E ALLR  DI+
Sbjct: 105 SQLQTPIGVQAE-ALLRCSDII 125

The SMN complex plays an essential role in spliceosomal snRNP assembly in the cytoplasm and is required for pre-mRNA splicing in the nucleus.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	86
197313773	112	gem (nuclear organelle) associated prote	0.860	0.660	0.44	2e-11
383852449	104	PREDICTED: gem-associated protein 7-like	0.860	0.711	0.413	2e-09
340719732	104	PREDICTED: gem-associated protein 7-like	0.860	0.711	0.413	6e-09
402592491	109	hypothetical protein WUBG_02668 [Wuchere	0.918	0.724	0.412	1e-08
357604681	92	gem associated protein 7 [Danaus plexipp	0.848	0.793	0.424	1e-08
170573358	109	Gem-associated protein 7 [Brugia malayi]	0.860	0.678	0.44	2e-08
350410710	104	PREDICTED: gem-associated protein 7-like	0.860	0.711	0.4	2e-08
393911667	109	gem-associated protein 7 [Loa loa]	0.848	0.669	0.418	3e-08
312071033	108	gem-associated protein 7 [Loa loa]	0.848	0.675	0.418	3e-08
345311537	297	PREDICTED: hypothetical protein LOC10009	0.767	0.222	0.417	4e-08

>gi|197313773|ref|NP_001127920.1| gem (nuclear organelle) associated protein 7 [Nasonia vitripennis]

 Score = 73.2 bits (178), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 53/75 (70%), Gaps = 1/75 (1%)

Query: 12  EEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFH 71
           +E  A +RE+FL+ ++ + G+P   +++E T VTAEF+G + D  E YVRNL TP+GT  
Sbjct: 36  QEARAFLRERFLRVITGIVGKPAKFHLYENTSVTAEFRGCDIDFLELYVRNLTTPLGTIP 95

Query: 72  EHALLRVDDIVDIEI 86
           E A+LR +D++ +E+
Sbjct: 96  E-AVLRTNDVILLEM 109

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383852449|ref|XP_003701739.1| PREDICTED: gem-associated protein 7-like [Megachile rotundata]

 Score = 66.2 bits (160), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 51/75 (68%), Gaps = 1/75 (1%)

Query: 12 EEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFH 71
          +E  A +RE+FL+ ++ + G+     ++E T V+AEF+G + D  E YVRNL+TP+G   
Sbjct: 25 QEARAFLRERFLRVITGIVGKKAEFYLYENTRVSAEFRGCDIDCLEIYVRNLETPLGKVP 84

Query: 72 EHALLRVDDIVDIEI 86
          E A+LR +DI+ +E+
Sbjct: 85 E-AILRANDIIHMEV 98

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719732|ref|XP_003398301.1| PREDICTED: gem-associated protein 7-like isoform 1 [Bombus terrestris] gi|340719734|ref|XP_003398302.1| PREDICTED: gem-associated protein 7-like isoform 2 [Bombus terrestris]

 Score = 65.1 bits (157), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 50/75 (66%), Gaps = 1/75 (1%)

Query: 12 EEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFH 71
          +E  A +RE+FL+ ++ + G+     ++E T V+A+F+G + D  E YVRNL+TP+GT  
Sbjct: 25 QEARAFLRERFLRVITGIVGKQAEFYLYENTQVSAQFRGCDVDCLEVYVRNLETPLGTIP 84

Query: 72 EHALLRVDDIVDIEI 86
          E A+LR  DI+ + I
Sbjct: 85 E-AVLRASDIIYLNI 98

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|402592491|gb|EJW86419.1| hypothetical protein WUBG_02668 [Wuchereria bancrofti]

 Score = 63.9 bits (154), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/80 (41%), Positives = 50/80 (62%), Gaps = 1/80 (1%)

Query: 5  RTSSRSDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK 64
          + S  S++E  AE+RE+FL+ MS L G+   ++M ERT V  +F    +D T + V  L 
Sbjct: 16 KQSGTSEQEQRAELRERFLRLMSFLGGKQIELDMHERTQVAGKFCAVKADQTHYIVDALI 75

Query: 65 TPIGTFHEHALLRVDDIVDI 84
          TPIG  + HA+LR++D + I
Sbjct: 76 TPIGLIN-HAILRMNDTITI 94

Source: Wuchereria bancrofti

Species: Wuchereria bancrofti

Genus: Wuchereria

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|357604681|gb|EHJ64288.1| gem associated protein 7 [Danaus plexippus]

 Score = 63.9 bits (154), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 43/73 (58%)

Query: 12 EEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFH 71
          +E   ++RE FL+ +S L GQPC I  +E++ + A F+G   D +E  V NLKTP     
Sbjct: 11 QEARRQLRESFLRDVSELKGQPCHILTYEQSTLEATFKGWKPDGSEVLVSNLKTPANIIM 70

Query: 72 EHALLRVDDIVDI 84
            ALLR  DI+ I
Sbjct: 71 SSALLRTPDILAI 83

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170573358|ref|XP_001892437.1| Gem-associated protein 7 [Brugia malayi] gi|158602003|gb|EDP38724.1| Gem-associated protein 7, putative [Brugia malayi]

 Score = 63.5 bits (153), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 49/75 (65%), Gaps = 1/75 (1%)

Query: 10 SDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGT 69
          S++E  AE+RE+FL+ MS L G+   ++M ERT VT +F    +D T + V  L TPIG 
Sbjct: 21 SEQEQRAELRERFLRLMSFLGGKQIELDMHERTQVTGKFCAVKADQTHYIVDALITPIGL 80

Query: 70 FHEHALLRVDDIVDI 84
           + HA+LR++D + I
Sbjct: 81 IN-HAILRMNDTIMI 94

Source: Brugia malayi

Species: Brugia malayi

Genus: Brugia

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|350410710|ref|XP_003489116.1| PREDICTED: gem-associated protein 7-like [Bombus impatiens]

 Score = 63.2 bits (152), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 50/75 (66%), Gaps = 1/75 (1%)

Query: 12 EEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFH 71
          +E  A +RE+FL+ ++ + G+     ++E T V+A+F+G + D  E +VRNL+TP+GT  
Sbjct: 25 QEARAFLRERFLRVITGIVGKQAEFYLYENTQVSAQFRGCDVDCLEVFVRNLETPLGTIP 84

Query: 72 EHALLRVDDIVDIEI 86
          E A+LR  DI+ + I
Sbjct: 85 E-AVLRASDIIYLNI 98

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|393911667|gb|EFO25647.2| gem-associated protein 7 [Loa loa]

 Score = 62.4 bits (150), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 1/74 (1%)

Query: 11 DEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTF 70
          ++E   E+RE+FL+ MS L G+   ++M ERT V  +F    +DLT + V  L TPIG  
Sbjct: 21 EQEQRTELRERFLRMMSFLGGKQVELDMHERTQVVGKFGAVKADLTHYIVDALITPIGVI 80

Query: 71 HEHALLRVDDIVDI 84
          + HA+LR++D + I
Sbjct: 81 N-HAILRMNDTIII 93

Source: Loa loa

Species: Loa loa

Genus: Loa

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|312071033|ref|XP_003138421.1| gem-associated protein 7 [Loa loa]

 Score = 62.4 bits (150), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 47/74 (63%), Gaps = 1/74 (1%)

Query: 11 DEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTF 70
          ++E   E+RE+FL+ MS L G+   ++M ERT V  +F    +DLT + V  L TPIG  
Sbjct: 20 EQEQRTELRERFLRMMSFLGGKQVELDMHERTQVVGKFGAVKADLTHYIVDALITPIGVI 79

Query: 71 HEHALLRVDDIVDI 84
          + HA+LR++D + I
Sbjct: 80 N-HAILRMNDTIII 92

Source: Loa loa

Species: Loa loa

Genus: Loa

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|345311537|ref|XP_001520699.2| PREDICTED: hypothetical protein LOC100091962 [Ornithorhynchus anatinus]

 Score = 62.4 bits (150), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 28/67 (41%), Positives = 46/67 (68%), Gaps = 1/67 (1%)

Query: 16  AEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHAL 75
           AE+RE++L+++ ++SG+P    + ER  V A F  ++ D+  F+V +L+TP+GT  E AL
Sbjct: 211 AELRERYLRSLLAMSGRPVRFALHERVRVAARFAASDLDVANFHVADLQTPLGTQRE-AL 269

Query: 76  LRVDDIV 82
           LR  DI+
Sbjct: 270 LRCSDII 276

Source: Ornithorhynchus anatinus

Species: Ornithorhynchus anatinus

Genus: Ornithorhynchus

Family: Ornithorhynchidae

Order: Monotremata

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

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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	86
MGI|MGI:1916981	129	Gemin7 "gem (nuclear organelle	0.837	0.558	0.418	1.8e-09
RGD|1597035	132	Gemin7 "gem (nuclear organelle	0.837	0.545	0.418	2.2e-09
UNIPROTKB|E2RHG3	131	GEMIN7 "Uncharacterized protei	0.918	0.603	0.35	7.6e-09
UNIPROTKB|Q17QA0	125	GEMIN7 "Gem-associated protein	0.825	0.568	0.375	9.7e-09
UNIPROTKB|I3LCH5	115	GEMIN7 "Uncharacterized protei	0.825	0.617	0.375	9.7e-09
UNIPROTKB|Q9H840	131	GEMIN7 "Gem-associated protein	0.918	0.603	0.370	3.3e-08
WB|WBGene00007702	92	C24H11.5 [Caenorhabditis elega	0.790	0.739	0.391	3.4e-06

MGI|MGI:1916981 Gemin7 "gem (nuclear organelle) associated protein 7" [Mus musculus (taxid:10090)]

 Score = 138 (53.6 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 31/74 (41%), Positives = 47/74 (63%)

Query:    10 SDEEIA-AEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIG 68
             S E+ A A +RE++L+++ ++ G P +  + E   VTA+F  T+ D+  FYV  L+TPIG
Sbjct:    51 SQEQRARATLRERYLRSLLAMVGHPVSFTLHEGVHVTAQFGATDLDVANFYVSQLQTPIG 110

Query:    69 TFHEHALLRVDDIV 82
                E ALLR  DI+
Sbjct:   111 VQAE-ALLRCSDII 123

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016604 "nuclear body" evidence=ISO

GO:0032797 "SMN complex" evidence=IEA

RGD|1597035 Gemin7 "gem (nuclear organelle) associated protein 7" [Rattus norvegicus (taxid:10116)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 31/74 (41%), Positives = 47/74 (63%)

Query:    10 SDEEIA-AEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIG 68
             S E+ A A +RE++L+++ ++ G P +  + E   VTA+F  T+ D+  FYV  L+TPIG
Sbjct:    54 SQEQRARAVLRERYLRSLLAMVGHPVSFTLHEGVHVTAQFGATDLDVANFYVSQLQTPIG 113

Query:    69 TFHEHALLRVDDIV 82
                E ALLR  DI+
Sbjct:   114 VQAE-ALLRCSDII 126

GO:0005654 "nucleoplasm" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0016604 "nuclear body" evidence=ISO

GO:0032797 "SMN complex" evidence=IEA

UNIPROTKB|E2RHG3 GEMIN7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 28/80 (35%), Positives = 46/80 (57%)

