Psyllid ID: psy9934

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------16
Protein Sequence
MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDEEGEMRE
Secondary Structure (PSIPRED)
cccccccccHHHHHHccccEEEEEEcccEEEEEEEEEEcccEEEEEccEEEEEccccccccccEEEEEEccccccccccHHHHHHccccEEEEEEcccEEEEEEEEEEEcEEEEEEccEEEEEccEEccccccEEEEcccEEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHccccEEEEEEcccEEEEEEEEEEcccccEEEEEEEEEEccEEEEEEEEEEEcHHHEEEEcccccHHHHHHHcccEEEEEEcccEEEEEEEEEEcccccEEEEEEEEEEccEEEEEEEEEEEcHHHEEEEEccccccccccccc
Coil and Loop (DISEMBL)
mstplpcnpkpflnlltgksvicklkwgheykgilvstdgymncqlasteeiidghctgKLGEVLIRSLtmstplpcnpkpflnlltgksvicklkwgheykgilvstdgymncqlasteeiidghctGKLGEVLIRCNNILyirgaeegdeegemre
Flexible Loop (DISEMBL)
mstplpcnpkpflnLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNIlyirgaeegdeegemre
Low Complexity Region (SEG)
MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRgaeegdeegemre
Disordered region (IsUnstruct)
**********PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG************
Disordered Region (DISOPRED)
******C***PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII**HCTGKLGEVLIRSLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILY***************
Disordered Region (DISEMBL)
MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE**********
Disordered Region (DISPRO)
*****PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE**********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDEEGEMRE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	158	2.2.26 [Sep-21-2011]
Q24297	88	Small nuclear ribonucleop	yes	N/A	0.556	1.0	0.727	7e-33
Q9SUM2	88	Probable small nuclear ri	yes	N/A	0.493	0.886	0.692	5e-27
P62321	86	Small nuclear ribonucleop	N/A	N/A	0.462	0.848	0.767	2e-26
P62307	86	Small nuclear ribonucleop	yes	N/A	0.462	0.848	0.767	2e-26
P62306	86	Small nuclear ribonucleop	yes	N/A	0.462	0.848	0.767	2e-26
Q3T0Z8	86	Small nuclear ribonucleop	yes	N/A	0.462	0.848	0.767	2e-26
P34659	85	Probable small nuclear ri	yes	N/A	0.518	0.964	0.646	5e-26
O59734	78	Small nuclear ribonucleop	yes	N/A	0.443	0.897	0.614	2e-20
Q54XP2	91	Small nuclear ribonucleop	yes	N/A	0.5	0.868	0.587	4e-20
Q9P5Z8	90	Probable small nuclear ri	N/A	N/A	0.525	0.922	0.523	7e-20

>sp|Q24297|RUXF_DROME Small nuclear ribonucleoprotein F OS=Drosophila melanogaster GN=SmF PE=3 SV=2

 Score =  139 bits (350), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 64/88 (72%), Positives = 73/88 (82%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           MS  +P NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE+I+G  TG 
Sbjct: 1   MSAGMPINPKPFLNGLTGKPVLVKLKWGQEYKGFLVSVDGYMNMQLANTEEVIEGSVTGN 60

Query: 131 LGEVLIRCNNILYIRGAEEGDEEGEMRE 158
           LGEVLIRCNN+LYI+G E+ DEEGEMR+
Sbjct: 61  LGEVLIRCNNVLYIKGMEDDDEEGEMRD 88

Associated with snRNP U1, U2, U4/U6 and U5.
Drosophila melanogaster (taxid: 7227)

>sp|Q9SUM2|RUXF_ARATH Probable small nuclear ribonucleoprotein F OS=Arabidopsis thaliana GN=At4g30220 PE=2 SV=1

 Score =  119 bits (299), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 54/78 (69%), Positives = 61/78 (78%)

Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           +P NPKPFLN LTGK+VI KLKWG EYKG L S D YMN QL +TEE IDG  TG LGE+
Sbjct: 4   IPVNPKPFLNNLTGKTVIVKLKWGMEYKGFLASVDSYMNLQLGNTEEYIDGQLTGNLGEI 63

Query: 135 LIRCNNILYIRGAEEGDE 152
           LIRCNN+LY+RG  E +E
Sbjct: 64  LIRCNNVLYVRGVPEDEE 81

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

Arabidopsis thaliana (taxid: 3702)

>sp|P62321|RUXF_XENLA Small nuclear ribonucleoprotein F OS=Xenopus laevis GN=snrpf PE=3 SV=1

 Score =  117 bits (294), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/73 (76%), Positives = 60/73 (82%)

Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct: 3   LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query: 135 LIRCNNILYIRGA 147
           LIRCNN+LYIRG 
Sbjct: 63  LIRCNNVLYIRGV 75

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

Xenopus laevis (taxid: 8355)

>sp|P62307|RUXF_MOUSE Small nuclear ribonucleoprotein F OS=Mus musculus GN=Snrpf PE=2 SV=1

 Score =  117 bits (294), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/73 (76%), Positives = 60/73 (82%)

Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct: 3   LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query: 135 LIRCNNILYIRGA 147
           LIRCNN+LYIRG 
Sbjct: 63  LIRCNNVLYIRGV 75

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

Mus musculus (taxid: 10090)

>sp|P62306|RUXF_HUMAN Small nuclear ribonucleoprotein F OS=Homo sapiens GN=SNRPF PE=1 SV=1

 Score =  117 bits (294), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/73 (76%), Positives = 60/73 (82%)

Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct: 3   LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query: 135 LIRCNNILYIRGA 147
           LIRCNN+LYIRG 
Sbjct: 63  LIRCNNVLYIRGV 75

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

Homo sapiens (taxid: 9606)

>sp|Q3T0Z8|RUXF_BOVIN Small nuclear ribonucleoprotein F OS=Bos taurus GN=SNRPF PE=3 SV=2

 Score =  117 bits (294), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/73 (76%), Positives = 60/73 (82%)

Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct: 3   LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query: 135 LIRCNNILYIRGA 147
           LIRCNN+LYIRG 
Sbjct: 63  LIRCNNVLYIRGV 75

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

Bos taurus (taxid: 9913)

>sp|P34659|RUXF_CAEEL Probable small nuclear ribonucleoprotein F OS=Caenorhabditis elegans GN=snr-5 PE=1 SV=1

 Score =  116 bits (291), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 53/82 (64%), Positives = 62/82 (75%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           MS   P NPKPFLN LTGK V+CKLKWG EYKG+LV+ D YMN QLA  EE IDG+  G 
Sbjct: 1   MSAVQPVNPKPFLNSLTGKFVVCKLKWGMEYKGVLVAVDSYMNLQLAHAEEYIDGNSQGN 60

Query: 131 LGEVLIRCNNILYIRGAEEGDE 152
           LGE+LIRCNN+LY+ G +  +E
Sbjct: 61  LGEILIRCNNVLYVGGVDGENE 82

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

Caenorhabditis elegans (taxid: 6239)

>sp|O59734|RUXF_SCHPO Small nuclear ribonucleoprotein F OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smf1 PE=1 SV=1

 Score = 98.6 bits (244), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 43/70 (61%), Positives = 53/70 (75%)

Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           +P NPKPFL  L GK V+ +LKWG EYKG L S D YMN QL + EE++DG  TG LGE+
Sbjct: 4   VPVNPKPFLQGLIGKPVLVRLKWGQEYKGTLQSVDSYMNLQLLNAEELVDGVKTGDLGEI 63

Query: 135 LIRCNNILYI 144
           LIRCNN+L++
Sbjct: 64  LIRCNNVLWV 73

Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site.

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

>sp|Q54XP2|RUXF_DICDI Small nuclear ribonucleoprotein F OS=Dictyostelium discoideum GN=snrpf PE=3 SV=1

 Score = 97.1 bits (240), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 47/80 (58%), Positives = 56/80 (70%), Gaps = 1/80 (1%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTG 129
           MS      PKPFL  L GK +  +LKWG  EY+GIL S D YMN QLA+TEE IDG   G
Sbjct: 1   MSKIEALAPKPFLYDLKGKKIAVRLKWGGMEYRGILASVDSYMNLQLAATEEWIDGANKG 60

Query: 130 KLGEVLIRCNNILYIRGAEE 149
            LGEVLIRCNN+L++RG ++
Sbjct: 61  PLGEVLIRCNNVLFVRGIDD 80

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

Dictyostelium discoideum (taxid: 44689)

>sp|Q9P5Z8|RUXF_NEUCR Probable small nuclear ribonucleoprotein F OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=B2O8.190 PE=3 SV=1

 Score = 96.3 bits (238), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 44/84 (52%), Positives = 58/84 (69%), Gaps = 1/84 (1%)

Query: 75  LPCNPKPFLNLLTGKSVICKLKWGH-EYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGE 133
           +P NP+PFL  L    V  +LKWG  EY G LVS D YMN QL+ T+E I+   TG LG+
Sbjct: 4   VPVNPRPFLQDLVNSFVTIRLKWGETEYVGRLVSIDSYMNIQLSDTKEYINRKFTGALGQ 63

Query: 134 VLIRCNNILYIRGAEEGDEEGEMR 157
           VLIRCNN+LYI+ A+E +  G+++
Sbjct: 64  VLIRCNNVLYIKKADEAETSGDVK 87

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

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

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	158
290561351	86	Small nuclear ribonucleoprotein F [Lepeo	0.531	0.976	0.785	1e-32
31212897	88	AGAP002658-PA [Anopheles gambiae str. PE	0.556	1.0	0.75	2e-32
312371148	88	hypothetical protein AND_30966 [Anophele	0.556	1.0	0.738	5e-32
170032813	88	small nuclear ribonucleoprotein F [Culex	0.556	1.0	0.738	5e-32
225709496	86	Small nuclear ribonucleoprotein F [Calig	0.531	0.976	0.761	7e-32
332031555	88	Small nuclear ribonucleoprotein F [Acrom	0.556	1.0	0.738	1e-31
22024001	88	small ribonucleoprotein particle protein	0.556	1.0	0.727	4e-31
307186677	84	Small nuclear ribonucleoprotein F [Campo	0.531	1.0	0.773	4e-31
153792507	88	small nuclear ribonucleoprotein protein	0.493	0.886	0.769	5e-30
357605279	88	small nuclear ribonucleoprotein F [Danau	0.487	0.875	0.766	2e-29

>gi|290561351|gb|ADD38076.1| Small nuclear ribonucleoprotein F [Lepeophtheirus salmonis]

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 66/84 (78%), Positives = 74/84 (88%)

Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           +P NPKPFLN LTGK+V+ KLKWGHEYKG LVSTDGYMN QLA+TEE IDG+CTG LGEV
Sbjct: 3   MPINPKPFLNELTGKAVMVKLKWGHEYKGYLVSTDGYMNVQLANTEEYIDGNCTGTLGEV 62

Query: 135 LIRCNNILYIRGAEEGDEEGEMRE 158
           L+RCNN+LYIRG +E DEEGE RE
Sbjct: 63  LVRCNNVLYIRGVQEDDEEGETRE 86

Source: Lepeophtheirus salmonis

Species: Lepeophtheirus salmonis

Genus: Lepeophtheirus

Family: Caligidae

Order: Siphonostomatoida

Class: Maxillopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|31212897|ref|XP_312266.1| AGAP002658-PA [Anopheles gambiae str. PEST] gi|30177439|gb|EAA07677.2| AGAP002658-PA [Anopheles gambiae str. PEST]