Query:     3 VDRTSSRSDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRN 62
             V  +    +++  A +RE++L+++ ++ G   +  + E   VTA F  T+ D+  FYV  
Sbjct:    47 VQESRESQEQQARAALRERYLRSLLAMVGHQVSFTLHEGVHVTAHFGATDLDVANFYVSQ 106

Query:    63 LKTPIGTFHEHALLRVDDIV 82
             L+TPIG   E ALLR  DI+
Sbjct:   107 LQTPIGVQAE-ALLRCSDII 125

GO:0016604 "nuclear body" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0032797 "SMN complex" evidence=IEA

UNIPROTKB|Q17QA0 GEMIN7 "Gem-associated protein 7" [Bos taurus (taxid:9913)]

 Score = 131 (51.2 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 27/72 (37%), Positives = 44/72 (61%)

Query:    11 DEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTF 70
             +++  A +RE++L+++ ++ G+P    + E   V A F  T+ D+  FYV  L+TPIG  
Sbjct:    49 EQQARASLRERYLRSLLAMVGRPVCFTLHEGVQVIAHFGATDLDVANFYVSQLQTPIGIQ 108

Query:    71 HEHALLRVDDIV 82
              E ALLR  DI+
Sbjct:   109 AE-ALLRCSDII 119

GO:0015030 "Cajal body" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0032797 "SMN complex" evidence=IEA

UNIPROTKB|I3LCH5 GEMIN7 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 131 (51.2 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 27/72 (37%), Positives = 45/72 (62%)

Query:    11 DEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTF 70
             +++  A +RE++L+++ ++ G+  +  + E   VTA F  T+ D+  FYV  L+TPIG  
Sbjct:    39 EQQARAALRERYLRSLLAMVGRQVSFTLHEGVQVTAHFGATDLDVANFYVSQLQTPIGVQ 98

Query:    71 HEHALLRVDDIV 82
              E ALLR  DI+
Sbjct:    99 AE-ALLRCSDII 109

GO:0016604 "nuclear body" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0032797 "SMN complex" evidence=IEA

UNIPROTKB|Q9H840 GEMIN7 "Gem-associated protein 7" [Homo sapiens (taxid:9606)]

 Score = 126 (49.4 bits), Expect = 3.3e-08, P = 3.3e-08
 Identities = 30/81 (37%), Positives = 47/81 (58%)

Query:     3 VDRTSSRSDEEIA-AEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVR 61
             + + S  S E+ A A +RE++L+++ ++ G   +  + E   V A F  T+ D+  FYV 
Sbjct:    46 IAQESLESQEQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVS 105

Query:    62 NLKTPIGTFHEHALLRVDDIV 82
              L+TPIG   E ALLR  DI+
Sbjct:   106 QLQTPIGVQAE-ALLRCSDII 125

GO:0032797 "SMN complex" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0015030 "Cajal body" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0000387 "spliceosomal snRNP assembly" evidence=TAS

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

GO:0005654 "nucleoplasm" evidence=IDA;TAS

GO:0005737 "cytoplasm" evidence=IDA

GO:0016604 "nuclear body" evidence=IDA

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0034660 "ncRNA metabolic process" evidence=TAS

WB|WBGene00007702 C24H11.5 [Caenorhabditis elegans (taxid:6239)]

 Score = 107 (42.7 bits), Expect = 3.4e-06, P = 3.4e-06
 Identities = 27/69 (39%), Positives = 35/69 (50%)

Query:    16 AEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHAL 75
             A +RE++L  +   + +P TI M ERT VTA  +          V  L TPIG   + A 
Sbjct:    17 AVLRERYLSFLQKSADKPATIEMCERTTVTATIKAFQPSSEHVIVEKLATPIGIL-DKAA 75

Query:    76 LRVDDIVDI 84
             LR  DIV I
Sbjct:    76 LRSTDIVKI 84


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.132   0.362    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       86        86   0.00091  102 3  11 22  0.43    29
                                                     29  0.47    30


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  7
  No. of states in DFA:  500 (53 KB)
  Total size of DFA:  89 KB (2066 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  9.88u 0.11s 9.99t   Elapsed:  00:00:07
  Total cpu time:  9.88u 0.11s 9.99t   Elapsed:  00:00:08
  Start:  Thu Aug 15 15:04:22 2013   End:  Thu Aug 15 15:04:30 2013

GO:0032797 "SMN complex" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9H840	GEMI7_HUMAN	No assigned EC number	0.3658	0.9302	0.6106	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	86
cd11677	77	cd11677, Gemin7, Gemin 7	1e-24
pfam11095	80	pfam11095, Gemin7, Gem-associated protein 7 (Gemin	2e-17

>gnl|CDD|212488 cd11677, Gemin7, Gemin 7

 Score = 87.3 bits (217), Expect = 1e-24
 Identities = 32/77 (41%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 10 SDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGT 69
           ++E  A +RE+FL+++ +L+G+P    M E T VTA F+  + D+  F V NLKTP+G 
Sbjct: 1  LEQEARAFLRERFLRSLLALAGKPVEFTMHENTTVTATFKACDIDVENFQVSNLKTPLGI 60

Query: 70 FHEHALLRVDDIVDIEI 86
              ALLR  DI+ I  
Sbjct: 61 Q-PEALLRTSDIISITF 76

Gemins 7, together with the survival motor neuron (SMN) protein, other Gemins, and Unr-interacting protein (UNRIP) form the SMN complex, which plays an important role in the Sm core assembly reaction, by binding directly to the Sm proteins, as well as UsnRNAs. Gemin 7 forms a heterodimer with Gemin 6, which serve as a surrogate for the SmB-SmD3 dimer during the formation of the heptameric Sm ring. Length = 77

>gnl|CDD|151540 pfam11095, Gemin7, Gem-associated protein 7 (Gemin7)

 Score = 69.0 bits (169), Expect = 2e-17
 Identities = 28/73 (38%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 12 EEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFH 71
          +   A +RE++L+++ ++ G+P    + ER  VTA F  T+ D+  FYV  L+TPIG   
Sbjct: 5  QRARAVLRERYLRSLLAMVGKPVEFTLHERVSVTAVFGATDIDVENFYVSQLQTPIGVQK 64

Query: 72 EHALLRVDDIVDI 84
          E ALLR  D++  
Sbjct: 65 E-ALLRCSDVISF 76

Gemin7 is a novel component of the survival of motor neuron complex which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE. Length = 80

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	86
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	100.0
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	97.32
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	96.77
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	96.69
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	96.46
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	96.38
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	96.32
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	96.12
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	96.06
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	95.99
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	95.95
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	95.91
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	95.83
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	95.74
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	95.49
PRK00737	72	small nuclear ribonucleoprotein; Provisional	95.25
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	94.13
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	93.68
KOG3482|consensus	79		93.54
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	92.59
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	91.6
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	89.68
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	89.58
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	89.34
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	87.18

>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins

Probab=100.00  E-value=5.8e-45  Score=239.94  Aligned_cols=78  Identities=36%  Similarity=0.667  Sum_probs=73.2

Q ss_pred             CcHHHHHHHHHHHHHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCccccceeeecCceeEEeC
Q psy488            8 SRSDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDIEI   86 (86)
Q Consensus         8 ~~~eQ~aRa~LRerfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e~AlLR~~DIi~~~~   86 (86)
                      +++||+||++||||||++|++|+||||+|+|||||+|+|+|+|||+|++||+||||+||||++|+ |+|||+|||+|+|
T Consensus         1 ~~~eQ~aR~~LRerfLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~TPlGv~~e-AlLR~~DVi~~~f   78 (80)
T PF11095_consen    1 ESEEQEARAFLRERFLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQTPLGVQPE-ALLRCSDVISISF   78 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEETTTTEEEE-EEEEGGGEEEEEE
T ss_pred             ChHHHHHHHHHHHHHHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCCCcccChh-heeecCCEEEEEe
Confidence            47899999999999999999999999999999999999999999999999999999999999999 9999999999975

Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.

>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=97.32  E-value=0.0017  Score=41.91  Aligned_cols=62  Identities=13%  Similarity=0.322  Sum_probs=50.2

Q ss_pred             HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC--CC-----cCccccceeeecCceeEEe
Q psy488           22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK--TP-----IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~--TP-----iGv~~e~AlLR~~DIi~~~   85 (86)
                      ||.+|.++.|++|.+.|..+.++.|+..++|..- |+..+|-+  .|     .+..++ ..+|++-|..+.
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~M-Ni~L~n~~~~~~~~~~~~~~~~~-v~IRG~~I~~I~   70 (81)
T cd01725           2 FFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYL-NIKLTNISVTDPEKYPHMLSVKN-CFIRGSVVRYVQ   70 (81)
T ss_pred             hhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCc-ccEEEEEEEEcCCCcccccccCe-EEEECCEEEEEE
Confidence            7889999999999999999999999999999764 77777664  12     233456 899999887664

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.

>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=96.77  E-value=0.0058  Score=36.16  Aligned_cols=57  Identities=11%  Similarity=0.225  Sum_probs=44.9

Q ss_pred             HhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-----CCcCccccceeeecCceeEEe
Q psy488           27 SSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-----TPIGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        27 ~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-----TPiGv~~e~AlLR~~DIi~~~   85 (86)
                      .++.|++|.+.+.++....|++.++|... |+..++-.     ..-...+. .++|.+.|..++
T Consensus         2 ~~~~g~~V~V~l~~g~~~~G~L~~~D~~~-Ni~L~~~~~~~~~~~~~~~~~-~~irG~~I~~I~   63 (63)
T cd00600           2 KDLVGKTVRVELKDGRVLEGVLVAFDKYM-NLVLDDVEETIKEGKKRVLGL-VLIRGDNVRLVT   63 (63)
T ss_pred             hHHCCCEEEEEECCCcEEEEEEEEECCCC-CEEECCEEEEecCCcEEECCe-EEEECCEEEEEC
Confidence            46689999999999999999999999766 77766653     22334556 899999998763

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.

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

Probab=96.69  E-value=0.0038  Score=39.16  Aligned_cols=36  Identities=14%  Similarity=0.331  Sum_probs=28.7

Q ss_pred             HHHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCc
Q psy488           20 EKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDL   55 (86)
Q Consensus        20 erfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~   55 (86)
                      +|++..+..+.|++|++++.++..-+|.|.+++.+.
T Consensus         1 dRl~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~   36 (77)
T PF14438_consen    1 DRLVYLLTNLVGQTVEVTTKNGSVYEGIFHSASPES   36 (77)
T ss_dssp             ---HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T--
T ss_pred             ChHHHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcc
Confidence            589999999999999999999999999999999964

>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=96.46  E-value=0.029  Score=34.84  Aligned_cols=60  Identities=15%  Similarity=0.274  Sum_probs=47.7

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CCcC----ccccceeeecCceeEE
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TPIG----TFHEHALLRVDDIVDI   84 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TPiG----v~~e~AlLR~~DIi~~   84 (86)
                      +..|.++.|++|.+.|.++.++.|+..++| +..|+..++-. +.-|    ..+. .++|.+-|+.|
T Consensus         3 ~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D-~~mNi~L~~~~e~~~~~~~~~lg~-~~IRG~~I~~i   67 (68)
T cd01722           3 KPFLNDLTGKPVIVKLKWGMEYKGTLVSVD-SYMNLQLANTEEYIDGKSTGNLGE-VLIRCNNVLYI   67 (68)
T ss_pred             HHHHHHcCCCEEEEEECCCcEEEEEEEEEC-CCEEEEEeeEEEEeCCccccCcCc-EEEECCEEEEE
Confidence            456778899999999999999999999999 67777777763 2222    3355 89999998765

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.

>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=96.38  E-value=0.022  Score=35.18  Aligned_cols=60  Identities=10%  Similarity=0.247  Sum_probs=47.5

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCC-CcC----ccccceeeecCceeEE
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKT-PIG----TFHEHALLRVDDIVDI   84 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T-PiG----v~~e~AlLR~~DIi~~   84 (86)
                      |.+|.++.|++|.+.|..+..+.|+..++| +..|+..++-.. .-|    ..+. .++|++-|+.+
T Consensus         2 ~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D-~~mNlvL~~~~~~~~~~~~~~~~~-v~IRG~~I~~I   66 (67)
T cd01726           2 SEFLKAIIGRPVVVKLNSGVDYRGILACLD-GYMNIALEQTEEYVNGQLKNKYGD-AFIRGNNVLYI   66 (67)
T ss_pred             HHHHHhhCCCeEEEEECCCCEEEEEEEEEc-cceeeEEeeEEEEeCCceeeEeCC-EEEECCEEEEE
Confidence            456778899999999999999999999999 677888887642 222    2345 88999888765

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

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

Probab=96.32  E-value=0.019  Score=34.56  Aligned_cols=60  Identities=10%  Similarity=0.076  Sum_probs=44.4

Q ss_pred             HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCc-----cccceeeecCceeEEe
Q psy488           25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGT-----FHEHALLRVDDIVDIE   85 (86)
Q Consensus        25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv-----~~e~AlLR~~DIi~~~   85 (86)
                      +|.++.|++|.+.|.++..+.|++.++|....-.+-.--++.-+.     .+. .++|.+-|+.+.
T Consensus         2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~-~~irG~~I~~I~   66 (67)
T PF01423_consen    2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGL-VFIRGSNIRYIS   66 (67)
T ss_dssp             HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEE-EEEEGGGEEEEE
T ss_pred             hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcE-EEEECCEEEEEE
Confidence            467788999999999999999999999975444443333443332     345 788998888764

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 ....

>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=96.12  E-value=0.036  Score=36.66  Aligned_cols=63  Identities=16%  Similarity=0.271  Sum_probs=49.2

Q ss_pred             HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CC----CcCccccceeeecCceeEEeC
Q psy488           22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KT----PIGTFHEHALLRVDDIVDIEI   86 (86)
Q Consensus        22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~T----PiGv~~e~AlLR~~DIi~~~~   86 (86)
                      ++++|.++.|++|.+.|..++++.|+..++|..- |+..+|- .|    .....++ ..||.+-|..+.+
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~M-Nl~L~~a~~~~~~~~~~~~~~-v~IRG~nI~yi~l   69 (90)
T cd01724           2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSM-NTHLKNVKLTLKGRNPVPLDT-LSIRGNNIRYFIL   69 (90)
T ss_pred             HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCce-eEEEEEEEEEcCCCceeEcce-EEEeCCEEEEEEc
Confidence            5788899999999999999999999999999765 6666653 11    1223455 8999999987764

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.

>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=96.06  E-value=0.039  Score=34.92  Aligned_cols=59  Identities=10%  Similarity=0.216  Sum_probs=45.7

Q ss_pred             HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CC----CcCccccceeeecCceeEEe
Q psy488           25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KT----PIGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~T----PiGv~~e~AlLR~~DIi~~~   85 (86)
                      .|..+.||+|.+.|.++..+.|++.|+| ...|+..++- ++    .-..... .++|.+.|+++.
T Consensus         4 ~L~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~lg~-v~IRG~~I~~i~   67 (72)
T cd01719           4 ELKKYMDKKLSLKLNGNRKVSGILRGFD-PFMNLVLDDAVEVNSGGEKNNIGM-VVIRGNSIVMLE   67 (72)
T ss_pred             hhHHhCCCeEEEEECCCeEEEEEEEEEc-ccccEEeccEEEEccCCceeEece-EEECCCEEEEEE
Confidence            4667799999999999999999999999 6677766554 11    1223345 899999998874

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.

>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=95.99  E-value=0.057  Score=34.22  Aligned_cols=62  Identities=11%  Similarity=0.239  Sum_probs=48.7

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc--CCCcCc----cccceeeecCceeEEeC
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL--KTPIGT----FHEHALLRVDDIVDIEI   86 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L--~TPiGv----~~e~AlLR~~DIi~~~~   86 (86)
                      |.+|.++.|++|.+.|..+.++.|+..++|.. .|+..+|-  .+|=|.    .++ ..+|.+-|..+.+
T Consensus         3 l~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~-mNi~L~~~~~~~~~g~~~~~~~~-v~IRG~~I~~i~~   70 (76)
T cd01723           3 LSLLKTAQNHPMLVELKNGETYNGHLVNCDNW-MNIHLREVICTSKDGDKFWKMPE-CYIRGNTIKYLRV   70 (76)
T ss_pred             hHHHHhcCCCEEEEEECCCCEEEEEEEEEcCC-CceEEEeEEEECCCCcEeeeCCc-EEEeCCEEEEEEc
Confidence            56788899999999999999999999999974 56666665  234442    245 8899999987753

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

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

Probab=95.95  E-value=0.055  Score=33.85  Aligned_cols=62  Identities=11%  Similarity=0.198  Sum_probs=48.1

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-C-Cc---CccccceeeecCceeEEeC
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-T-PI---GTFHEHALLRVDDIVDIEI   86 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-T-Pi---Gv~~e~AlLR~~DIi~~~~   86 (86)
                      +++|..+.|++|.+.|..++++.|+..++|.. .|+..++-+ + |=   ....+ -.+|.+-|..+.+
T Consensus         2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~-MNl~L~~~~~~~~~g~~~~~~~-v~IRG~nI~~v~l   68 (70)
T cd01721           2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDN-MNCQLKDVTVTARDGRVSQLEQ-VYIRGSKIRFFIL   68 (70)
T ss_pred             hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCC-ceeEEEEEEEECCCCcEeEcCc-EEEeCCEEEEEEe
Confidence            56788899999999999999999999999984 477776662 2 22   23345 7899998877654

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.

>smart00651 Sm snRNP Sm proteins

Probab=95.91  E-value=0.056  Score=32.42  Aligned_cols=59  Identities=14%  Similarity=0.203  Sum_probs=44.2

Q ss_pred             HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CC-----cCccccceeeecCceeEEe
Q psy488           25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TP-----IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TP-----iGv~~e~AlLR~~DIi~~~   85 (86)
                      +|..+.|++|.+.|.++..+.|++.++|.. .|+..++-. +.     -...+. .++|.+-|..+.
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~-~NlvL~~~~e~~~~~~~~~~~~~-~~IrG~~I~~i~   66 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQF-MNLVLEDVEETVKDGEKKRKLGL-VFIRGNNIVYII   66 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECcc-ccEEEccEEEEecCCcEEeEeCC-EEEcCCEEEEEe
Confidence            467789999999999999999999999975 555554431 22     123345 789999888775

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

>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=95.83  E-value=0.061  Score=33.12  Aligned_cols=61  Identities=11%  Similarity=0.314  Sum_probs=45.5

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CC----CcCccccceeeecCceeEEe
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KT----PIGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~T----PiGv~~e~AlLR~~DIi~~~   85 (86)
                      |.+|..+.|++|.+.|.++..+.|++.++|.. .|+..++- ++    .-..... -+||...|+.+.
T Consensus         2 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~-mNlvL~~~~e~~~~~~~~~lg~-~~iRG~~I~~i~   67 (68)
T cd01731           2 LDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQH-MNLVLEDAEEIDDGEPVRKYGR-VVIRGDNVLFIS   67 (68)
T ss_pred             hHHHHHhcCCEEEEEECCCCEEEEEEEEECCc-ceEEEeeEEEEecCCeEeEcCc-EEEeCCEEEEEc
Confidence            46677889999999999999999999999974 44444443 22    1223345 789999998763

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.

>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=95.74  E-value=0.08  Score=34.09  Aligned_cols=62  Identities=16%  Similarity=0.285  Sum_probs=47.7

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC--CCcC---ccccceeeecCceeEEeC
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK--TPIG---TFHEHALLRVDDIVDIEI   86 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~--TPiG---v~~e~AlLR~~DIi~~~~   86 (86)
                      +.+|..+.|++|.+.|..++.+.|+..++|..- |+..+|-+  .|-|   ..++ -.+|++-|..++|
T Consensus        11 ~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~M-Nl~L~~~~~~~~~~~~~~~~~-v~IRG~nI~yI~l   77 (78)
T cd01733          11 IILLQGLQGKVVTVELRNETTVTGRIASVDAFM-NIRLAKVTIIDRNGKQVQVEE-IMVTGRNIRYVHI   77 (78)
T ss_pred             HHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCc-eeEEEEEEEEcCCCceeECCc-EEEECCEEEEEEc
Confidence            456688999999999999999999999999765 66665542  2222   2355 8899999988764

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.

>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=95.49  E-value=0.049  Score=34.62  Aligned_cols=60  Identities=15%  Similarity=0.255  Sum_probs=43.4

Q ss_pred             HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCC-----------Cc----CccccceeeecCceeEEeC
Q psy488           25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKT-----------PI----GTFHEHALLRVDDIVDIEI   86 (86)
Q Consensus        25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T-----------Pi----Gv~~e~AlLR~~DIi~~~~   86 (86)
                      -|.++.|+++.+.|.++-.+.|+|.|+|... |+..+|-.=           |.    ..... .++|..-|+++.+
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 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHM-NLVLSDCEEFRKVKKKKSKNSEREEKRTLGL-VLLRGENIVSMTV   78 (79)
T ss_pred             hhHHHcCCEEEEEECCCcEEEEEEEEEcCcc-CEEcCCEEEEEeccccccccccCcceeEeee-EEEcCCEEEEEEE
Confidence            3667899999999999999999999999653 444333211           01    12234 7999999999864

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=95.25  E-value=0.17  Score=31.76  Aligned_cols=61  Identities=15%  Similarity=0.263  Sum_probs=46.6

Q ss_pred             HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-C----CcCccccceeeecCceeEE
Q psy488           22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-T----PIGTFHEHALLRVDDIVDI   84 (86)
Q Consensus        22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-T----PiGv~~e~AlLR~~DIi~~   84 (86)
                      -+..|....|++|.+.|.++..+.|+..++|. ..|+..+|-. +    +...... .++|.+-|+.+
T Consensus         5 P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~~lg~-v~iRG~~V~~i   70 (72)
T PRK00737          5 PLDVLNNALNSPVLVRLKGGREFRGELQGYDI-HMNLVLDNAEEIQDGEVVRKLGK-VVIRGDNVVYV   70 (72)
T ss_pred             hHHHHHHhCCCEEEEEECCCCEEEEEEEEEcc-cceeEEeeEEEEcCCCeEeEcCc-EEEeCCEEEEE
Confidence            35677788999999999999999999999997 5666666631 1    2223334 78999999876

>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=94.13  E-value=0.29  Score=31.38  Aligned_cols=60  Identities=20%  Similarity=0.254  Sum_probs=41.8

Q ss_pred             HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecc-cCCCcC----------ccccceeeecCceeEEeC
Q psy488           25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRN-LKTPIG----------TFHEHALLRVDDIVDIEI   86 (86)
Q Consensus        25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~-L~TPiG----------v~~e~AlLR~~DIi~~~~   86 (86)
                      .|.++.|+++.+.+.++..+.|+|.++|....-+ .++ -++..+          ...- .++|..-|+++++
T Consensus         4 ~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~Niv-L~~~~E~~~~~~~~~~~~~r~lGl-v~IrG~~Iv~i~v   74 (75)
T cd06168           4 KLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNII-LGSAQEYRPPPDSFSPTEPRVLGL-VMIPGHHIVSIEV   74 (75)
T ss_pred             HHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEE-ecCcEEEEcccCccCCccEEEeee-EEEeCCeEEEEEE
Confidence            3556689999999999999999999999765433 332 222111          1222 5788988888864

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.