 Score =  143 bits (360), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 66/88 (75%), Positives = 74/88 (84%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           M+T +P NPKPFLN LTGK VI KLKWGHEYKG LVS DGYMN QLA+TEE +DG  TG 
Sbjct: 1   MTTAMPINPKPFLNGLTGKPVIIKLKWGHEYKGFLVSVDGYMNMQLANTEEFVDGQNTGH 60

Query: 131 LGEVLIRCNNILYIRGAEEGDEEGEMRE 158
           LGEVLIRCNN+LYIRG ++ DEEGEMR+
Sbjct: 61  LGEVLIRCNNVLYIRGIDDEDEEGEMRD 88

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312371148|gb|EFR19407.1| hypothetical protein AND_30966 [Anopheles darlingi]

 Score =  142 bits (358), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 74/88 (84%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           M+T +P NPKPFLN LTGK V+ KLKWGHEYKG LVS DGYMN QLA+TEE +DG  TG 
Sbjct: 1   MATAMPINPKPFLNGLTGKPVMIKLKWGHEYKGFLVSVDGYMNMQLANTEEFVDGQNTGH 60

Query: 131 LGEVLIRCNNILYIRGAEEGDEEGEMRE 158
           LGEVLIRCNN+LYIRG ++ DEEGEMR+
Sbjct: 61  LGEVLIRCNNVLYIRGIDDEDEEGEMRD 88

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170032813|ref|XP_001844274.1| small nuclear ribonucleoprotein F [Culex quinquefasciatus] gi|167873231|gb|EDS36614.1| small nuclear ribonucleoprotein F [Culex quinquefasciatus]

 Score =  142 bits (358), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 74/88 (84%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           M+T +P NPKPFLN LTGK VI KLKWGHEYKG LVS DGYMN QLA+T+E +DG  TG 
Sbjct: 1   MTTAMPINPKPFLNGLTGKPVIIKLKWGHEYKGFLVSVDGYMNMQLANTDEYVDGQNTGH 60

Query: 131 LGEVLIRCNNILYIRGAEEGDEEGEMRE 158
           LGEVLIRCNN+LYIRG ++ DEEGEMR+
Sbjct: 61  LGEVLIRCNNVLYIRGIDDDDEEGEMRD 88

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225709496|gb|ACO10594.1| Small nuclear ribonucleoprotein F [Caligus rogercresseyi]

 Score =  141 bits (356), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 64/84 (76%), Positives = 74/84 (88%)

Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           +P NPKPFLN LTGK+V+ KLKWGHEYKG LVS+DGYMN QLA+TEE IDG+CTG LGEV
Sbjct: 3   MPINPKPFLNELTGKAVMVKLKWGHEYKGYLVSSDGYMNVQLANTEEYIDGNCTGTLGEV 62

Query: 135 LIRCNNILYIRGAEEGDEEGEMRE 158
           L+RCNN+LYIRG +E DEEGE +E
Sbjct: 63  LVRCNNVLYIRGVQEDDEEGETKE 86

Source: Caligus rogercresseyi

Species: Caligus rogercresseyi

Genus: Caligus

Family: Caligidae

Order: Siphonostomatoida

Class: Maxillopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332031555|gb|EGI71027.1| Small nuclear ribonucleoprotein F [Acromyrmex echinatior]

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 75/88 (85%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           M+  +P NPKPFLN LTGK V+ KLKWGHEYKG LVS DGYMN QLA+TEE I+G+CTG 
Sbjct: 1   MAATMPINPKPFLNGLTGKPVMVKLKWGHEYKGYLVSVDGYMNLQLANTEEHIEGNCTGN 60

Query: 131 LGEVLIRCNNILYIRGAEEGDEEGEMRE 158
           LGEVLIRCNN++YIRG EE DEEGEM++
Sbjct: 61  LGEVLIRCNNVMYIRGVEESDEEGEMKD 88

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|22024001|ref|NP_523708.2| small ribonucleoprotein particle protein SmF [Drosophila melanogaster] gi|125807333|ref|XP_001360364.1| GA14154 [Drosophila pseudoobscura pseudoobscura] gi|194754150|ref|XP_001959360.1| GF12081 [Drosophila ananassae] gi|194883764|ref|XP_001975970.1| GG22599 [Drosophila erecta] gi|195056665|ref|XP_001995140.1| GH22983 [Drosophila grimshawi] gi|195122320|ref|XP_002005660.1| GI18952 [Drosophila mojavensis] gi|195149774|ref|XP_002015830.1| GL11267 [Drosophila persimilis] gi|195333646|ref|XP_002033498.1| GM20378 [Drosophila sechellia] gi|195381309|ref|XP_002049395.1| GJ21558 [Drosophila virilis] gi|195436262|ref|XP_002066088.1| GK22120 [Drosophila willistoni] gi|195485487|ref|XP_002091113.1| GE13467 [Drosophila yakuba] gi|195551853|ref|XP_002076311.1| GD15243 [Drosophila simulans] gi|195551862|ref|XP_002076315.1| DebB [Drosophila simulans] gi|29337191|sp|Q24297.2|RUXF_DROME RecName: Full=Small nuclear ribonucleoprotein F; Short=snRNP-F; AltName: Full=Membrane-associated protein Deb-B; AltName: Full=Sm protein F; Short=Sm-F; Short=SmF gi|21430088|gb|AAM50722.1| GM23968p [Drosophila melanogaster] gi|21645477|gb|AAF58559.2| small ribonucleoprotein particle protein SmF [Drosophila melanogaster] gi|54635536|gb|EAL24939.1| GA14154 [Drosophila pseudoobscura pseudoobscura] gi|190620658|gb|EDV36182.1| GF12081 [Drosophila ananassae] gi|190659157|gb|EDV56370.1| GG22599 [Drosophila erecta] gi|193899346|gb|EDV98212.1| GH22983 [Drosophila grimshawi] gi|193910728|gb|EDW09595.1| GI18952 [Drosophila mojavensis] gi|194109677|gb|EDW31720.1| GL11267 [Drosophila persimilis] gi|194125468|gb|EDW47511.1| GM20378 [Drosophila sechellia] gi|194144192|gb|EDW60588.1| GJ21558 [Drosophila virilis] gi|194162173|gb|EDW77074.1| GK22120 [Drosophila willistoni] gi|194177214|gb|EDW90825.1| GE13467 [Drosophila yakuba] gi|194201960|gb|EDX15536.1| GD15243 [Drosophila simulans] gi|194201964|gb|EDX15540.1| DebB [Drosophila simulans] gi|220956990|gb|ACL91038.1| DebB-PA [synthetic construct]

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 64/88 (72%), Positives = 73/88 (82%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           MS  +P NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE+I+G  TG 
Sbjct: 1   MSAGMPINPKPFLNGLTGKPVLVKLKWGQEYKGFLVSVDGYMNMQLANTEEVIEGSVTGN 60

Query: 131 LGEVLIRCNNILYIRGAEEGDEEGEMRE 158
           LGEVLIRCNN+LYI+G E+ DEEGEMR+
Sbjct: 61  LGEVLIRCNNVLYIKGMEDDDEEGEMRD 88

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307186677|gb|EFN72155.1| Small nuclear ribonucleoprotein F [Camponotus floridanus]

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 65/84 (77%), Positives = 72/84 (85%)

Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           +P NPKPFLN LTGK V+ KLKWGHEYKG LVS DGYMN QLA+TEE IDG CTG LGEV
Sbjct: 1   MPINPKPFLNGLTGKPVMVKLKWGHEYKGYLVSVDGYMNLQLANTEEHIDGSCTGNLGEV 60

Query: 135 LIRCNNILYIRGAEEGDEEGEMRE 158
           LIRCNN++YIRG EE DEEGEM++
Sbjct: 61  LIRCNNVMYIRGVEESDEEGEMKD 84

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|153792507|ref|NP_001093276.1| small nuclear ribonucleoprotein protein F [Bombyx mori] gi|95102986|gb|ABF51434.1| small nuclear ribonucleoprotein protein F [Bombyx mori]

 Score =  135 bits (341), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 60/78 (76%), Positives = 70/78 (89%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           M+  +P NPKPFLN LTGKSV+ KLKWGHEYKG+LVSTDGYMN QLA+TEE++DG CTG 
Sbjct: 1   MAAAMPINPKPFLNSLTGKSVLVKLKWGHEYKGLLVSTDGYMNLQLANTEELVDGTCTGN 60

Query: 131 LGEVLIRCNNILYIRGAE 148
           LGEVLIRCNN+LY+RGA+
Sbjct: 61  LGEVLIRCNNVLYVRGAD 78

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357605279|gb|EHJ64538.1| small nuclear ribonucleoprotein F [Danaus plexippus]

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 59/77 (76%), Positives = 68/77 (88%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           M+  +P NPKPFLN LTGK+V+ KLKWGHEYKG+LVS DGYMN QLA+TEEI+DG CTG 
Sbjct: 1   MAASMPINPKPFLNSLTGKAVLVKLKWGHEYKGLLVSADGYMNLQLANTEEIVDGSCTGN 60

Query: 131 LGEVLIRCNNILYIRGA 147
           LGEVLIRCNN+LY+RGA
Sbjct: 61  LGEVLIRCNNVLYVRGA 77

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	158
FB|FBgn0000426	88	SmF "Small ribonucleoprotein p	0.474	0.852	0.733	2.5e-26
UNIPROTKB|F1Q0L5	111	SNRPF "Uncharacterized protein	0.582	0.828	0.655	2.5e-26
UNIPROTKB|F1P4B8	85	SNRPF "Uncharacterized protein	0.449	0.835	0.774	4.6e-25
UNIPROTKB|Q3T0Z8	86	SNRPF "Small nuclear ribonucle	0.449	0.825	0.774	4.6e-25
UNIPROTKB|P62306	86	SNRPF "Small nuclear ribonucle	0.449	0.825	0.774	4.6e-25
UNIPROTKB|F1SQR4	86	SNRPF "Uncharacterized protein	0.449	0.825	0.774	4.6e-25
MGI|MGI:1917128	86	Snrpf "small nuclear ribonucle	0.449	0.825	0.774	4.6e-25
RGD|1588229	86	Snrpf "small nuclear ribonucle	0.449	0.825	0.774	4.6e-25
ZFIN|ZDB-GENE-040930-9	86	snrpf "small nuclear ribonucle	0.449	0.825	0.760	7.6e-25
WB|WBGene00004918	85	snr-5 [Caenorhabditis elegans	0.468	0.870	0.689	9.7e-25

FB|FBgn0000426 SmF "Small ribonucleoprotein particle protein SmF" [Drosophila melanogaster (taxid:7227)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 55/75 (73%), Positives = 62/75 (82%)

Query:    71 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
             MS  +P NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE+I+G  TG 
Sbjct:     1 MSAGMPINPKPFLNGLTGKPVLVKLKWGQEYKGFLVSVDGYMNMQLANTEEVIEGSVTGN 60

Query:   131 LGEVLIRCNNILYIR 145
             LGEVLIRCNN+LYI+
Sbjct:    61 LGEVLIRCNNVLYIK 75

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

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

GO:0005681 "spliceosomal complex" evidence=ISS;NAS

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

UNIPROTKB|F1Q0L5 SNRPF "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 61/93 (65%), Positives = 68/93 (73%)

Query:    54 DGHCT-GKLGEVLIRSLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYM 112
             +G  T G     L R L ++  LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYM
Sbjct:     6 EGRTTAGSAASGLQRWLVVAMSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYM 65

Query:   113 NCQLASTEEIIDGHCTGKLGEVLIRCNNILYIR 145
             N QLA+TEE IDG  +G LGEVLIRCNN+LYIR
Sbjct:    66 NMQLANTEEYIDGALSGHLGEVLIRCNNVLYIR 98

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

GO:0008380 "RNA splicing" evidence=IEA

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

GO:0005683 "U7 snRNP" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1P4B8 SNRPF "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:    75 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     2 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 61

Query:   135 LIRCNNILYIR 145
             LIRCNN+LYIR
Sbjct:    62 LIRCNNVLYIR 72

GO:0003723 "RNA binding" evidence=IEA

GO:0005683 "U7 snRNP" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

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

UNIPROTKB|Q3T0Z8 SNRPF "Small nuclear ribonucleoprotein F" [Bos taurus (taxid:9913)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:    75 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query:   135 LIRCNNILYIR 145
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

GO:0005683 "U7 snRNP" evidence=ISS

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

GO:0008380 "RNA splicing" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|P62306 SNRPF "Small nuclear ribonucleoprotein F" [Homo sapiens (taxid:9606)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:    75 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query:   135 LIRCNNILYIR 145
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0008380 "RNA splicing" evidence=IMP;TAS

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

GO:0003723 "RNA binding" evidence=IMP

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

GO:0005683 "U7 snRNP" evidence=IDA

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

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

GO:0000387 "spliceosomal snRNP assembly" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

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

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

GO:0006397 "mRNA processing" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0034660 "ncRNA metabolic process" evidence=TAS

UNIPROTKB|F1SQR4 SNRPF "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:    75 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query:   135 LIRCNNILYIR 145
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

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

GO:0008380 "RNA splicing" evidence=IEA

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

GO:0005683 "U7 snRNP" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

MGI|MGI:1917128 Snrpf "small nuclear ribonucleoprotein polypeptide F" [Mus musculus (taxid:10090)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:    75 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query:   135 LIRCNNILYIR 145
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

GO:0003723 "RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0005683 "U7 snRNP" evidence=ISO

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

GO:0006396 "RNA processing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

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

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

RGD|1588229 Snrpf "small nuclear ribonucleoprotein polypeptide F" [Rattus norvegicus (taxid:10116)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:    75 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query:   135 LIRCNNILYIR 145
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

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

GO:0005681 "spliceosomal complex" evidence=ISO

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

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

GO:0008380 "RNA splicing" evidence=IEA;ISO

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

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

ZFIN|ZDB-GENE-040930-9 snrpf "small nuclear ribonucleoprotein polypeptide F" [Danio rerio (taxid:7955)]

 Score = 283 (104.7 bits), Expect = 7.6e-25, P = 7.6e-25
 Identities = 54/71 (76%), Positives = 58/71 (81%)

Query:    75 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE +DG   G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYVDGALAGHLGEV 62

Query:   135 LIRCNNILYIR 145
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

GO:0005634 "nucleus" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

WB|WBGene00004918 snr-5 [Caenorhabditis elegans (taxid:6239)]

 Score = 282 (104.3 bits), Expect = 9.7e-25, P = 9.7e-25
 Identities = 51/74 (68%), Positives = 58/74 (78%)

Query:    71 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
             MS   P NPKPFLN LTGK V+CKLKWG EYKG+LV+ D YMN QLA  EE IDG+  G 
Sbjct:     1 MSAVQPVNPKPFLNSLTGKFVVCKLKWGMEYKGVLVAVDSYMNLQLAHAEEYIDGNSQGN 60

Query:   131 LGEVLIRCNNILYI 144
             LGE+LIRCNN+LY+
Sbjct:    61 LGEILIRCNNVLYV 74

GO:0005634 "nucleus" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

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

GO:0000003 "reproduction" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0040039 "inductive cell migration" evidence=IMP

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

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0032940 "secretion by cell" evidence=IMP

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

GO:0006915 "apoptotic process" evidence=IMP

---

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)
Q3T0Z8	RUXF_BOVIN	No assigned EC number	0.7671	0.4620	0.8488	yes	N/A
Q24297	RUXF_DROME	No assigned EC number	0.7272	0.5569	1.0	yes	N/A
P34659	RUXF_CAEEL	No assigned EC number	0.6463	0.5189	0.9647	yes	N/A
Q9SUM2	RUXF_ARATH	No assigned EC number	0.6923	0.4936	0.8863	yes	N/A
P62307	RUXF_MOUSE	No assigned EC number	0.7671	0.4620	0.8488	yes	N/A
P62306	RUXF_HUMAN	No assigned EC number	0.7671	0.4620	0.8488	yes	N/A
O26745	RUXX_METTH	No assigned EC number	0.5185	0.3417	0.6666	yes	N/A
Q54XP2	RUXF_DICDI	No assigned EC number	0.5875	0.5	0.8681	yes	N/A
P54999	RUXF_YEAST	No assigned EC number	0.5316	0.4936	0.9069	yes	N/A
O59734	RUXF_SCHPO	No assigned EC number	0.6142	0.4430	0.8974	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	158
cd01722	69	cd01722, Sm_F, Sm protein F	9e-44
cd01722	69	cd01722, Sm_F, Sm protein F	8e-35
cd01726	68	cd01726, LSm6, Like-Sm protein 6	3e-23
pfam01423	66	pfam01423, LSM, LSM domain	5e-20
smart00651	67	smart00651, Sm, snRNP Sm proteins	1e-19
cd01726	68	cd01726, LSm6, Like-Sm protein 6	4e-18
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	8e-17
pfam01423	66	pfam01423, LSM, LSM domain	2e-15
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	3e-15
smart00651	67	smart00651, Sm, snRNP Sm proteins	6e-15
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	3e-14
cd00600	63	cd00600, Sm_like, Sm and related proteins	2e-13
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	2e-12
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	4e-12
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	1e-11
cd00600	63	cd00600, Sm_like, Sm and related proteins	3e-09
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	7e-06
cd01723	76	cd01723, LSm4, Like-Sm protein 4	5e-05
cd01733	78	cd01733, LSm10, Like-Sm protein 10	0.001

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

 Score =  138 bits (350), Expect = 9e-44
 Identities = 54/69 (78%), Positives = 56/69 (81%)

Query: 78  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 137
           NPKPFLN LTGK VI KLKWG EYKG LVS D YMN QLA+TEE IDG  TG LGEVLIR
Sbjct: 1   NPKPFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIR 60

Query: 138 CNNILYIRG 146
           CNN+LYIR 
Sbjct: 61  CNNVLYIRE 69

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers. Length = 69

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

 Score =  115 bits (291), Expect = 8e-35
 Identities = 47/60 (78%), Positives = 48/60 (80%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
          NPKPFLN LTGK VI KLKWG EYKG LVS D YMN QLA+TEE IDG  TG LGEVLIR
Sbjct: 1  NPKPFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIR 60

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers. Length = 69

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

 Score = 86.0 bits (214), Expect = 3e-23
 Identities = 34/68 (50%), Positives = 41/68 (60%)

Query: 78  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 137
            P  FL  + GK V+ KLK G EY+G+L   DGYMN  L  TEE +DG    K G+  IR
Sbjct: 1   TPSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIR 60

Query: 138 CNNILYIR 145
            NN+LYI 
Sbjct: 61  GNNVLYIS 68

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 68

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

 Score = 78.0 bits (193), Expect = 5e-20
 Identities = 30/64 (46%), Positives = 34/64 (53%)

Query: 81  PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNN 140
            FL  L GK V  +LK G E +G L   D +MN  L   EE I      KLG VLIR NN
Sbjct: 1   KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60

Query: 141 ILYI 144
           I+ I
Sbjct: 61  IVLI 64

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

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

 Score = 77.2 bits (191), Expect = 1e-19
 Identities = 32/66 (48%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 81  PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCN 139
            FL  L GK V+ +LK G EY+G L   D +MN  L   EE + DG    KLG V IR N
Sbjct: 1   KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60

Query: 140 NILYIR 145
           NI+YI 
Sbjct: 61  NIVYII 66

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

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

 Score = 73.3 bits (181), Expect = 4e-18
 Identities = 29/60 (48%), Positives = 35/60 (58%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
           P  FL  + GK V+ KLK G EY+G+L   DGYMN  L  TEE +DG    K G+  IR
Sbjct: 1  TPSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIR 60

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 68

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

 Score = 70.0 bits (172), Expect = 8e-17
 Identities = 34/76 (44%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 73  TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG----HCT 128
           + L   P  FL  L  K V+ KLK G EY+G LV  D YMN  L   EEII      +  
Sbjct: 2   SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVR 61

Query: 129 GKLGEVLIRCNNILYI 144
              GEVLIR +NI+ I
Sbjct: 62  RLGGEVLIRGDNIVLI 77

Length = 79

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

 Score = 66.0 bits (162), Expect = 2e-15
 Identities = 26/57 (45%), Positives = 29/57 (50%)

Query: 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
           FL  L GK V  +LK G E +G L   D +MN  L   EE I      KLG VLIR
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIR 57

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

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

 Score = 66.2 bits (162), Expect = 3e-15
 Identities = 24/56 (42%), Positives = 36/56 (64%)

Query: 89  KSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
             V+ +LK G E++G L   D +MN  L + EEI DG    KLG+V+IR +N++Y+
Sbjct: 15  SPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYV 70

Length = 72

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

 Score = 64.8 bits (159), Expect = 6e-15
 Identities = 27/58 (46%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIR 67
           FL  L GK V+ +LK G EY+G L   D +MN  L   EE + DG    KLG V IR
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIR 58

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

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

 Score = 63.0 bits (154), Expect = 3e-14
 Identities = 25/57 (43%), Positives = 38/57 (66%)

Query: 88  GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
            K+V+ KLK G E +G+L   D ++N  L + EEII+G    KLG VL+R +N+++I
Sbjct: 11  NKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNVVFI 67

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

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

 Score = 60.7 bits (148), Expect = 2e-13
 Identities = 26/63 (41%), Positives = 31/63 (49%)

Query: 83  LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNIL 142
           L    GK+V  +LK G    G LV+ D YMN  L    E         LG VLIR +NI+
Sbjct: 1   LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIV 60

Query: 143 YIR 145
            IR
Sbjct: 61  SIR 63

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

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

 Score = 58.9 bits (143), Expect = 2e-12
 Identities = 31/69 (44%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 3  TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG----HCT 58
          + L   P  FL  L  K V+ KLK G EY+G LV  D YMN  L   EEII      +  
Sbjct: 2  SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVR 61

Query: 59 GKLGEVLIR 67
             GEVLIR
Sbjct: 62 RLGGEVLIR 70

Length = 79

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

 Score = 57.7 bits (140), Expect = 4e-12
 Identities = 22/49 (44%), Positives = 30/49 (61%)

Query: 19 KSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
            V+ +LK G E++G L   D +MN  L + EEI DG    KLG+V+IR
Sbjct: 15 SPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIR 63