>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=93.68  E-value=0.57  Score=30.01  Aligned_cols=61  Identities=16%  Similarity=0.208  Sum_probs=44.0

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc----CCCc----CccccceeeecCceeEEe
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL----KTPI----GTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L----~TPi----Gv~~e~AlLR~~DIi~~~   85 (86)
                      |..|.++.+++|.+.+.++..+.|+..|+|.- .|+..++-    .+|=    ..... -+||..-|+.+.
T Consensus         5 ~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~-mNlvL~da~E~~~~~~~~~~~~lg~-v~iRG~nV~~i~   73 (76)
T cd01732           5 LELIDKCIGSRIWIVMKSDKEFVGTLLGFDDY-VNMVLEDVTEYEITPEGRKITKLDQ-ILLNGNNICMLV   73 (76)
T ss_pred             HHHHHHhCCCEEEEEECCCeEEEEEEEEeccc-eEEEEccEEEEEEcCCCceeeEcCe-EEEeCCeEEEEE
Confidence            45677788999999999999999999999964 44444441    1222    12334 789999988763

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.

>KOG3482|consensus

Probab=93.54  E-value=0.33  Score=32.33  Aligned_cols=58  Identities=16%  Similarity=0.325  Sum_probs=46.3

Q ss_pred             HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCC-----CcCccccceeeecCceeEE
Q psy488           25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKT-----PIGTFHEHALLRVDDIVDI   84 (86)
Q Consensus        25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T-----PiGv~~e~AlLR~~DIi~~   84 (86)
                      +|++|.||+|-+.|.=+..-+|+..++|.. -|++..+-+-     .-|...| -++||+.|..+
T Consensus        12 FL~~l~gk~V~vkLKwg~eYkG~LvsvD~Y-mNlqL~~~eE~idG~~~g~lGE-ilIRCNNvlyi   74 (79)
T KOG3482|consen   12 FLNGLTGKPVLVKLKWGQEYKGTLVSVDNY-MNLQLANAEEYIDGVSTGNLGE-ILIRCNNVLYI   74 (79)
T ss_pred             HHhhccCCeEEEEEecCcEEEEEEEEecch-hheehhhhhhhhccccccccee-EEEEeccEEEE
Confidence            678899999999999999999999999964 4555544332     3467778 99999999765

>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=92.59  E-value=0.57  Score=29.40  Aligned_cols=58  Identities=12%  Similarity=0.307  Sum_probs=41.2

Q ss_pred             HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCc-----Cc----cccceeeecCceeEE
Q psy488           25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPI-----GT----FHEHALLRVDDIVDI   84 (86)
Q Consensus        25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPi-----Gv----~~e~AlLR~~DIi~~   84 (86)
                      .|....++++.+.|.++-.+.|+|++.|.. .|+..++=.-++     |.    ..- .++|..-|+.+
T Consensus         3 ~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~-~NlvL~~~~E~~~~~~~~~~~~~lG~-~~iRG~~I~~i   69 (74)
T cd01727           3 TLEDYLNKTVSVITVDGRVIVGTLKGFDQA-TNLILDDSHERVYSSDEGVEQVVLGL-YIIRGDNIAVV   69 (74)
T ss_pred             hHHHhcCCEEEEEECCCcEEEEEEEEEccc-cCEEccceEEEEecCCCCceeeEece-EEECCCEEEEE
Confidence            366778999999999999999999999985 444444421111     11    222 68888888765

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.

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

Probab=91.60  E-value=1.1  Score=28.15  Aligned_cols=64  Identities=16%  Similarity=0.059  Sum_probs=46.4

Q ss_pred             HHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCC--------cCccccceeeecCceeEEe
Q psy488           21 KFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTP--------IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        21 rfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TP--------iGv~~e~AlLR~~DIi~~~   85 (86)
                      ..+.+|..+.|++|.+.|.++.++.|+-.|+|....-++-..-++.        .....+ -+||...|+.|.
T Consensus         7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~-~~IRG~~I~~I~   78 (79)
T COG1958           7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGE-VLIRGDNIVLIS   78 (79)
T ss_pred             CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccE-EEEECCcEEEEe
Confidence            4567788888899999999999999999999975544332222221        122235 899999998774

>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=89.68  E-value=1.9  Score=27.52  Aligned_cols=60  Identities=7%  Similarity=0.154  Sum_probs=42.0

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCC------------------cCccccceeeecCceeEE
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTP------------------IGTFHEHALLRVDDIVDI   84 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TP------------------iGv~~e~AlLR~~DIi~~   84 (86)
                      |..|....+++|.+.|.++..+.|+..|+|.-- |+..++-+--                  ...... .+||..-|+++
T Consensus         3 l~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~m-NlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~-~~iRGd~Vv~i   80 (82)
T cd01730           3 LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHL-NMILGDVEETITTVEIDEETYEEIVKTTKRNIPM-LFVRGDSVILV   80 (82)
T ss_pred             hHHHHHhCCCEEEEEECCCCEEEEEEEEEccce-EEeccceEEEeecccccccccccccceeEEEcCe-EEEeCCEEEEE
Confidence            345566689999999999999999999999754 5554433111                  111223 68888888776

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.

>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=89.58  E-value=2.5  Score=26.98  Aligned_cols=60  Identities=3%  Similarity=0.015  Sum_probs=42.4

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CCCcCc-------cccceeeecCceeEE
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KTPIGT-------FHEHALLRVDDIVDI   84 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~TPiGv-------~~e~AlLR~~DIi~~   84 (86)
                      +..|.+..++++.+.+.++..+.|+++++|.- .|+..++- ++-...       ... .++|..-|+.+
T Consensus         4 ~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~-~NlvL~d~~E~~~~~~~~~~~~lG~-~viRG~~V~~i   71 (74)
T cd01728           4 TASLVDDLDKKVVVLLRDGRKLIGILRSFDQF-ANLVLQDTVERIYVGDKYGDIPRGI-FIIRGENVVLL   71 (74)
T ss_pred             hHHHHHhcCCEEEEEEcCCeEEEEEEEEECCc-ccEEecceEEEEecCCccceeEeeE-EEEECCEEEEE
Confidence            34567789999999999999999999999954 45555443 221111       113 58898888765

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.

>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=89.34  E-value=2  Score=27.67  Aligned_cols=58  Identities=14%  Similarity=0.147  Sum_probs=40.7

Q ss_pred             HHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CC------------CcCccccceeeecCceeEEe
Q psy488           26 MSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KT------------PIGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        26 l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~T------------PiGv~~e~AlLR~~DIi~~~   85 (86)
                      |.++.|+++.+.|.++..+.|++.+.|..- |+..++= +.            .-..... .++|+.-|+++.
T Consensus         7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~~m-NlvL~~~~E~~~~~~~~~~~~~~~~~lG~-v~iRG~nV~~i~   77 (81)
T cd01729           7 LSKYVDKKIRVKFQGGREVTGILKGYDQLL-NLVLDDTVEYLRDPDDPYKLTDKTRQLGL-VVCRGTSVVLIS   77 (81)
T ss_pred             HHHhcCCeEEEEECCCcEEEEEEEEEcCcc-cEEecCEEEEEccCCcccccccceeEccE-EEEcCCEEEEEe
Confidence            677899999999999999999999999743 2222221 11            1111234 799999998763

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.

>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=87.18  E-value=3.3  Score=27.30  Aligned_cols=60  Identities=12%  Similarity=0.213  Sum_probs=40.6

Q ss_pred             HHHHhc--CCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CC----Cc------------C-ccccceeeecCceeE
Q psy488           24 KAMSSL--SGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KT----PI------------G-TFHEHALLRVDDIVD   83 (86)
Q Consensus        24 r~l~~~--~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~T----Pi------------G-v~~e~AlLR~~DIi~   83 (86)
                      ..|...  .|++|.+.|..+..+.|++.|+|.- .|+..++- ++    |-            . .... .+||..-||+
T Consensus         5 ~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~h-mNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~-v~iRGd~Vv~   82 (87)
T cd01720           5 SLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRH-CNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISK-MFLRGDSVIL   82 (87)
T ss_pred             HHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCc-cEEEEcceEEEeeccccccccccccceeeeeEccc-EEEeCCEEEE
Confidence            344444  4899999999999999999999974 34443332 11    11            1 1244 7899988887


Q ss_pred             Ee
Q psy488           84 IE   85 (86)
Q Consensus        84 ~~   85 (86)
                      +.
T Consensus        83 Is   84 (87)
T cd01720          83 VL   84 (87)
T ss_pred             Ee
Confidence            63

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	86
1y96_B	85	Crystal Structure Of The Gemin6GEMIN7 HETERODIMER F		2e-08

>pdb|1Y96|B Chain B, Crystal Structure Of The Gemin6GEMIN7 HETERODIMER FROM THE Human Smn Complex Length = 85

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 1/68 (1%)
Query: 16 AEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHAL 75
          A +RE++L+++ ++ G   +  + E   V A F  T+ D+  FYV  L+TPIG   E AL
Sbjct: 14 AALRERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQTPIGVQAE-AL 72
Query: 76 LRVDDIVD 83
          LR  DI+ 
Sbjct: 73 LRCSDIIS 80

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	86
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	4e-21

>1y96_B Gemin7, SIP3, GEM-associated protein 7; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} Length = 85

 Score = 78.1 bits (192), Expect = 4e-21
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 7  SSRSDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTP 66
              ++   A +RE++L+++ ++ G   +  + E   V A F  T+ D+  FYV  L+TP
Sbjct: 5  LESQEQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQTP 64

Query: 67 IGTFHEHALLRVDDIVDIEI 86
          IG   E ALLR  DI+    
Sbjct: 65 IGVQAE-ALLRCSDIISYTF 83

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	86
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	100.0
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	96.53
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	96.49
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	96.48
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	96.47
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	96.36
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	96.23
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	96.21
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	96.2
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	96.04
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	95.97
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	95.81
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	95.75
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	95.68
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	95.63
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	95.56
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	95.39
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	94.94
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	94.66
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	93.65
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	92.72
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	91.9
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	91.03
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	89.62
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	88.62
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	88.58

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

Probab=100.00  E-value=1.8e-44  Score=239.34  Aligned_cols=81  Identities=32%  Similarity=0.606  Sum_probs=77.9

Q ss_pred             cCCCcHHHHHHHHHHHHHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCccccceeeecCceeEE
Q psy488            5 RTSSRSDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDI   84 (86)
Q Consensus         5 ~~~~~~eQ~aRa~LRerfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e~AlLR~~DIi~~   84 (86)
                      ...++++|+|||+|||||||+|++|.|+||+|+|||||+|+|+|+|+|+|++||+||+|+||||++|| |+|||+|||+|
T Consensus         3 ~~~~~~~Q~aRa~LReRfLr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e-AlLR~~Dii~~   81 (85)
T 1y96_B            3 ESLESQEQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQTPIGVQAE-ALLRCSDIISY   81 (85)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEECCTTCCEEE-EEEEGGGEEEE
T ss_pred             cccchHHHHHHHHHHHHHHHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcCCCcccchh-hhhhcCCEEEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999999 99999999999