Length = 72

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

 Score = 56.8 bits (138), Expect = 1e-11
 Identities = 23/50 (46%), Positives = 32/50 (64%)

Query: 18 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
           K+V+ KLK G E +G+L   D ++N  L + EEII+G    KLG VL+R
Sbjct: 11 NKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVR 60

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

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

 Score = 50.3 bits (121), Expect = 3e-09
 Identities = 22/55 (40%), Positives = 25/55 (45%)

Query: 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
          L    GK+V  +LK G    G LV+ D YMN  L    E         LG VLIR
Sbjct: 1  LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIR 55

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

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

 Score = 41.3 bits (97), Expect = 7e-06
 Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 86  LTGKSVICKLKW-GHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
           L G  +  ++K   ++ +G LV+ D YMN  L  T E +       LG V++R NNIL I
Sbjct: 8   LVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLRGNNILLI 67

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

>gnl|CDD|212470 cd01723, LSm4, Like-Sm protein 4

 Score = 39.5 bits (93), Expect = 5e-05
 Identities = 27/71 (38%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 83  LNLLT---GKSVICKLKWGHEYKGILVSTDGYMNCQLAS-TEEIIDGHCTGKLGEVLIRC 138
           L+LL    G  V+ +LK G  Y G LV+ D +MN  L +      DG    K+ E  IR 
Sbjct: 3   LSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRG 62

Query: 139 NNILYIRGAEE 149
           N I Y+R  +E
Sbjct: 63  NTIKYLRLPDE 73

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

>gnl|CDD|212480 cd01733, LSm10, Like-Sm protein 10

 Score = 36.0 bits (84), Expect = 0.001
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 82  FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA-STEEIIDGHCTGKLGEVLIRCNN 140
            L  L G+    +L+     +GI+ + DG+MN  L+ +T     G       E  ++  N
Sbjct: 13  LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH-HFDEFFVQGRN 71

Query: 141 ILYI 144
           I Y+
Sbjct: 72  IRYV 75

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 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-membered 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. Length = 78

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	158
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.88
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
KOG3482|consensus	79		99.88
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.87
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.87
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.86
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
KOG3482|consensus	79		99.84
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.83
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.82
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.81
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.81
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.8
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.8
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.8
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.8
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.79
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.79
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.78
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.78
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.78
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.78
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.78
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.77
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.77
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.76
KOG1780|consensus	77		99.75
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.75
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.74
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.74
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.74
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.74
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.73
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.73
KOG1783|consensus	77		99.72
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.71
KOG1780|consensus	77		99.71
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.7
KOG1783|consensus	77		99.68
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.67
KOG3293|consensus	134		99.61
KOG3460|consensus	91		99.59
KOG1781|consensus	108		99.53
KOG3460|consensus	91		99.53
KOG1775|consensus	84		99.51
KOG1775|consensus	84		99.45
KOG1774|consensus	88		99.4
KOG1782|consensus	129		99.4
KOG3172|consensus	119		99.39
KOG1781|consensus	108		99.38
KOG3293|consensus	134		99.38
KOG3448|consensus	96		99.35
KOG1784|consensus	96		99.34
KOG3428|consensus	109		99.31
KOG1774|consensus	88		99.28
KOG3172|consensus	119		99.21
KOG3448|consensus	96		99.2
KOG3168|consensus	177		99.14
KOG3168|consensus	177		99.05
KOG1784|consensus	96		98.97
KOG1782|consensus	129		98.96
KOG3428|consensus	109		98.8
KOG3459|consensus	114		98.63
PRK14091	165	RNA-binding protein Hfq; Provisional	98.17
KOG3459|consensus	114		97.91
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.85
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	97.76
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.59
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	96.97
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	96.62
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	95.89
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	95.87
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	95.73
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	95.55
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	95.55
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	95.5
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	95.24
COG1923	77	Hfq Uncharacterized host factor I protein [General	95.11
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	94.73
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	94.59
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	94.23
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	94.19
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	93.76
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	93.24
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	92.7
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	92.65
PRK14638	150	hypothetical protein; Provisional	92.47
PRK14091	165	RNA-binding protein Hfq; Provisional	91.49
PRK14639	140	hypothetical protein; Provisional	91.45
PRK02001	152	hypothetical protein; Validated	91.36
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	90.92
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	90.65
PRK14644	136	hypothetical protein; Provisional	89.95
COG1923	77	Hfq Uncharacterized host factor I protein [General	89.93
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	89.42
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	88.5
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	87.49
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	87.35
PRK14642	197	hypothetical protein; Provisional	86.9
PRK14640	152	hypothetical protein; Provisional	86.86
PRK14633	150	hypothetical protein; Provisional	86.78
PRK14645	154	hypothetical protein; Provisional	86.74
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	86.68
PRK14638	150	hypothetical protein; Provisional	84.43
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	84.34
PRK14634	155	hypothetical protein; Provisional	83.19
PRK14636	176	hypothetical protein; Provisional	82.82
PRK00092	154	ribosome maturation protein RimP; Reviewed	82.15
PRK14632	172	hypothetical protein; Provisional	81.87
PRK14647	159	hypothetical protein; Provisional	81.57
PRK02001	152	hypothetical protein; Validated	80.95
PRK14639	140	hypothetical protein; Provisional	80.78
PRK14646	155	hypothetical protein; Provisional	80.01

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.88  E-value=6.6e-23  Score=137.36  Aligned_cols=70  Identities=37%  Similarity=0.468  Sum_probs=65.4

Q ss_pred             CCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         7 ~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      ..|+++|+++++++|.|+|+||++|.|+|.+||+|||++|+||+|+++++..+.+|.++|||++|.++.|
T Consensus         3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~~   72 (72)
T PRK00737          3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVSP   72 (72)
T ss_pred             cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEcC
Confidence            5899999999999999999999999999999999999999999998777667899999999999998754

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

Probab=99.88  E-value=7.2e-23  Score=135.32  Aligned_cols=66  Identities=39%  Similarity=0.705  Sum_probs=62.6

Q ss_pred             chHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCC
Q psy9934           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTP   74 (158)
Q Consensus         9 p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I   74 (158)
                      |+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||++..+++..+.+|.++|||++|.++
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I   66 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYI   66 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEE
Confidence            899999999999999999999999999999999999999999987776678999999999999875

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.

>KOG3482|consensus

Probab=99.88  E-value=5.7e-23  Score=135.02  Aligned_cols=76  Identities=71%  Similarity=1.165  Sum_probs=72.1

Q ss_pred             CCCCCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          74 PLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        74 I~p~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      .+|.+|.+||+.+.+++|.|+||+|.+|+|+|.+.|.|||++|.+|+|+++|.....+|.++||++||.+|...++
T Consensus         4 ~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~gv~~   79 (79)
T KOG3482|consen    4 KQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIRGVPE   79 (79)
T ss_pred             cccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEecCCC
Confidence            4688999999999999999999999999999999999999999999999999888899999999999999987653

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

Probab=99.88  E-value=1.9e-22  Score=135.12  Aligned_cols=71  Identities=30%  Similarity=0.387  Sum_probs=66.0

Q ss_pred             CCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        79 P~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      |.++|+++++|+|.|+|++|++|+|+|.|||+||||+|+||+|+..+...+++|.++|||++|++|++.|+
T Consensus         1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~~   71 (72)
T cd01719           1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALER   71 (72)
T ss_pred             CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEcccc
Confidence            56789999999999999999999999999999999999999999766667899999999999999998864

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.

>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences

Probab=99.87  E-value=2.6e-22  Score=132.96  Aligned_cols=68  Identities=40%  Similarity=0.423  Sum_probs=63.8

Q ss_pred             chHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         9 p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      |+++|++++|++|.|+|+||++|.|+|.+||+|||++|+||+|++.+...+.+|.++|||++|.++.|
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEcC
Confidence            89999999999999999999999999999999999999999999766567899999999999998764

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.87  E-value=2.3e-22  Score=134.68  Aligned_cols=70  Identities=39%  Similarity=0.557  Sum_probs=65.3

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEe
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      ..|.++|+++++++|.|+|+||++|+|+|.|||+|||++|+||+|..+++..+++|.++|||++|++|++
T Consensus         3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~~   72 (72)
T PRK00737          3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVSP   72 (72)
T ss_pred             cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEcC
Confidence            3688899999999999999999999999999999999999999998777667899999999999999974

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

Probab=99.87  E-value=3.7e-22  Score=132.28  Aligned_cols=67  Identities=70%  Similarity=1.016  Sum_probs=63.0

Q ss_pred             CchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCC
Q psy9934           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTP   74 (158)
Q Consensus         8 ~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I   74 (158)
                      +|+++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+|+.++.....+|.++|||++|.++
T Consensus         1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i   67 (68)
T cd01722           1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYI   67 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEE
Confidence            5999999999999999999999999999999999999999999987666578899999999999875

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=99.86  E-value=4.7e-22  Score=131.43  Aligned_cols=67  Identities=46%  Similarity=0.850  Sum_probs=63.1

Q ss_pred             CCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEE
Q psy9934          79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIR  145 (158)
Q Consensus        79 P~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~  145 (158)
                      |.++|+++++++|.|+|++|++|+|+|.|||+|||++|+||++..++.....+|.++|||++|++|+
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence            6789999999999999999999999999999999999999999877777789999999999999985

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.

>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences

Probab=99.86  E-value=5.3e-22  Score=131.45  Aligned_cols=68  Identities=43%  Similarity=0.527  Sum_probs=63.5

Q ss_pred             CCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEe
Q psy9934          79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        79 P~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      |.++|+++++++|.|+|++|++|+|+|.|||+|||++|+||+|+..+...+.+|.++|||++|++|++
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEcC
Confidence            66789999999999999999999999999999999999999998776667899999999999999975

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

>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.86  E-value=7.1e-22  Score=133.65  Aligned_cols=70  Identities=26%  Similarity=0.395  Sum_probs=64.0

Q ss_pred             CCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEe---cCeeeeecCcEEEeeCcEEEEEeC
Q psy9934          78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII---DGHCTGKLGEVLIRCNNILYIRGA  147 (158)
Q Consensus        78 dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~~g~~~iRG~~I~~i~~~  147 (158)
                      -|.++|+++++++|.|++++|+++.|+|.|||+|||++|+||+|+.   ++++.+.+|.++|||+||++|+|.
T Consensus         3 ~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~   75 (76)
T cd01732           3 LPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG   75 (76)
T ss_pred             ChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence            3678899999999999999999999999999999999999999986   454567899999999999999974

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.

>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.86  E-value=1e-21  Score=132.85  Aligned_cols=70  Identities=23%  Similarity=0.385  Sum_probs=64.3

Q ss_pred             CCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEE---eccceecceeEEEEecCCCCCCC
Q psy9934           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII---DGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         7 ~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      -.|+++|+++++++|+|++++|+++.|+|.|||+|||++|+||+|++   ++++.+.+|.++|||++|..+.|
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p   74 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVP   74 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEEC
Confidence            36999999999999999999999999999999999999999999986   44446789999999999998876

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.

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

Probab=99.86  E-value=7.1e-22  Score=132.38  Aligned_cols=71  Identities=25%  Similarity=0.287  Sum_probs=65.8

Q ss_pred             chHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCCC
Q psy9934           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNP   79 (158)
Q Consensus         9 p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~dP   79 (158)
                      |-++|+++++|+|.|+|++|++|.|+|.|||+|||++|+||+|+..+...+.+|.++|||++|.++.+.+|
T Consensus         1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~~   71 (72)
T cd01719           1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALER   71 (72)
T ss_pred             CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEcccc
Confidence            56899999999999999999999999999999999999999999766567899999999999999887765

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.

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

Probab=99.85  E-value=1.2e-21  Score=129.90  Aligned_cols=68  Identities=79%  Similarity=1.246  Sum_probs=63.2

Q ss_pred             CCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEE
Q psy9934          78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIR  145 (158)
Q Consensus        78 dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~  145 (158)
                      .|.++|+++++++|.|+|++|++|+|+|.|||+|||++|+||+|+.++.....+|.++|||++|++|+
T Consensus         1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence            47789999999999999999999999999999999999999999877766678999999999999984

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.

>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.84  E-value=4.8e-21  Score=131.08  Aligned_cols=68  Identities=28%  Similarity=0.343  Sum_probs=61.3

Q ss_pred             cccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecC--------eeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG--------HCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      -|.++++++|.|+|++||+|.|+|.|||+||||+|++|+|+..+        ...+.+|.++|||+||++|++.++
T Consensus         6 ~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~~   81 (81)
T cd01729           6 DLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVDG   81 (81)
T ss_pred             hHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCCC
Confidence            47889999999999999999999999999999999999998653        245789999999999999998763

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.

>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.84  E-value=3.8e-21  Score=131.81  Aligned_cols=68  Identities=22%  Similarity=0.347  Sum_probs=61.7

Q ss_pred             CCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecC-------------eeeeecCcEEEeeCcEEEEE
Q psy9934          79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG-------------HCTGKLGEVLIRCNNILYIR  145 (158)
Q Consensus        79 P~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------------~~~~~~g~~~iRG~~I~~i~  145 (158)
                      |.++|+...+++|.|++++||++.|+|.|||+||||+|+||+|++.+             ...+.+|.+||||++|++|+
T Consensus         2 pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~   81 (82)
T cd01730           2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS   81 (82)
T ss_pred             chHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence            67889999999999999999999999999999999999999998643             13578999999999999997


Q ss_pred             e
Q psy9934         146 G  146 (158)
Q Consensus       146 ~  146 (158)
                      +
T Consensus        82 ~   82 (82)
T cd01730          82 P   82 (82)
T ss_pred             C
Confidence            4

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 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.

>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.84  E-value=4.9e-21  Score=131.30  Aligned_cols=69  Identities=23%  Similarity=0.299  Sum_probs=62.4

Q ss_pred             CchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEecc-------------ceecceeEEEEecCCCCC
Q psy9934           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-------------CTGKLGEVLIRSLTMSTP   74 (158)
Q Consensus         8 ~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~-------------~~~~lg~~~iRG~~i~~I   74 (158)
                      .|+++|+.+++++|.|+|+|||+|.|+|.|||.|||++|+||+|++.+.             ..+.+|.++|||++|.++
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i   80 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV   80 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence            4999999999999999999999999999999999999999999996431             256899999999999987


Q ss_pred             CC
Q psy9934          75 LP   76 (158)
Q Consensus        75 ~p   76 (158)
                      .|
T Consensus        81 ~~   82 (82)
T cd01730          81 SP   82 (82)
T ss_pred             CC
Confidence            64

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.

>KOG3482|consensus

Probab=99.84  E-value=2.7e-21  Score=127.12  Aligned_cols=75  Identities=61%  Similarity=0.911  Sum_probs=72.0

Q ss_pred             CCCCCCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCC
Q psy9934           1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus         1 m~~~~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~   75 (158)
                      ||+..|.+|.+||+.+.||+|.|+||.|.+|.|+|++.|.|||+.|.+|+|+++|.....+|+++||+++|.++.
T Consensus         1 ~~a~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~   75 (79)
T KOG3482|consen    1 SSAKQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIR   75 (79)
T ss_pred             CCCcccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEe
Confidence            688899999999999999999999999999999999999999999999999999988889999999999999874

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

Probab=99.84  E-value=8.3e-21  Score=126.53  Aligned_cols=70  Identities=29%  Similarity=0.441  Sum_probs=63.1

Q ss_pred             CCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCC
Q psy9934          79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE  148 (158)
Q Consensus        79 P~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~  148 (158)
                      |.++|+++.+++|.|+||||.+|+|+|.++|+|||++|+||++...+.+..+++.+||||+||.+|..||
T Consensus         1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd   70 (70)
T cd01721           1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence            6678999999999999999999999999999999999999987643333578899999999999999886

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.

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

Probab=99.84  E-value=5.7e-21  Score=127.30  Aligned_cols=67  Identities=31%  Similarity=0.496  Sum_probs=61.5

Q ss_pred             chHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEE-eccceecceeEEEEecCCCCCCC
Q psy9934           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         9 p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      |+++|+++.|++|+|+||||.+|+|+|.++|.|||++|+||++.. +++ ..+++.+||||++|+++..
T Consensus         1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~-~~~~~~v~IRG~nI~~v~l   68 (70)
T cd01721           1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGR-VSQLEQVYIRGSKIRFFIL   68 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCc-EeEcCcEEEeCCEEEEEEe
Confidence            899999999999999999999999999999999999999999874 444 6788999999999999763

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

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

Probab=99.83  E-value=9.4e-21  Score=128.14  Aligned_cols=69  Identities=29%  Similarity=0.348  Sum_probs=62.8

Q ss_pred             CchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEE-EeccceecceeEEEEecCCCCCCC
Q psy9934           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         8 ~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~-~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      .|+++|+++.|++|.|+|+||++|+|+|.+||+|||++|+||+++ .+|+....++.+||||++|+++..
T Consensus         1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~   70 (76)
T cd01723           1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRV   70 (76)
T ss_pred             CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEc
Confidence            499999999999999999999999999999999999999999998 455545678999999999999763

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.

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

Probab=99.82  E-value=5e-20  Score=123.94  Aligned_cols=69  Identities=26%  Similarity=0.194  Sum_probs=62.2

Q ss_pred             CcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEec----CeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----GHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        81 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      +.|+++++++|.|++++||.|.|+|.|||+|||++|++|+|+..    +...+.+|.+++||+||++|++.|+
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~   74 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE   74 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence            46788999999999999999999999999999999999999853    3345789999999999999999875

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.

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

Probab=99.81  E-value=3.3e-20  Score=128.39  Aligned_cols=69  Identities=14%  Similarity=0.162  Sum_probs=61.6

Q ss_pred             CchHHHhhcC--CCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEecc-------------ceecceeEEEEecCCC
Q psy9934           8 NPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-------------CTGKLGEVLIRSLTMS   72 (158)
Q Consensus         8 ~p~~~L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~-------------~~~~lg~~~iRG~~i~   72 (158)
                      -|+++|++++  +++|.|+|++|+++.|+|.|||.|||++|+||+|.+.+.             ..+.+|.+||||++|.
T Consensus         2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv   81 (87)
T cd01720           2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI   81 (87)
T ss_pred             ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence            5999999996  899999999999999999999999999999999986442             1457899999999999


Q ss_pred             CCCC
Q psy9934          73 TPLP   76 (158)
Q Consensus        73 ~I~p   76 (158)
                      ++.+
T Consensus        82 ~Is~   85 (87)
T cd01720          82 LVLR   85 (87)
T ss_pred             EEec
Confidence            8764

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.

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

Probab=99.81  E-value=7.1e-20  Score=124.57  Aligned_cols=71  Identities=48%  Similarity=0.626  Sum_probs=62.9

Q ss_pred             CCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEE--eccc-eecce-eEEEEecCCCCCC
Q psy9934           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII--DGHC-TGKLG-EVLIRSLTMSTPL   75 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~--~~~~-~~~lg-~~~iRG~~i~~I~   75 (158)
                      ....|+++|+++++++|.|+|+||++|.|+|.|||+|||++|+||+|..  ++.. ....+ .++|||++|.++.
T Consensus         4 ~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~   78 (79)
T COG1958           4 LGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLIS   78 (79)
T ss_pred             ccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEe
Confidence            4567999999999999999999999999999999999999999999996  5543 24455 9999999998864

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

Probab=99.81  E-value=4.9e-20  Score=124.62  Aligned_cols=71  Identities=34%  Similarity=0.486  Sum_probs=64.7

Q ss_pred             CCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEE-ecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        79 P~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~-~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      |..+|+++.+++|.|+|+||++|+|+|.+||+|||++|+||++. .+|+....++.+||||++|.+|+.+++
T Consensus         2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~   73 (76)
T cd01723           2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDE   73 (76)
T ss_pred             chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHH
Confidence            77899999999999999999999999999999999999999987 456555678999999999999998764

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.

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

Probab=99.81  E-value=5.3e-20  Score=127.39  Aligned_cols=69  Identities=13%  Similarity=0.203  Sum_probs=60.6

Q ss_pred             CCCcccccc--cceeeEeeccccEEEEEEEEeccccceeecceEEEecCe-------------eeeecCcEEEeeCcEEE
Q psy9934          79 PKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-------------CTGKLGEVLIRCNNILY  143 (158)
Q Consensus        79 P~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~-------------~~~~~g~~~iRG~~I~~  143 (158)
                      |.++|+..+  +++|.|+|++|+++.|+|.|||+||||+|+||+|.+.+.             ..+.+|.+||||++|++
T Consensus         3 Pl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~   82 (87)
T cd01720           3 PLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVIL   82 (87)
T ss_pred             hHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEE
Confidence            677888886  899999999999999999999999999999999976432             24578999999999999


Q ss_pred             EEeC
Q psy9934         144 IRGA  147 (158)
Q Consensus       144 i~~~  147 (158)
                      |++-
T Consensus        83 Is~~   86 (87)
T cd01720          83 VLRN   86 (87)
T ss_pred             EecC
Confidence            9864

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.

>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.81  E-value=6.2e-20  Score=124.81  Aligned_cols=69  Identities=25%  Similarity=0.347  Sum_probs=60.5

Q ss_pred             CCCCcccccccc--eeeEeec--cccEEEEEEEEeccccceeecceEEEec-CeeeeecCcEEEeeCcEEEEEe
Q psy9934          78 NPKPFLNLLTGK--SVICKLK--WGHEYKGILVSTDGYMNCQLASTEEIID-GHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        78 dP~~~L~~~~~k--~V~V~L~--~g~~~~G~L~~~D~~mNlvL~~~~e~~~-~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      .|...+.+++++  +|.|+++  +|+++.|+|.|||+|||++|+||+|+.. +...+.+|.++|||+||++|+|
T Consensus         6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p   79 (79)
T cd01718           6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN   79 (79)
T ss_pred             CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence            466677777777  8888887  8999999999999999999999999975 5566789999999999999985

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.80  E-value=1.1e-19  Score=126.59  Aligned_cols=69  Identities=25%  Similarity=0.251  Sum_probs=64.0

Q ss_pred             chHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCC
Q psy9934           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPC   77 (158)
Q Consensus         9 p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~   77 (158)
                      |+.||+++.|++|+|+|+||.+|+|+|.++|+|||++|+||+++.+++....++.++|||++|+++..+
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lP   70 (90)
T cd01724           2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILP   70 (90)
T ss_pred             HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcC
Confidence            678999999999999999999999999999999999999999986665678899999999999998743

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.