Q ss_pred             eC
Q psy488           85 EI   86 (86)
Q Consensus        85 ~~   86 (86)
                      +|
T Consensus        82 sF   83 (85)
T 1y96_B           82 TF   83 (85)
T ss_dssp             EE
T ss_pred             Ee
Confidence            75

>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1

Probab=96.53  E-value=0.0078  Score=41.30  Aligned_cols=63  Identities=14%  Similarity=0.273  Sum_probs=49.4

Q ss_pred             HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCccccceeeecCceeEEe
Q psy488           22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e~AlLR~~DIi~~~   85 (86)
                      |..+|..+.|++|.+.|.++..+.|+..++| +..|+..+|-.=-.|..-...+||++-|+.+.
T Consensus         1 f~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D-~~MNlvL~d~~E~~~~~lg~v~IRG~nI~~I~   63 (130)
T 1m5q_A            1 FVAELNNLLGREVQVVLSNGEVYKGVLHAVD-NQLNIVLANASNKAGEKFNRVFIMYRYIVHID   63 (130)
T ss_dssp             CHHHHHHTTTSEEEEEETTSCEEEEEEEEEC-TTCCEEEEEEECTTCCEEEEEEECGGGEEEEE
T ss_pred             ChhHHHHhCCCeEEEEECCCcEEEEEEEEEc-ccceeEEeeEEEEcCCEeceEEEeCCeEEEEE
Confidence            5678899999999999999999999999999 66777777653112332223899999998764

>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=96.49  E-value=0.008  Score=36.68  Aligned_cols=61  Identities=10%  Similarity=0.192  Sum_probs=46.4

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CC----cCccccceeeecCceeEEe
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TP----IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TP----iGv~~e~AlLR~~DIi~~~   85 (86)
                      +..|.++.|++|.+.|.++..+.|++.++|. ..|+..+|-. +.    -..... .++|.+-|+.+.
T Consensus         6 ~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~~lg~-v~iRG~~I~~i~   71 (77)
T 1i4k_A            6 LDVLNRSLKSPVIVRLKGGREFRGTLDGYDI-HMNLVLLDAEEIQNGEVVRKVGS-VVIRGDTVVFVS   71 (77)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECT-TCCEEEEEEEEEETTEEEEEEEE-EEECGGGEEEEE
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEcC-CCCeEEeeEEEEecCCcEeECCE-EEECCCEEEEEE
Confidence            5677888999999999999999999999994 4666666542 21    112234 899999998774

>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=96.48  E-value=0.011  Score=36.53  Aligned_cols=62  Identities=15%  Similarity=0.149  Sum_probs=48.5

Q ss_pred             HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-C----CcCccccceeeecCceeEEe
Q psy488           22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-T----PIGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-T----PiGv~~e~AlLR~~DIi~~~   85 (86)
                      .+.+|.++.|++|.+.|..+.++.|+..++| +.-|+..++-. |    .....++ .++|.+-|..+.
T Consensus         6 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D-~~MNl~L~~~~e~~~~~~~~~lg~-v~IRG~nI~~i~   72 (75)
T 1d3b_A            6 PIKVLHEAEGHIVTCETNTGEVYRGKLIEAE-DNMNCQMSNITVTYRDGRVAQLEQ-VYIRGCKIRFLI   72 (75)
T ss_dssp             HHHHHHHTTTSEEEEEETTSCEEEEEEEEEC-TTCCEEEEEEEEECTTSCEEEEEE-EEECGGGEEEEE
T ss_pred             HHHHHHHhCCCEEEEEECCCcEEEEEEEEEc-cceeEEEEeEEEECCCCcEEEcCe-EEEeCCEEEEEE
Confidence            4788999999999999999999999999999 55677776642 2    1122335 899999987765

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

Probab=96.47  E-value=0.0098  Score=36.21  Aligned_cols=62  Identities=10%  Similarity=0.127  Sum_probs=47.0

Q ss_pred             HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CCCcC----ccccceeeecCceeEEe
Q psy488           22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KTPIG----TFHEHALLRVDDIVDIE   85 (86)
Q Consensus        22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~TPiG----v~~e~AlLR~~DIi~~~   85 (86)
                      -+..|.++.|++|.+.|.++..+.|++.++| +..|+..++- ++--|    .... .++|.+-|+.+.
T Consensus         5 P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D-~~mNlvL~d~~e~~~~~~~~~lg~-v~iRG~~I~~i~   71 (75)
T 1h64_1            5 PLDVIHRSLDKDVLVILKKGFEFRGRLIGYD-IHLNVVLADAEMIQDGEVVKRYGK-IVIRGDNVLAIS   71 (75)
T ss_dssp             HHHHHHTTTTSEEEEEETTSEEEEEEEEEEC-TTCCEEEEEEEEEETTEEEEEEEE-EEECGGGEEEEE
T ss_pred             HHHHHHHHCCCEEEEEECCCCEEEEEEEEEe-CCCCeEEeeEEEEeeCCceeECCE-EEECCCEEEEEE
Confidence            4678889999999999999999999999999 4556666554 22111    1224 799999998764

>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=96.36  E-value=0.014  Score=39.78  Aligned_cols=63  Identities=16%  Similarity=0.177  Sum_probs=50.6

Q ss_pred             HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-C-CcC---ccccceeeecCceeEEeC
Q psy488           22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-T-PIG---TFHEHALLRVDDIVDIEI   86 (86)
Q Consensus        22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-T-PiG---v~~e~AlLR~~DIi~~~~   86 (86)
                      .+.+|..+.|++|.+.|..+.++.|+..++| +..|+..+|-. | +=|   ..++ .+||.+-|..|.+
T Consensus         6 P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D-~~MNi~L~dv~e~~~~g~~~~l~~-v~IRGnnI~~I~l   73 (126)
T 2y9a_D            6 PIKVLHEAEGHIVTCETNTGEVYRGKLIEAE-DNMNCQMSNITVTYRDGRVAQLEQ-VYIRGSKIRFLIL   73 (126)
T ss_dssp             SHHHHHSCSSCEEEEEESSCCEEEEEEEEEC-TTSCEEEEEEEEECTTSCCEEEEE-EEECGGGEEEEEC
T ss_pred             HHHHHHHhCCCEEEEEECCCcEEEEEEEEEc-CceEEEEeeEEEEcCCCcEeeccc-EEEeCCEEEEEEc
Confidence            3678899999999999999999999999999 56788877764 2 222   3345 8999999988764

>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=96.23  E-value=0.018  Score=38.52  Aligned_cols=63  Identities=17%  Similarity=0.193  Sum_probs=49.0

Q ss_pred             HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CCc----CccccceeeecCceeEEeC
Q psy488           22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TPI----GTFHEHALLRVDDIVDIEI   86 (86)
Q Consensus        22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TPi----Gv~~e~AlLR~~DIi~~~~   86 (86)
                      .+.+|..+.|++|.+.|..+.++.|+..++| +..|+..+|-+ |.-    ..... .+||.+-|+.|.+
T Consensus         3 p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D-~~MNlvL~d~~e~~~~~~~~~lg~-v~IRG~nI~~I~~   70 (119)
T 1b34_A            3 LVRFLMKLSHETVTIELKNGTQVHGTITGVD-VSMNTHLKAVKMTLKNREPVQLET-LSIRGNNIRYFIL   70 (119)
T ss_dssp             HHHHHHTCTTCEEEEEETTCCEEEEEEEEEC-TTCCEEEEEEEEECTTSCCEEEEE-EEECGGGEEEEEC
T ss_pred             hHHHHHHhCCCEEEEEEcCCCEEEEEEEEEc-ccceEEeccEEEecCCCceeEcce-EEEcCCeEEEEEe
Confidence            5788999999999999999999999999999 45677766653 211    12234 8999999988753

>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=96.21  E-value=0.01  Score=36.41  Aligned_cols=61  Identities=7%  Similarity=0.179  Sum_probs=47.0

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCc-----CccccceeeecCceeEEe
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPI-----GTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPi-----Gv~~e~AlLR~~DIi~~~   85 (86)
                      +.+|.++.|++|.+.|.++.++.|++.++|. ..|+..++-..-.     ..... .+||.+-|+.+.
T Consensus         6 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~~lg~-v~iRG~~I~~i~   71 (75)
T 4emk_B            6 NEFLNKVIGKKVLIRLSSGVDYKGILSCLDG-YMNLALERTEEYVNGKKTNVYGD-AFIRGNNVLYVS   71 (75)
T ss_dssp             HHHHHHTTTSEEEEECTTSCEEEEEEEEECT-TCEEEEEEEEEEETTEEEEEEEE-EEEEGGGSSEEE
T ss_pred             HHHHHHhCCCeEEEEEcCCcEEEEEEEEEcC-cceEEEccEEEEecCCcccEecE-EEEcCCeEEEEE
Confidence            5678888999999999999999999999996 5677776653321     12234 789998887663

>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=96.20  E-value=0.014  Score=36.93  Aligned_cols=61  Identities=16%  Similarity=0.299  Sum_probs=48.4

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCc-C----ccccceeeecCceeEEe
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPI-G----TFHEHALLRVDDIVDIE   85 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPi-G----v~~e~AlLR~~DIi~~~   85 (86)
                      +.+|.++.|++|.+.|.++..+.|++.++|. ..|+..++-..-. |    .... .+||.+-|+.+.
T Consensus         8 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~~g~~~~~lg~-v~IRG~nI~~i~   73 (86)
T 3s6n_F            8 KPFLNGLTGKPVMVKLKWGMEYKGYLVSVDG-YMNMQLANTEEYIDGALSGHLGE-VLIRCNNVLYIR   73 (86)
T ss_dssp             HHHHHHHTTSEEEEEETTSCEEEEEEEEECT-TCCEEEEEEEEEETTEEEEEESS-EEECGGGEEEEE
T ss_pred             HHHHHHhCCCeEEEEEcCCeEEEEEEEEEcC-ceEEEEeeEEEEcCCceeeEccE-EEEeCCeEEEEE
Confidence            5677888999999999999999999999996 5677777765322 2    2235 899999998764

>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=96.04  E-value=0.011  Score=39.20  Aligned_cols=62  Identities=15%  Similarity=0.292  Sum_probs=42.4

Q ss_pred             HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CC-cC----ccccceeeecCceeEEe
Q psy488           22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TP-IG----TFHEHALLRVDDIVDIE   85 (86)
Q Consensus        22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TP-iG----v~~e~AlLR~~DIi~~~   85 (86)
                      -+.+|.++.|++|.+.|.++.++.|+..++|. ..|+..++-. |. =|    .... .+||.+-|..+.
T Consensus        17 p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~-~MNlvL~d~~e~~~dg~~~~~lg~-v~IRG~nI~~I~   84 (105)
T 4emh_A           17 PLTLLNATQGRPILVELKNGETFNGHLENCDN-YMNLTLREVIRTMPDGDKFFRLPE-CYIRGNNIKYLR   84 (105)
T ss_dssp             ---------CCEEEEEETTSCEEEEEEEEECT-TCCEEEEEEEEECTTSCEEEEEEE-EEECGGGEEEEE
T ss_pred             HHHHHHHhCCCEEEEEECCCCEEEEEEEEEcC-CceEEEEEEEEEccCCceeeEcCe-EEEeCCeEEEEe
Confidence            36678889999999999999999999999996 5588877754 32 22    3345 899999998775