>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.80  E-value=1e-19  Score=124.55  Aligned_cols=69  Identities=28%  Similarity=0.291  Sum_probs=60.6

Q ss_pred             chHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEec--------cceecceeEEEEecCCCCCCCC
Q psy9934           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG--------HCTGKLGEVLIRSLTMSTPLPC   77 (158)
Q Consensus         9 p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~lg~~~iRG~~i~~I~p~   77 (158)
                      +..-|.++++++|.|.|+|||+|.|+|.+||+||||+|+||+|+..+        +..+.+|.++|||++|.++.|.
T Consensus         3 ~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~   79 (81)
T cd01729           3 SILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPV   79 (81)
T ss_pred             chhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecC
Confidence            34459999999999999999999999999999999999999998543        2357899999999999987654

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.

>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.80  E-value=1.5e-19  Score=125.94  Aligned_cols=72  Identities=29%  Similarity=0.337  Sum_probs=66.3

Q ss_pred             CCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCCC
Q psy9934          80 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD  151 (158)
Q Consensus        80 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~~  151 (158)
                      ..||+++.+++|.|+|+||.+|+|+|.++|+|||++|+||++...+.....++.++|||+||.||..|+.-.
T Consensus         3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~   74 (90)
T cd01724           3 VRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLN   74 (90)
T ss_pred             hHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCC
Confidence            458899999999999999999999999999999999999999877666778999999999999999998753

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.

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

Probab=99.80  E-value=1.8e-19  Score=122.59  Aligned_cols=71  Identities=51%  Similarity=0.699  Sum_probs=62.7

Q ss_pred             CCCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEe--cCee-eeecC-cEEEeeCcEEEEEe
Q psy9934          76 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII--DGHC-TGKLG-EVLIRCNNILYIRG  146 (158)
Q Consensus        76 p~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~--~~~~-~~~~g-~~~iRG~~I~~i~~  146 (158)
                      ...|.++|+++++++|.|+|++|++|.|+|.|||+|||++|+||+|+.  ++.. .+.++ .++|||++|++|.+
T Consensus         5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958           5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence            346788999999999999999999999999999999999999999987  5554 34555 99999999999974

>smart00651 Sm snRNP Sm proteins

Probab=99.79  E-value=4.3e-19  Score=116.51  Aligned_cols=66  Identities=45%  Similarity=0.646  Sum_probs=60.7

Q ss_pred             CcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecC-eeeeecCcEEEeeCcEEEEEe
Q psy9934          81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG-HCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        81 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      ++|+++.+++|.|+|+||+++.|+|.+||+|||++|+||+|+..+ ...+++|.++|||++|++|++
T Consensus         1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence            368889999999999999999999999999999999999998765 567899999999999999974

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

>smart00651 Sm snRNP Sm proteins

Probab=99.79  E-value=2.4e-19  Score=117.75  Aligned_cols=65  Identities=38%  Similarity=0.560  Sum_probs=59.9

Q ss_pred             HHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEec-cceecceeEEEEecCCCCCC
Q psy9934          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG-HCTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus        11 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-~~~~~lg~~~iRG~~i~~I~   75 (158)
                      .+|++++|++|+|+|+||+++.|+|.+||+|||++|+||+|+..+ ...+.++.++|||++|.++.
T Consensus         1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~   66 (67)
T smart00651        1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYII   66 (67)
T ss_pred             ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEe
Confidence            378999999999999999999999999999999999999999654 45789999999999999865

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

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

Probab=99.78  E-value=3.4e-19  Score=121.08  Aligned_cols=71  Identities=23%  Similarity=0.237  Sum_probs=64.3

Q ss_pred             CCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCC
Q psy9934           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~   75 (158)
                      +.-++..||+++.|++|.|+||||.+|+|+|.++|.|||++|+||++...+....+++.++|||++|++++
T Consensus         6 ~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~   76 (78)
T cd01733           6 LENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVH   76 (78)
T ss_pred             hhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEE
Confidence            45678899999999999999999999999999999999999999998865544568999999999999875

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.

>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.78  E-value=4.3e-19  Score=120.68  Aligned_cols=72  Identities=19%  Similarity=0.247  Sum_probs=63.9

Q ss_pred             CCCCchHHHhhcCCC--EEEEEEe--CCcEEEEEEeEecCcceeEEceeeEEEe-ccceecceeEEEEecCCCCCCC
Q psy9934           5 LPCNPKPFLNLLTGK--SVICKLK--WGHEYKGILVSTDGYMNCQLASTEEIID-GHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k--~V~V~l~--~g~~~~G~L~~~D~~mNlvL~~~~e~~~-~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      +-..|+..+.+++++  +|.|+++  +|+.+.|+|.|||+|||++|+||+|+.. ++....+|.++|||++|.++.|
T Consensus         3 ~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p   79 (79)
T cd01718           3 VMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN   79 (79)
T ss_pred             cccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence            446899999999999  7888887  9999999999999999999999999964 4556789999999999998764

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

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

Probab=99.78  E-value=4.5e-19  Score=119.36  Aligned_cols=68  Identities=29%  Similarity=0.274  Sum_probs=59.8

Q ss_pred             CCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEec-Ce--eeeecCcEEEeeCcEEEEEeC
Q psy9934          80 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID-GH--CTGKLGEVLIRCNNILYIRGA  147 (158)
Q Consensus        80 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~-~~--~~~~~g~~~iRG~~I~~i~~~  147 (158)
                      ...|.++++++|.|++++||+|.|+|.|||+|||++|+||+|+.. +.  ..+.+|.++|||+||++|++.
T Consensus         4 ~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~~   74 (74)
T cd01728           4 TASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGEI   74 (74)
T ss_pred             hHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEcC
Confidence            456888999999999999999999999999999999999999742 21  357899999999999999863

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.

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

Probab=99.78  E-value=7.3e-19  Score=115.50  Aligned_cols=65  Identities=45%  Similarity=0.591  Sum_probs=61.0

Q ss_pred             cccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCe-eeeecCcEEEeeCcEEEEEe
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-CTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~-~~~~~g~~~iRG~~I~~i~~  146 (158)
                      +|+++++++|.|.|++|++|+|+|.+||+|||++|+||.+...+. ..+.+|.+||||++|.+|++
T Consensus         2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred             hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence            578899999999999999999999999999999999999997765 77899999999999999985

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 ....

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

Probab=99.78  E-value=3.9e-19  Score=116.79  Aligned_cols=64  Identities=39%  Similarity=0.511  Sum_probs=59.7

Q ss_pred             HHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEecc-ceecceeEEEEecCCCCCC
Q psy9934          12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-CTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus        12 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~-~~~~lg~~~iRG~~i~~I~   75 (158)
                      +|++++|++|+|+|+||++|.|+|.+||+|||++|+||+++.... ..+.+|.++|||++|.++.
T Consensus         2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~   66 (67)
T PF01423_consen    2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYIS   66 (67)
T ss_dssp             HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEE
T ss_pred             hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEE
Confidence            799999999999999999999999999999999999999997654 6789999999999999865

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 ....

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

Probab=99.77  E-value=1e-18  Score=118.71  Aligned_cols=69  Identities=26%  Similarity=0.309  Sum_probs=62.6

Q ss_pred             CCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeC
Q psy9934          79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGA  147 (158)
Q Consensus        79 P~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~  147 (158)
                      +..||+.+.+++|.|+||||.+|+|+|.++|+|||++|+||++...+....++|.++|||++|.+|..|
T Consensus        10 l~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733          10 LIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             HHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence            446889999999999999999999999999999999999999876555556899999999999999875

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=99.77  E-value=1e-18  Score=118.97  Aligned_cols=65  Identities=26%  Similarity=0.286  Sum_probs=58.0

Q ss_pred             cccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecC----------eeeeecCcEEEeeCcEEEEEe
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG----------HCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----------~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      -|..+++++|.|+|++||++.|+|.|||+||||+|+||+|+...          .+.+.+|.++|||++|++|+.
T Consensus         4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            46778999999999999999999999999999999999997532          245789999999999999974

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.

>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.76  E-value=1.4e-18  Score=118.83  Aligned_cols=69  Identities=23%  Similarity=0.222  Sum_probs=60.5

Q ss_pred             CchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEecc--ceecceeEEEEecCCCCCCC
Q psy9934           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH--CTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         8 ~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~--~~~~lg~~~iRG~~i~~I~p   76 (158)
                      .|+.||+++.|++|+|+||||.+|+|+|.++|+|||++|+||+++....  ....+++++|||++|+++..
T Consensus         1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~l   71 (81)
T cd01725           1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQL   71 (81)
T ss_pred             ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEe
Confidence            3789999999999999999999999999999999999999998874221  23567899999999999863

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.

>KOG1780|consensus

Probab=99.75  E-value=6.6e-19  Score=116.33  Aligned_cols=74  Identities=28%  Similarity=0.326  Sum_probs=64.6

Q ss_pred             CCCCCCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCC
Q psy9934           1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus         1 m~~~~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      ||+  ...|  .|++|++|++.++|.+||++.|.|+|||+|||+||++|+|.........+|.++|||++|..+.+.+
T Consensus         1 Msk--sg~P--eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~   74 (77)
T KOG1780|consen    1 MSK--SGHP--ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALE   74 (77)
T ss_pred             CCc--ccCc--hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeecc
Confidence            664  3346  8999999999999999999999999999999999999999854445778999999999999876544

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

Probab=99.75  E-value=2e-18  Score=117.45  Aligned_cols=65  Identities=23%  Similarity=0.246  Sum_probs=57.6

Q ss_pred             HHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEec----------cceecceeEEEEecCCCCCC
Q psy9934          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG----------HCTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus        11 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----------~~~~~lg~~~iRG~~i~~I~   75 (158)
                      +-|.+++|++|.|.|+|||.+.|+|.|||+|||++|+||+|++..          .+.+.+|.++|||++|.++.
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~   77 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMT   77 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEE
Confidence            458899999999999999999999999999999999999998532          23578999999999998753

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.

>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.74  E-value=3.6e-18  Score=110.65  Aligned_cols=62  Identities=40%  Similarity=0.464  Sum_probs=57.4

Q ss_pred             HhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCC
Q psy9934          13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTP   74 (158)
Q Consensus        13 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I   74 (158)
                      |++++|++|+|+|+||+.|.|+|.+||+|||++|+||+++..+...+.++.++|||++|.++
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I   62 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLV   62 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEE
Confidence            57889999999999999999999999999999999999997655678999999999999875

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.

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

Probab=99.74  E-value=3.1e-18  Score=115.22  Aligned_cols=68  Identities=22%  Similarity=0.111  Sum_probs=60.6

Q ss_pred             HHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEe----ccceecceeEEEEecCCCCCCCCC
Q psy9934          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----GHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus        11 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      +.|.++++++|.|.+++||.|.|+|.+||+|||++|++|.|...    +.....+|.++|||++|.++.|.+
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d   73 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID   73 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence            46899999999999999999999999999999999999999842    224568999999999999988765

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

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

Probab=99.74  E-value=5.9e-18  Score=113.90  Aligned_cols=68  Identities=28%  Similarity=0.177  Sum_probs=59.5

Q ss_pred             CchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEE-ecc--ceecceeEEEEecCCCCCC
Q psy9934           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGH--CTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus         8 ~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~--~~~~lg~~~iRG~~i~~I~   75 (158)
                      .++..|.++++++|.|.++|||+|.|+|.|||+|||++|+||.|.. .++  ..+.+|.++|||++|.++.
T Consensus         2 ~~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig   72 (74)
T cd01728           2 PGTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLG   72 (74)
T ss_pred             CchHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEE
Confidence            3577899999999999999999999999999999999999999984 221  2568999999999998754

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.

>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.74  E-value=4.5e-18  Score=116.38  Aligned_cols=74  Identities=23%  Similarity=0.290  Sum_probs=64.1

Q ss_pred             CCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCe--eeeecCcEEEeeCcEEEEEeCCCCCc
Q psy9934          79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH--CTGKLGEVLIRCNNILYIRGAEEGDE  152 (158)
Q Consensus        79 P~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~--~~~~~g~~~iRG~~I~~i~~~~~~~~  152 (158)
                      |..||+++.+++|.|+||+|.+|+|+|.++|+|||++|+||++...+.  ....++.++|||++|.+|..|+...+
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~   77 (81)
T cd01725           2 FFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVD   77 (81)
T ss_pred             hhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcC
Confidence            346889999999999999999999999999999999999998764322  23457899999999999999987765

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=99.73  E-value=1.4e-17  Score=107.91  Aligned_cols=63  Identities=41%  Similarity=0.523  Sum_probs=57.8

Q ss_pred             ccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEE
Q psy9934          83 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIR  145 (158)
Q Consensus        83 L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~  145 (158)
                      |+++++++|.|+|++|+.|.|+|.+||+|||++|++|.++..+...++++.++|||++|.+|.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEEC
Confidence            467889999999999999999999999999999999999876556789999999999999984

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.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.73  E-value=1e-17  Score=116.28  Aligned_cols=70  Identities=26%  Similarity=0.312  Sum_probs=57.5

Q ss_pred             CCCCccccccc--ceeeEeecc--ccEEEEEEEEeccccceeecceEEEec-CeeeeecCcEEEeeCcEEEEEeC
Q psy9934          78 NPKPFLNLLTG--KSVICKLKW--GHEYKGILVSTDGYMNCQLASTEEIID-GHCTGKLGEVLIRCNNILYIRGA  147 (158)
Q Consensus        78 dP~~~L~~~~~--k~V~V~L~~--g~~~~G~L~~~D~~mNlvL~~~~e~~~-~~~~~~~g~~~iRG~~I~~i~~~  147 (158)
                      .|...+..+..  .+|.|++.+  ++++.|+|.|||+|||++|+||+|+.. +...+.+|.++||||||++|++.
T Consensus        14 ~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~~   88 (89)
T PTZ00138         14 QPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAA   88 (89)
T ss_pred             CCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEcC
Confidence            45555555543  388888877  489999999999999999999999865 34567899999999999999875

>KOG1783|consensus

Probab=99.72  E-value=4e-19  Score=116.97  Aligned_cols=72  Identities=44%  Similarity=0.784  Sum_probs=68.3

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCC
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE  148 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~  148 (158)
                      ..|.+||++.++++|.|+|.+|-.|+|+|.++|.|||+.|+.|+|+.+|+.++++|..||||+||.+|+...
T Consensus         5 ~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~~   76 (77)
T KOG1783|consen    5 SMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQK   76 (77)
T ss_pred             cCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEecc
Confidence            357789999999999999999999999999999999999999999999999999999999999999999754

>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.71  E-value=3.5e-17  Score=110.43  Aligned_cols=66  Identities=26%  Similarity=0.278  Sum_probs=59.4

Q ss_pred             CcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecC------eeeeecCcEEEeeCcEEEEEe
Q psy9934          81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG------HCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        81 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~------~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      +.|++++++++.|+|+|||.|.|+|.+||++||++|++|.|+..+      ...+.+|.++|||++|+.|+.
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence            357788999999999999999999999999999999999998632      356899999999999999874

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.

>KOG1780|consensus

Probab=99.71  E-value=1.2e-17  Score=110.34  Aligned_cols=68  Identities=31%  Similarity=0.386  Sum_probs=61.7

Q ss_pred             cccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      -|++|.+|++.++|++||...|+|+|||.|||+||++|+|.........+|.++|||++|+.+.+.+.
T Consensus         8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~~   75 (77)
T KOG1780|consen    8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALER   75 (77)
T ss_pred             hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeeccc
Confidence            78999999999999999999999999999999999999997544445789999999999999988763

>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.70  E-value=3.2e-17  Score=110.63  Aligned_cols=64  Identities=23%  Similarity=0.251  Sum_probs=58.2

Q ss_pred             HHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEec------cceecceeEEEEecCCCCC
Q psy9934          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG------HCTGKLGEVLIRSLTMSTP   74 (158)
Q Consensus        11 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~------~~~~~lg~~~iRG~~i~~I   74 (158)
                      +.|+++++++|.|.|+|||.|.|+|.|||.|||++|+||.|++..      .+.+.+|+++|||++|..+
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i   72 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSI   72 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEE
Confidence            568999999999999999999999999999999999999999532      3578999999999999865

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.

>KOG1783|consensus

Probab=99.68  E-value=2.5e-18  Score=113.21  Aligned_cols=74  Identities=39%  Similarity=0.623  Sum_probs=69.8

Q ss_pred             CCCCCCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         1 m~~~~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      ||  ....|.+||++.+||+|.|+|.+|-.|+|+|.|.|.|||+-|+.++|+.+|+.++..|..||||++|.+|..
T Consensus         1 ~s--~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~   74 (77)
T KOG1783|consen    1 MS--EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYIST   74 (77)
T ss_pred             CC--cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEe
Confidence            56  578899999999999999999999999999999999999999999999999999999999999999998753

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.67  E-value=1.2e-16  Score=110.96  Aligned_cols=72  Identities=19%  Similarity=0.245  Sum_probs=61.0

Q ss_pred             CCCCchHHHhhcCCC--EEEEEEeCC--cEEEEEEeEecCcceeEEceeeEEEe-ccceecceeEEEEecCCCCCCC
Q psy9934           5 LPCNPKPFLNLLTGK--SVICKLKWG--HEYKGILVSTDGYMNCQLASTEEIID-GHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k--~V~V~l~~g--~~~~G~L~~~D~~mNlvL~~~~e~~~-~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      .-..|+..+.+++.+  +|.|+++++  +++.|+|.|||+|||++|+||+|... ++..+.+|.++|||++|.++.+
T Consensus        11 ~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~   87 (89)
T PTZ00138         11 IMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA   87 (89)
T ss_pred             eecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEc
Confidence            346799999999665  488888774  89999999999999999999999864 3446789999999999998754

>KOG3293|consensus

Probab=99.61  E-value=5.4e-16  Score=111.67  Aligned_cols=76  Identities=26%  Similarity=0.359  Sum_probs=67.3

Q ss_pred             CchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEE-EeccceecceeEEEEecCCCCCCCCCCCCcccc
Q psy9934           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCTGKLGEVLIRSLTMSTPLPCNPKPFLNL   85 (158)
Q Consensus         8 ~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~-~~~~~~~~lg~~~iRG~~i~~I~p~dP~~~L~~   85 (158)
                      .||++|+...++++.|+||||.+|.|.|+.||.||||.|.+|+++ .++.....+++++|||++|.|+..  |.+.+.+
T Consensus         2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri--~d~iid~   78 (134)
T KOG3293|consen    2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRI--PDEIIDK   78 (134)
T ss_pred             cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEec--cHHHHHH
Confidence            599999999999999999999999999999999999999999999 456668899999999999999763  3344443

>KOG3460|consensus

Probab=99.59  E-value=2.5e-16  Score=106.23  Aligned_cols=73  Identities=23%  Similarity=0.235  Sum_probs=64.7

Q ss_pred             CCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEe---c----------cceecceeEEEEecCC
Q psy9934           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID---G----------HCTGKLGEVLIRSLTM   71 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~---~----------~~~~~lg~~~iRG~~i   71 (158)
                      +...|+++|+-+++.+|.|+++++|+++|+|.|||.|+|++|.||+|+..   .          +..+.+..+|+||++|
T Consensus         2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~V   81 (91)
T KOG3460|consen    2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGV   81 (91)
T ss_pred             cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeE
Confidence            45789999999999999999999999999999999999999999999842   1          1256888999999999


Q ss_pred             CCCCCC
Q psy9934          72 STPLPC   77 (158)
Q Consensus        72 ~~I~p~   77 (158)
                      .++.|+
T Consensus        82 ilvspp   87 (91)
T KOG3460|consen   82 ILVSPP   87 (91)
T ss_pred             EEEcCc
Confidence            998763

>KOG1781|consensus

Probab=99.53  E-value=5.5e-16  Score=107.56  Aligned_cols=73  Identities=30%  Similarity=0.327  Sum_probs=65.0

Q ss_pred             cccccccceeeEeeccccEEEEEEEEeccccceeecceEEEec--------CeeeeecCcEEEeeCcEEEEEeCCCCCcc
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID--------GHCTGKLGEVLIRCNNILYIRGAEEGDEE  153 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~--------~~~~~~~g~~~iRG~~I~~i~~~~~~~~~  153 (158)
                      -|.+++++.|+|++.+||+..|+|.|||+.|||||++|+|+..        +.+.|++|.+++||..+++|++.|+.+++
T Consensus        21 DLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e~I  100 (108)
T KOG1781|consen   21 DLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSEEI  100 (108)
T ss_pred             hHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchhhh
Confidence            3778999999999999999999999999999999999999832        12458999999999999999999998865


Q ss_pred             c
Q psy9934         154 G  154 (158)
Q Consensus       154 ~  154 (158)
                      .
T Consensus       101 ~  101 (108)
T KOG1781|consen  101 A  101 (108)
T ss_pred             c
Confidence            3

>KOG3460|consensus

Probab=99.53  E-value=1.6e-15  Score=102.35  Aligned_cols=73  Identities=22%  Similarity=0.313  Sum_probs=64.0

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEe---cC----------eeeeecCcEEEeeCcEEE
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII---DG----------HCTGKLGEVLIRCNNILY  143 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~---~~----------~~~~~~g~~~iRG~~I~~  143 (158)
                      ..|..+++-.++.+|.|+++++|+++|+|.+||+|+|++|.|++|.+   ++          ..++.+..+|+||++|++
T Consensus         4 ~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vil   83 (91)
T KOG3460|consen    4 EEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVIL   83 (91)
T ss_pred             cccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEE
Confidence            36788999999999999999999999999999999999999999874   21          124678899999999999


Q ss_pred             EEeCCC
Q psy9934         144 IRGAEE  149 (158)
Q Consensus       144 i~~~~~  149 (158)
                      |+++-.
T Consensus        84 vspp~~   89 (91)
T KOG3460|consen   84 VSPPLR   89 (91)
T ss_pred             EcCccc
Confidence            999864