>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=95.97  E-value=0.023  Score=36.51  Aligned_cols=63  Identities=13%  Similarity=0.076  Sum_probs=47.9

Q ss_pred             HHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CC-----------cCccccceeeecCceeEEe
Q psy488           21 KFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TP-----------IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        21 rfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TP-----------iGv~~e~AlLR~~DIi~~~   85 (86)
                      -++..|.+..|++|.+.|.++..+.|++.|+|. ..|+..++-. +.           -..... .+||..-|+++.
T Consensus        10 ~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~-~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~-v~IRG~nVv~I~   84 (96)
T 3bw1_A           10 TPLDLLKLNLDERVYIKLRGARTLVGTLQAFDS-HCNIVLSDAVETIYQLNNEELSESERRCEM-VFIRGDTVTLIS   84 (96)
T ss_dssp             CHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECT-TCCEEEEEEEEEEECCSTTCCCEEEEEEEE-EEECGGGEEEEE
T ss_pred             hHHHHHHHHCCCeEEEEECCCcEEEEEEEEECC-CCcEEEcCEEEEeccccccccCcceeEcCE-EEECCCEEEEEE
Confidence            367889999999999999999999999999995 4566655532 11           111234 789999998874

>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=95.81  E-value=0.032  Score=34.48  Aligned_cols=63  Identities=8%  Similarity=0.101  Sum_probs=48.1

Q ss_pred             HHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CC----cCccccceeeecCceeEEe
Q psy488           21 KFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TP----IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        21 rfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TP----iGv~~e~AlLR~~DIi~~~   85 (86)
                      .-+..|....|++|.+.|.++.++.|++.++|. ..|+..+|-. +.    -..... .+||..-|+.+.
T Consensus         9 ~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~~lg~-v~iRG~~I~~i~   76 (81)
T 1th7_A            9 TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQ-HMNLVLSDSEEIQSDGSGKKLGT-IVIRGDNVILIS   76 (81)
T ss_dssp             HHHHHHHHHTTSEEEEEETTTEEEEEEEEEECT-TCCEEEEEEEEECSSSCEEEEEE-EEECGGGEEEEE
T ss_pred             chHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcC-CCCEEEccEEEEecCCceeECCE-EEECCCEEEEEE
Confidence            456788888999999999999999999999995 4566666542 21    122334 899999998774

>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=95.75  E-value=0.017  Score=37.25  Aligned_cols=67  Identities=12%  Similarity=0.142  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHhcCCCceEEEeecC-cEEEEEEeeecCCcceeeecccC-CC----cCccccceeeecCceeEEe
Q psy488           17 EMREKFLKAMSSLSGQPCTINMFER-TVVTAEFQGTNSDLTEFYVRNLK-TP----IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        17 ~LRerfLr~l~~~~gk~v~f~m~E~-t~V~a~F~a~d~d~~~f~Vs~L~-TP----iGv~~e~AlLR~~DIi~~~   85 (86)
                      +....-+.+|.++.|++|.+.|.++ .++.|+..++| +..|+..++-. +.    ...... .+||.+-|+.+.
T Consensus        17 ~~~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D-~~MNlvL~d~~E~~~~~~~~~lg~-v~IRG~nI~~I~   89 (93)
T 1n9r_A           17 MQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTD-NYFNLQLNEAEEFVAGVSHGTLGE-IFIRCNNVLYIR   89 (93)
T ss_dssp             ---------CGGGTTSEEEEEESSTTEEEEEEEEECC-TTTCEEEEEEEEEETTEEEEECCS-EEECGGGEEEEE
T ss_pred             cccCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEc-cccEEEEeeEEEEcCCCeEeEcCE-EEEcCCeEEEEE
Confidence            3345667888899999999999999 99999999999 55677666553 21    112335 899999998764

>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=95.68  E-value=0.034  Score=33.95  Aligned_cols=61  Identities=20%  Similarity=0.387  Sum_probs=46.7

Q ss_pred             HHHHHhcCCCceEEEeecC-cEEEEEEeeecCCcceeeecccC-CC----cCccccceeeecCceeEEe
Q psy488           23 LKAMSSLSGQPCTINMFER-TVVTAEFQGTNSDLTEFYVRNLK-TP----IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~-t~V~a~F~a~d~d~~~f~Vs~L~-TP----iGv~~e~AlLR~~DIi~~~   85 (86)
                      +.+|.++.|+++.+.|.++ .++.|++.++| +..|+..++-. +.    -..... .+||.+-|+.+.
T Consensus         7 ~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D-~~mNlvL~d~~e~~~~~~~~~lg~-v~iRG~nI~~i~   73 (77)
T 1ljo_A            7 NQMVKSMVGKIIRVEMKGEENQLVGKLEGVD-DYMNLYLTNAMECKGEEKVRSLGE-IVLRGNNVVLIQ   73 (77)
T ss_dssp             HHHHHHTTTSEEEEEETTCSSEEEEEEEEEC-TTCCEEEEEEEEEETTEEEEEEEE-EEECGGGEEEEE
T ss_pred             HHHHHHHCCCEEEEEEeCCCEEEEEEEEEEC-CcceEEEeeEEEEecCCcEeECCe-EEEeCCeEEEEE
Confidence            5678889999999999999 99999999999 55676666652 11    111234 789999998764

>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=95.63  E-value=0.044  Score=33.61  Aligned_cols=60  Identities=8%  Similarity=0.192  Sum_probs=40.5

Q ss_pred             HHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CC----cCccccceeeecCceeEEe
Q psy488           24 KAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TP----IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        24 r~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TP----iGv~~e~AlLR~~DIi~~~   85 (86)
                      .+|.++.|+++.+.|.++..+.|++.++|. ..|+..++-. +.    -..... .++|.+-|+.+.
T Consensus         7 ~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~-~mNlvL~~~~e~~~~~~~~~lg~-v~iRG~~I~~i~   71 (76)
T 3s6n_G            7 PELKKFMDKKLSLKLNGGRHVQGILRGFDP-FMNLVIDECVEMATSGQQNNIGM-VVIRGNSIIMLE   71 (76)
T ss_dssp             -------CCEEEEEETTTEEEEEEEEEECT-TCCEEEEEEEECCCC----CBSS-EEECSSSEEEEE
T ss_pred             HHHHHhCCCeEEEEECCCcEEEEEEEEECC-cceEEEeceEEEccCCcEeEcCE-EEECCCeEEEEE
Confidence            456778899999999999999999999994 6677766642 11    122235 899999998875

>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=95.56  E-value=0.034  Score=34.62  Aligned_cols=63  Identities=16%  Similarity=0.209  Sum_probs=47.4

Q ss_pred             HHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CC----cCccccceeeecCceeEEe
Q psy488           21 KFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TP----IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        21 rfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TP----iGv~~e~AlLR~~DIi~~~   85 (86)
                      .-+.+|..+.|++|.+.|.++..+.|++.++|. ..|+..+|-. +.    -..... .++|.+-|+.+.
T Consensus        15 ~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~~lg~-v~IRG~~I~~i~   82 (83)
T 1mgq_A           15 RPLDALGNSLNSPVIIKLKGDREFRGVLKSFDL-HMNLVLNDAEELEDGEVTRRLGT-VLIRGDNIVYIS   82 (83)
T ss_dssp             CTTHHHHHTTTSEEEEEETTTEEEEEEEEEECT-TCCEEEEEEEEEETTEEEEEEEE-EEECGGGEEEEE
T ss_pred             ChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECC-CceeEEccEEEEecCCcccCCCE-EEECCCEEEEEE
Confidence            345677888899999999999999999999994 5677666642 21    112234 799999998764

>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=95.39  E-value=0.055  Score=33.48  Aligned_cols=63  Identities=5%  Similarity=0.134  Sum_probs=47.3

Q ss_pred             HHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-C---CcCccccceeeecCceeEEe
Q psy488           21 KFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-T---PIGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        21 rfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-T---PiGv~~e~AlLR~~DIi~~~   85 (86)
                      .-+..|....|++|.+.|.++..+.|++.++|. ..|+..+|-. +   .-..... .+||..-|+.+.
T Consensus        11 ~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~lg~-v~iRG~~I~~i~   77 (81)
T 1i8f_A           11 TLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQ-HVNLLLEDAEEIIDGNVYKRGT-MVVRGENVLFIS   77 (81)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECT-TCCEEEEEEEEEETTEEEEEEE-EEECGGGEEEEE
T ss_pred             chHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcC-CCeeEEccEEEEcCCcccCCCE-EEECCCEEEEEE
Confidence            456778888999999999999999999999994 4566665542 2   1111234 799999998774

>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=94.94  E-value=0.076  Score=34.43  Aligned_cols=61  Identities=13%  Similarity=0.175  Sum_probs=45.9

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-----CC-cCccccceeeecCceeEEe
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-----TP-IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-----TP-iGv~~e~AlLR~~DIi~~~   85 (86)
                      |.+|.+..|++|.+.|.++.++.|++.++|. ..|+..+|-+     +. -..... .+||.+-|+.+.
T Consensus        22 l~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~-~mNlvL~d~~E~~~~~~~~~~lg~-v~IRG~nI~~i~   88 (94)
T 4emk_A           22 LELIDKCIGSNLWVIMKSEREFAGTLVGFDD-YVNIVLKDVTEYDTVTGVTEKHSE-MLLNGNGMCMLI   88 (94)
T ss_dssp             HHHHHHTTTSEEEEEESSSEEEEEEEEEECT-TCCEEEEEEEEEETTTCCEEEEEE-EEECSTTEEEEE
T ss_pred             HHHHHHHcCCeEEEEECCCcEEEEEEEEEcc-cCCeEeeeEEEEecCCCcEeEcCE-EEEcCCEEEEEE
Confidence            5778889999999999999999999999995 5566655531     11 112234 899999988763

>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=94.66  E-value=0.041  Score=34.51  Aligned_cols=59  Identities=10%  Similarity=0.115  Sum_probs=43.8

Q ss_pred             HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCC---C--------cC----ccccceeeecCceeEEe
Q psy488           25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKT---P--------IG----TFHEHALLRVDDIVDIE   85 (86)
Q Consensus        25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T---P--------iG----v~~e~AlLR~~DIi~~~   85 (86)
                      .|.++.|++|.+.|.++..+.|++.|+|. ..|+..++-.-   .        -+    .... .+||..-|+++.
T Consensus         8 ~L~~~~~k~V~V~l~~gr~~~G~L~~~D~-~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~-v~iRG~~I~~i~   81 (91)
T 1d3b_B            8 KMLQHIDYRMRCILQDGRIFIGTFKAFDK-HMNLILCDCDEFRKIKPKNSKQAEREEKRVLGL-VLLRGENLVSMT   81 (91)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCT-TCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEE-EEECGGGEEEEE
T ss_pred             HHHHHcCCcEEEEECCCeEEEEEEEEECC-CCeEEecCEEEEeeccccccccccCccEeECCE-EEECCCeEEEEE
Confidence            35678899999999999999999999995 45666655321   1        11    1234 789999998875

>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=93.65  E-value=0.18  Score=33.54  Aligned_cols=62  Identities=10%  Similarity=0.141  Sum_probs=46.1

Q ss_pred             HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-C----------CcC---------ccccceeeecCce
Q psy488           22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-T----------PIG---------TFHEHALLRVDDI   81 (86)
Q Consensus        22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-T----------PiG---------v~~e~AlLR~~DI   81 (86)
                      =|.+|....|++|.+.|.++..+.|++.|+| ...|+..++-+ +          |-|         .... .+||..-|
T Consensus        29 Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD-~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~-v~IRG~nV  106 (121)
T 2fwk_A           29 PLALIDKCIGNRIYVVMKGDKEFSGVLRGFD-EYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLET-ILLSGNNV  106 (121)
T ss_dssp             HHHHHHHTBTSBCEEEETTTEEECCEEEEEC-TTCCEEEESCCEEEC---------------CEECCCCSE-EEECGGGE
T ss_pred             cHHHHHHHcCCeEEEEECCCcEEEEEEEEEc-ccCCeEeceEEEEEeccccccccccCcccccccceEcce-EEECCCEE
Confidence            4677788899999999999999999999999 44566655542 1          112         2234 79999999


Q ss_pred             eEEe
Q psy488           82 VDIE   85 (86)
Q Consensus        82 i~~~   85 (86)
                      +.+.
T Consensus       107 v~I~  110 (121)
T 2fwk_A          107 AMLV  110 (121)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8874

>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=92.72  E-value=0.27  Score=36.97  Aligned_cols=60  Identities=10%  Similarity=0.158  Sum_probs=43.7

Q ss_pred             HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCC---------------CcCccccceeeecCceeEEeC
Q psy488           25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKT---------------PIGTFHEHALLRVDDIVDIEI   86 (86)
Q Consensus        25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T---------------PiGv~~e~AlLR~~DIi~~~~   86 (86)
                      .|+++.||+|.+.|.++.++.|+|+++|.. .|+..+|-+=               --..... .+||...|++|.+
T Consensus         8 kL~klIdKrV~V~LkdGRel~GtLkgFDq~-MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGl-V~IRGdnIV~Isv   82 (231)
T 3pgw_B            8 KMLQHIDYRMRCILQDGRIFIGTFKAFDKH-MNLILCDCDEFRKIKPKNSKQAEREEKRVLGL-VLLRGENLVSMTV   82 (231)
T ss_pred             HHHHhcCCeEEEEECCCcEEEEEEEEEccc-ccEEecCEEEEEeccCcccccccccceeEece-EEECCCcEEEEEe
Confidence            467789999999999999999999999964 4554444211               0111223 7899999998864

>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=91.90  E-value=0.44  Score=31.58  Aligned_cols=64  Identities=14%  Similarity=0.207  Sum_probs=39.6

Q ss_pred             HHHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC----CC--------cCccccceeeecCceeEEe
Q psy488           20 EKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK----TP--------IGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        20 erfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~----TP--------iGv~~e~AlLR~~DIi~~~   85 (86)
                      ...+..|.++.|++|.+.|.++..+.|++.|+|.. .|+..++-.    .|        -..... .+||..-|+++.
T Consensus        22 ke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~-mNLVL~d~~E~~~~~~~~~~~~~~r~lG~-v~IRG~nIv~I~   97 (113)
T 4emk_C           22 KESILDLSRYQDQRIQATFTGGRQITGILKGFDQL-MNLVLDDVEEQLRNPEDGKLTGAIRKLGL-VVVRGTTLVLIA   97 (113)
T ss_dssp             ----------CCSEEEEEETTSCEEEEEEEEECTT-CCEEEEEEEEEC---------CCEEEEEE-EEECTTTEEEEE
T ss_pred             cchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCc-ccEEEeeEEEEEcCCCCcccccceeEccE-EEECCCeEEEEE
Confidence            34666778889999999999999999999999965 455544421    11        112234 789999998774

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

Probab=91.03  E-value=0.42  Score=30.49  Aligned_cols=61  Identities=7%  Similarity=0.127  Sum_probs=43.8

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCc------C------------ccccceeeecCceeEE
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPI------G------------TFHEHALLRVDDIVDI   84 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPi------G------------v~~e~AlLR~~DIi~~   84 (86)
                      |.+|....|++|.+.|.++..+.|++.|+|. ..|+..++-.=-+      |            .... .+||..-|+++
T Consensus        11 l~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~-~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~-v~iRG~nVv~I   88 (93)
T 4emg_A           11 LDLVRLSLDEIVYVKLRGDRELNGRLHAYDE-HLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEM-LFVRGDSVILI   88 (93)
T ss_dssp             THHHHTTTTSEEEEEETTTEEEEEEEEEECT-TCCEEEEEEEEEEC--------------CEEEEEEE-EEECGGGEEEE
T ss_pred             HHHHHHhCCCEEEEEECCCcEEEEEEEEECC-cccEEeecEEEEEeccccCCccccccccccEeEece-EEECCCeEEEE
Confidence            4566677899999999999999999999996 4566655432100      1            1223 78999998877


Q ss_pred             e
Q psy488           85 E   85 (86)
Q Consensus        85 ~   85 (86)
                      .
T Consensus        89 ~   89 (93)
T 4emg_A           89 A   89 (93)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=89.62  E-value=1.1  Score=29.54  Aligned_cols=62  Identities=13%  Similarity=0.139  Sum_probs=44.5

Q ss_pred             HHHHHHhcC--CCceEEEeecCcEEEEEEeeecCCcceeeecccC-CC----cC--------------ccccceeeecCc
Q psy488           22 FLKAMSSLS--GQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TP----IG--------------TFHEHALLRVDD   80 (86)
Q Consensus        22 fLr~l~~~~--gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TP----iG--------------v~~e~AlLR~~D   80 (86)
                      =|.+|....  |++|.+.|.++..+.|++.|+| ...|+..+|-. +-    -+              .... .+||..-
T Consensus        28 Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD-~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~-v~IRG~n  105 (118)
T 1b34_B           28 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFD-RHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISK-MFLRGDS  105 (118)
T ss_dssp             HHHHHHHHHHHTCEEEEEETTSCEEEEEEEEEC-TTCCEEEEEEEEC-------------------CEEEEE-EEECGGG
T ss_pred             hHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeC-CceEEEEeCEEEEEecccccccccccccccccccCcCe-EEEcCCE
Confidence            345666665  6999999999999999999999 55666665543 21    11              1334 8999999


Q ss_pred             eeEEe
Q psy488           81 IVDIE   85 (86)
Q Consensus        81 Ii~~~   85 (86)
                      |+.+.
T Consensus       106 Vv~I~  110 (118)
T 1b34_B          106 VIVVL  110 (118)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            98764

>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=88.62  E-value=0.66  Score=29.71  Aligned_cols=61  Identities=8%  Similarity=0.130  Sum_probs=44.6

Q ss_pred             HHHHHhcCCCceEEEe----ecCcEEEEEEeeecCCcceeeecccC-C-----CcCccccceeeecCceeEEe
Q psy488           23 LKAMSSLSGQPCTINM----FERTVVTAEFQGTNSDLTEFYVRNLK-T-----PIGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m----~E~t~V~a~F~a~d~d~~~f~Vs~L~-T-----PiGv~~e~AlLR~~DIi~~~   85 (86)
                      |.+|.+..++++.+.+    .++.++.|++.++|. ..|+..+|-+ +     +-..... .+||..-|+.+.
T Consensus        18 l~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~-~mNlvL~d~~E~~~~~~~~~~lg~-v~iRG~nV~~i~   88 (92)
T 3s6n_E           18 INLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDE-YMNLVLDDAEEIHSKTKSRKQLGR-IMLKGDNITLLQ   88 (92)
T ss_dssp             HHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECT-TCCEEEEEEEEECSSSCCEEEEEE-EEECGGGEEEEE
T ss_pred             HHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcC-cCcEEEeeeEEEecCCCceeEcCe-EEEeCCEEEEEE
Confidence            4566677788988888    899999999999995 5677666532 1     1223345 899999988764

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

Probab=88.58  E-value=0.95  Score=29.28  Aligned_cols=39  Identities=8%  Similarity=-0.003  Sum_probs=36.3

Q ss_pred             HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc
Q psy488           25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL   63 (86)
Q Consensus        25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L   63 (86)
                      -|..+.||.|.+++.|+.+-+|.--++|+...++...|.
T Consensus        11 el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~   49 (86)
T 1y96_A           11 EWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF   49 (86)
T ss_dssp             HHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE
T ss_pred             HHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec
Confidence            578899999999999999999999999999999888876

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	86
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	96.19
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	96.03
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	95.53
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	95.46
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	95.3
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	95.25
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	95.24
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	95.03
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	94.38
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	94.32
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	92.54
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	88.55

>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=96.19  E-value=0.01  Score=34.95  Aligned_cols=61  Identities=13%  Similarity=0.118  Sum_probs=46.9

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CCCcCc----cccceeeecCceeEEe
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KTPIGT----FHEHALLRVDDIVDIE   85 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~TPiGv----~~e~AlLR~~DIi~~~   85 (86)
                      |+.|..+.|++|.+.|.++.++.|+..++|.. .|+..++- +|+-+-    .++ ..+|.+-|..+.
T Consensus         4 l~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~-mNi~L~~~~~~~~~~~~~~~~~-v~IRG~~I~~i~   69 (72)
T d1d3ba_           4 IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDN-MNCQMSNITVTYRDGRVAQLEQ-VYIRGCKIRFLI   69 (72)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTT-CCEEEEEEEEECTTSCEEEEEE-EEECGGGEEEEE
T ss_pred             hHHHHhcCCCEEEEEECCCeEEEEEEEEEcCC-eeEEEEEEEEEcCCCcEeEcCe-EEEECCEEEEEE
Confidence            57788999999999999999999999999986 55655554 344332    334 678888887665

>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=96.03  E-value=0.007  Score=40.06  Aligned_cols=62  Identities=16%  Similarity=0.335  Sum_probs=50.2

Q ss_pred             HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcC-ccccceeeecCceeEEe
Q psy488           22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIG-TFHEHALLRVDDIVDIE   85 (86)
Q Consensus        22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiG-v~~e~AlLR~~DIi~~~   85 (86)
                      |+..|.++.|++|.+.|..+.++.|+..++| +..|+..+|-.-.-| -.++ -++|.+-|..+.
T Consensus         1 f~~~L~~~~gk~V~VeLkng~~~~G~L~~~D-~~mNivL~da~~~~~~k~~~-v~IRG~~I~~I~   63 (127)
T d1m5q1_           1 FVAELNNLLGREVQVVLSNGEVYKGVLHAVD-NQLNIVLANASNKAGEKFNR-VFIMYRYIVHID   63 (127)
T ss_dssp             CHHHHHTTTTSEEEEEETTSCEEEEEEEEEC-TTCCEEEEEEEETTCCEEEE-EEECGGGEEEEE
T ss_pred             ChhHHHHhCCCEEEEEECCCCEEEEEEEEEC-CCceEEEeEEEECCCCcccE-EEEeCCeEEEEE
Confidence            6889999999999999999999999999999 668888887753333 3444 778888876654

>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=95.53  E-value=0.047  Score=32.11  Aligned_cols=63  Identities=8%  Similarity=0.145  Sum_probs=47.2

Q ss_pred             HHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CCcCc----cccceeeecCceeEEe
Q psy488           21 KFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TPIGT----FHEHALLRVDDIVDIE   85 (86)
Q Consensus        21 rfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TPiGv----~~e~AlLR~~DIi~~~   85 (86)
                      .-.+.|....|++|.+.+.++..+.|++.++|... |+..++-. +.-+.    .+. .++|.+-|+.+.
T Consensus         7 ~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~m-NlvL~~~~e~~~~~~~~~~~~-v~iRG~~I~~I~   74 (76)
T d1th7a1           7 TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHM-NLVLSDSEEIQSDGSGKKLGT-IVIRGDNVILIS   74 (76)
T ss_dssp             HHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTC-CEEEEEEEEECSSSCEEEEEE-EEECGGGEEEEE
T ss_pred             cHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCC-CEEEeEEEEEecCCcccCcce-EEEECCEEEEEE
Confidence            34466778889999999999999999999999876 55554432 33332    245 789999888764

>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=95.46  E-value=0.038  Score=32.16  Aligned_cols=61  Identities=11%  Similarity=0.196  Sum_probs=44.9

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCc----cccceeeecCceeEE
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGT----FHEHALLRVDDIVDI   84 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv----~~e~AlLR~~DIi~~   84 (86)
                      |..|....|++|.+.+.++..+.|++.++|....-++-+--++.-+.    .+. .+||..-|+.+
T Consensus         5 l~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~-~~IRG~~I~~I   69 (72)
T d1i4k1_           5 LDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGS-VVIRGDTVVFV   69 (72)
T ss_dssp             HHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEE-EEECGGGEEEE
T ss_pred             HHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcce-EEEeCCeEEEE
Confidence            56788889999999999999999999999986544432222332222    335 88898888765

>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=95.30  E-value=0.028  Score=34.10  Aligned_cols=61  Identities=10%  Similarity=0.196  Sum_probs=46.9

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCC-C-------------------cCccccceeeecCcee
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKT-P-------------------IGTFHEHALLRVDDIV   82 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T-P-------------------iGv~~e~AlLR~~DIi   82 (86)
                      |.+|.+..|++|.+.+.++....|++.|+|-.. |+..++-.- .                   -..... ++||...|+
T Consensus         7 l~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~-NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~-~~iRG~~Vv   84 (92)
T d2fwka1           7 LALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYV-NMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLET-ILLSGNNVA   84 (92)
T ss_dssp             HHHHHHTBTSBCEEEETTTEEECCEEEEECTTC-CEEEESCCEEEC---------------CEECCCCSE-EEECGGGEE
T ss_pred             HHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCC-CEEEeeEEEEEecCCccccccccccccccceeEcce-EEEeCCEEE
Confidence            566778889999999999999999999999876 666665431 1                   112334 899999998


Q ss_pred             EEe
Q psy488           83 DIE   85 (86)
Q Consensus        83 ~~~   85 (86)
                      .+.
T Consensus        85 ~I~   87 (92)
T d2fwka1          85 MLV   87 (92)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            863

>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=95.25  E-value=0.065  Score=32.01  Aligned_cols=62  Identities=16%  Similarity=0.205  Sum_probs=48.0

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CCCcC-c---cccceeeecCceeEEeC
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KTPIG-T---FHEHALLRVDDIVDIEI   86 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~TPiG-v---~~e~AlLR~~DIi~~~~   86 (86)
                      .++|.++.|++|.+.|..++.+.|+..++|.. .|+..+|- .|+-+ .   .++ -.+|.+-|..+.+
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~-MNl~L~~~~~~~~~~~~~~~~~-v~IRG~~Ir~i~l   69 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVS-MNTHLKAVKMTLKNREPVQLET-LSIRGNNIRYFIL   69 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTT-CCEEEEEEEEECTTSCCEEEEE-EEECGGGEEEEEC
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCC-cEEEEEEEEEEcCCCCEEEccc-EEEcCCEEEEEEC
Confidence            67899999999999999999999999999985 66666663 33322 2   234 7888888876653

>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=95.24  E-value=0.032  Score=32.24  Aligned_cols=60  Identities=10%  Similarity=0.191  Sum_probs=44.8

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CC----CcCccccceeeecCceeEE
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KT----PIGTFHEHALLRVDDIVDI   84 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~T----PiGv~~e~AlLR~~DIi~~   84 (86)
                      |..|..+.|++|.+.|.++..+.|++.++|... |+..++- ++    .-...+. .+||.+-|+.+
T Consensus         4 l~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~m-NlvL~~~~e~~~~~~~~~l~~-~~IRG~~I~~I   68 (71)
T d1h641_           4 LDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHL-NVVLADAEMIQDGEVVKRYGK-IVIRGDNVLAI   68 (71)
T ss_dssp             HHHHHTTTTSEEEEEETTSEEEEEEEEEECTTC-CEEEEEEEEEETTEEEEEEEE-EEECGGGEEEE
T ss_pred             hHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCC-CeEEeeEEEEecCCcEeEcCc-EEEECCeEEEE
Confidence            567888999999999999999999999999665 5544443 11    1122234 78998888776

>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=95.03  E-value=0.036  Score=32.44  Aligned_cols=60  Identities=17%  Similarity=0.256  Sum_probs=43.9

Q ss_pred             HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CC----cCccccceeeecCceeEE
Q psy488           23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TP----IGTFHEHALLRVDDIVDI   84 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TP----iGv~~e~AlLR~~DIi~~   84 (86)
                      |..|.++.|++|.+.|.++..+.|++.++|... |+..++-. +.    -...+. .++|.+-|+.+
T Consensus         8 l~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~m-Nl~L~~~~e~~~~~~~~~~~~-~~IRG~~I~~I   72 (74)
T d1mgqa_           8 LDALGNSLNSPVIIKLKGDREFRGVLKSFDLHM-NLVLNDAEELEDGEVTRRLGT-VLIRGDNIVYI   72 (74)
T ss_dssp             THHHHHTTTSEEEEEETTTEEEEEEEEEECTTC-CEEEEEEEEEETTEEEEEEEE-EEECGGGEEEE
T ss_pred             HHHHHHhCCCeEEEEECCCCEEEEEEEEECCCC-CeEEeeEEEEeCCCeEeEcce-EEEeCCEEEEE
Confidence            456778899999999999999999999999765 55444331 21    122334 78888888765

>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=94.38  E-value=0.075  Score=30.99  Aligned_cols=59  Identities=7%  Similarity=0.189  Sum_probs=42.5

Q ss_pred             HHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CCCcC---ccccceeeecCceeEE
Q psy488           24 KAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KTPIG---TFHEHALLRVDDIVDI   84 (86)
Q Consensus        24 r~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~TPiG---v~~e~AlLR~~DIi~~   84 (86)
                      .+|.++.|++|.+.|.++..+.|++.++|-.. |+..++- ++.-|   -.+. .++|.+-|+.+
T Consensus         5 ~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~m-NivL~~~~e~~~~~~~~~g~-v~iRG~~I~~I   67 (71)
T d1i8fa_           5 ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHV-NLLLEDAEEIIDGNVYKRGT-MVVRGENVLFI   67 (71)
T ss_dssp             HHHHTTTTSEEEEEEGGGEEEEEEEEEECTTC-CEEEEEEEEEETTEEEEEEE-EEECGGGEEEE
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEECCCc-ceEEccEEEEECCCEEEcce-EEEeCCeEEEE
Confidence            46788999999999999999999999999854 4433332 11111   1123 78999888776

>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=94.32  E-value=0.068  Score=31.54  Aligned_cols=60  Identities=20%  Similarity=0.342  Sum_probs=42.6

Q ss_pred             HHHHHhcCCCceEEEee-cCcEEEEEEeeecCCcceeeeccc-CCCc----CccccceeeecCceeEE
Q psy488           23 LKAMSSLSGQPCTINMF-ERTVVTAEFQGTNSDLTEFYVRNL-KTPI----GTFHEHALLRVDDIVDI   84 (86)
Q Consensus        23 Lr~l~~~~gk~v~f~m~-E~t~V~a~F~a~d~d~~~f~Vs~L-~TPi----Gv~~e~AlLR~~DIi~~   84 (86)
                      +..|.++.|++|.+.|. +++.+.|++.++|.. .|+..+|- ++.-    ..... .+||.+-|+.+
T Consensus         7 ~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~-mNlvL~~~~e~~~~~~~~~~g~-~~IRG~~I~~I   72 (75)
T d1ljoa_           7 NQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDY-MNLYLTNAMECKGEEKVRSLGE-IVLRGNNVVLI   72 (75)
T ss_dssp             HHHHHHTTTSEEEEEETTCSSEEEEEEEEECTT-CCEEEEEEEEEETTEEEEEEEE-EEECGGGEEEE
T ss_pred             HHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCC-CcEEEeEEEEEcCCCcEeEcce-EEEeCCEEEEE
Confidence            46788899999999998 458999999999965 55555443 2221    12224 78888888765

>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=92.54  E-value=0.083  Score=31.31  Aligned_cols=59  Identities=10%  Similarity=0.158  Sum_probs=42.6

Q ss_pred             HHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-C-----CC-cCc--------cccceeeecCceeEEeC
Q psy488           26 MSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-K-----TP-IGT--------FHEHALLRVDDIVDIEI   86 (86)
Q Consensus        26 l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~-----TP-iGv--------~~e~AlLR~~DIi~~~~   86 (86)
                      |....|+++.+.+.++-.+.|+|.|+|....-++ ++- +     ++ -+.        ..- .++|..-|++|++
T Consensus         3 L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL-~~~~E~~~~~~~~~~~~~~~~~r~lG~-v~IRG~~Iv~i~~   76 (81)
T d1d3bb_           3 MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLIL-CDCDEFRKIKPKNSKQAEREEKRVLGL-VLLRGENLVSMTV   76 (81)
T ss_dssp             CGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEE-EEEEEEEEECCSSTTSCCEEEEEEEEE-EEECGGGEEEEEE
T ss_pred             hHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEE-cCEEEEEeecCccccccccceEEEeee-EEEeCCEEEEEEc
Confidence            4567899999999999999999999997654444 331 1     11 110        123 7999999999874

>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=88.55  E-value=0.67  Score=26.47  Aligned_cols=58  Identities=14%  Similarity=0.235  Sum_probs=40.9

Q ss_pred             HHhcCCCceEEEee-cCcEEEEEEeeecCCcceeeeccc-CC----CcCccccceeeecCceeEEe
Q psy488           26 MSSLSGQPCTINMF-ERTVVTAEFQGTNSDLTEFYVRNL-KT----PIGTFHEHALLRVDDIVDIE   85 (86)
Q Consensus        26 l~~~~gk~v~f~m~-E~t~V~a~F~a~d~d~~~f~Vs~L-~T----PiGv~~e~AlLR~~DIi~~~   85 (86)
                      |.++.|++|.+.|. +++...|+..++|..-.-.+ ++- ++    .....+. .+||.+-|+.+.
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL-~~~~e~~~~~~~~~lg~-~~IRG~nI~~I~   64 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQL-NEAEEFVAGVSHGTLGE-IFIRCNNVLYIR   64 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEE-EEEEEEETTEEEEECCS-EEECGGGEEEEE
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEE-eeEEEEecCCcccCcCe-EEEECCEEEEEE
Confidence            35678999999998 66889999999997654333 221 11    1223456 899999998774