>KOG1775|consensus

Probab=99.51  E-value=6.2e-15  Score=97.96  Aligned_cols=74  Identities=27%  Similarity=0.407  Sum_probs=66.4

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEe---cCeeeeecCcEEEeeCcEEEEEeCCCC
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII---DGHCTGKLGEVLIRCNNILYIRGAEEG  150 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~~g~~~iRG~~I~~i~~~~~~  150 (158)
                      .-|.+++.++++++++|.+++.|++.|+|.|||.|.|++|+|++|+-   +|+...+++++++.||||.++-|.-+.
T Consensus         6 llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGGe~   82 (84)
T KOG1775|consen    6 LLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGGEG   82 (84)
T ss_pred             cccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCCCC
Confidence            45788999999999999999999999999999999999999999983   466677999999999999999877643

>KOG1775|consensus

Probab=99.45  E-value=2.2e-14  Score=95.33  Aligned_cols=74  Identities=24%  Similarity=0.402  Sum_probs=66.0

Q ss_pred             CCCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEE-Ee--ccceecceeEEEEecCCCCCCCC
Q psy9934           4 PLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-ID--GHCTGKLGEVLIRSLTMSTPLPC   77 (158)
Q Consensus         4 ~~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~-~~--~~~~~~lg~~~iRG~~i~~I~p~   77 (158)
                      +....|+.++.+++|.++.|.+|+.+++.|+|.|||.|.|++|+||+|+ ..  +....+++++++.|++|..+.|.
T Consensus         3 ~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPG   79 (84)
T KOG1775|consen    3 PSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPG   79 (84)
T ss_pred             hhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecC
Confidence            4568899999999999999999999999999999999999999999998 32  33456899999999999987763

>KOG1774|consensus

Probab=99.40  E-value=2.1e-13  Score=91.75  Aligned_cols=66  Identities=33%  Similarity=0.420  Sum_probs=54.5

Q ss_pred             CcccccccceeeEeecc--ccEEEEEEEEeccccceeecceEEEe-cCeeeeecCcEEEeeCcEEEEEeCC
Q psy9934          81 PFLNLLTGKSVICKLKW--GHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAE  148 (158)
Q Consensus        81 ~~L~~~~~k~V~V~L~~--g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~~g~~~iRG~~I~~i~~~~  148 (158)
                      .||++..  +|.|||..  |-.+.|.+.|||+|||+||++|+|.. +.+..+.+|.++++|+||.+|....
T Consensus        19 r~Lq~~t--~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~~~   87 (88)
T KOG1774|consen   19 RFLQNRT--RVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQSAG   87 (88)
T ss_pred             HHHhcCC--ceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEeecC
Confidence            4555543  89999987  78999999999999999999999973 3333358999999999999997653

>KOG1782|consensus

Probab=99.40  E-value=2.8e-14  Score=102.72  Aligned_cols=70  Identities=27%  Similarity=0.359  Sum_probs=62.4

Q ss_pred             ccccccceeeEeeccccEEEEEEEEeccccceeecceEEEe-cCe--eeeecCcEEEeeCcEEEEEeCCCCCc
Q psy9934          83 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGH--CTGKLGEVLIRCNNILYIRGAEEGDE  152 (158)
Q Consensus        83 L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~--~~~~~g~~~iRG~~I~~i~~~~~~~~  152 (158)
                      +-+++++++.|-|+|||...|.|+|||||.|++|++|+|++ .++  .....|.++|||.||++++..|.+.|
T Consensus        14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE   86 (129)
T KOG1782|consen   14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE   86 (129)
T ss_pred             HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh
Confidence            66778999999999999999999999999999999999985 233  23567999999999999999999987

>KOG3172|consensus

Probab=99.39  E-value=5.1e-13  Score=94.26  Aligned_cols=73  Identities=25%  Similarity=0.337  Sum_probs=65.6

Q ss_pred             CCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCC
Q psy9934           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus         6 ~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      ...|+++|+...|.-|+++++.|..|+|+|...|++||++|+|++-+.......++..+||||+.|+++..++
T Consensus         3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPd   75 (119)
T KOG3172|consen    3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPD   75 (119)
T ss_pred             cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECch
Confidence            5679999999999999999999999999999999999999999999844435789999999999999976443

>KOG1781|consensus

Probab=99.38  E-value=2.3e-14  Score=99.45  Aligned_cols=70  Identities=30%  Similarity=0.281  Sum_probs=61.8

Q ss_pred             chHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEE-Eec-------cceecceeEEEEecCCCCCCCCC
Q psy9934           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDG-------HCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus         9 p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~-~~~-------~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      ..--|.+|++|+|+|++.+||...|+|.|||+.|||||+++.|+ ++.       .+.+++|.+++||..+..+.|.+
T Consensus        18 silDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~d   95 (108)
T KOG1781|consen   18 SILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPAD   95 (108)
T ss_pred             HHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCc
Confidence            34468999999999999999999999999999999999999998 332       23589999999999999998754

>KOG3293|consensus

Probab=99.38  E-value=4.4e-13  Score=96.66  Aligned_cols=73  Identities=30%  Similarity=0.406  Sum_probs=66.2

Q ss_pred             CCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEe-cCeeeeecCcEEEeeCcEEEEEeCCCCC
Q psy9934          79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAEEGD  151 (158)
Q Consensus        79 P~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~~g~~~iRG~~I~~i~~~~~~~  151 (158)
                      |..+|....+.++.|+||+|.+|.|.|..+|.+|||.|.++.++. +|.+...+..++|||++|.|+..+|+-.
T Consensus         3 PLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~ii   76 (134)
T KOG3293|consen    3 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEII   76 (134)
T ss_pred             chhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHH
Confidence            677888899999999999999999999999999999999999985 5666678899999999999999988643

>KOG3448|consensus

Probab=99.35  E-value=1.5e-12  Score=89.00  Aligned_cols=66  Identities=24%  Similarity=0.271  Sum_probs=57.9

Q ss_pred             hHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEecc--ceecceeEEEEecCCCCCC
Q psy9934          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH--CTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus        10 ~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~--~~~~lg~~~iRG~~i~~I~   75 (158)
                      .+|+++++|+.|.|+|||+-.+.|+|.++|+|+|+.|.|+.-....+  .-.....+||||+.|+|++
T Consensus         4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~   71 (96)
T KOG3448|consen    4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   71 (96)
T ss_pred             HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEE
Confidence            47899999999999999999999999999999999999998774322  2346778999999999987

>KOG1784|consensus

Probab=99.34  E-value=4.6e-13  Score=91.91  Aligned_cols=71  Identities=24%  Similarity=0.183  Sum_probs=64.5

Q ss_pred             cccccccceeeEeeccccEEEEEEEEeccccceeecceEEEe----cCeeeeecCcEEEeeCcEEEEEeCCCCCc
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----DGHCTGKLGEVLIRCNNILYIRGAEEGDE  152 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~----~~~~~~~~g~~~iRG~~I~~i~~~~~~~~  152 (158)
                      -|..|++++|.|...|||.+.|.|.|||+..||.|+++-|++    .|.....+|..+|||+||..|++.||+.+
T Consensus         4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d   78 (96)
T KOG1784|consen    4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELD   78 (96)
T ss_pred             hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhh
Confidence            467889999999999999999999999999999999999984    35556789999999999999999999875

>KOG3428|consensus

Probab=99.31  E-value=4.5e-12  Score=89.73  Aligned_cols=97  Identities=22%  Similarity=0.183  Sum_probs=77.2

Q ss_pred             hHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCCCCCcccccccc
Q psy9934          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNPKPFLNLLTGK   89 (158)
Q Consensus        10 ~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~dP~~~L~~~~~k   89 (158)
                      ..||+++.+.+|+|+|++|....|++.++|.+||..|.+++-+.++ ++.++..++|||++|+|+..+|+.++-.-+++.
T Consensus         4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l~ld~Llvd~   82 (109)
T KOG3428|consen    4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSLNLDTLLVDD   82 (109)
T ss_pred             HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCcCcceeeeeh
Confidence            5799999999999999999999999999999999999999988766 467889999999999998876765554445544


Q ss_pred             eeeEeecccc-EEEEEEEE
Q psy9934          90 SVICKLKWGH-EYKGILVS  107 (158)
Q Consensus        90 ~V~V~L~~g~-~~~G~L~~  107 (158)
                      .-.++++... ..+|..+|
T Consensus        83 ~~~~~~~~~~~~~rgrgrg  101 (109)
T KOG3428|consen   83 APRLHLRKNEKVGRGRGRG  101 (109)
T ss_pred             hhhhhhhcccccccccccc
Confidence            4445554332 45555544

>KOG1774|consensus

Probab=99.28  E-value=1.6e-12  Score=87.46  Aligned_cols=70  Identities=23%  Similarity=0.294  Sum_probs=56.2

Q ss_pred             CCchHHHhhcCC--CEEEEEEeC--CcEEEEEEeEecCcceeEEceeeEE-EeccceecceeEEEEecCCCCCCC
Q psy9934           7 CNPKPFLNLLTG--KSVICKLKW--GHEYKGILVSTDGYMNCQLASTEEI-IDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         7 ~~p~~~L~~~~~--k~V~V~l~~--g~~~~G~L~~~D~~mNlvL~~~~e~-~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      ..|+.++=.++.  .+|.|||.+  |-.+.|.++|||+|||+||++|+|. .+......+|.++++|++|..++.
T Consensus        11 v~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~   85 (88)
T KOG1774|consen   11 VQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQS   85 (88)
T ss_pred             cCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEee
Confidence            457666665543  458888887  7999999999999999999999998 333334589999999999988764

>KOG3172|consensus

Probab=99.21  E-value=4.5e-11  Score=84.46  Aligned_cols=73  Identities=26%  Similarity=0.387  Sum_probs=65.7

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      ..|.++|.+..+.-|.++++.|..|+|+|+..+++||++|+|.+-+..+.....+..+||||+.|.++-.||-
T Consensus         4 gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdm   76 (119)
T KOG3172|consen    4 GVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDM   76 (119)
T ss_pred             ccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchH
Confidence            3578899999999999999999999999999999999999999987555456789999999999999988764

>KOG3448|consensus

Probab=99.20  E-value=2.3e-11  Score=83.13  Aligned_cols=72  Identities=24%  Similarity=0.335  Sum_probs=60.7

Q ss_pred             CcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCee--eeecCcEEEeeCcEEEEEeCCCCCc
Q psy9934          81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHC--TGKLGEVLIRCNNILYIRGAEEGDE  152 (158)
Q Consensus        81 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~~g~~~iRG~~I~~i~~~~~~~~  152 (158)
                      .|++.+++++|.|.||++-.+.|+|.|+|+|+|+.|.|.......+-  -.....+||||+.|.||..+.+..+
T Consensus         5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vd   78 (96)
T KOG3448|consen    5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVD   78 (96)
T ss_pred             HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHHH
Confidence            46788999999999999999999999999999999999986643321  1245689999999999999877654

>KOG3168|consensus

Probab=99.14  E-value=5.8e-12  Score=95.44  Aligned_cols=70  Identities=26%  Similarity=0.257  Sum_probs=59.7

Q ss_pred             cccccccceeeEeeccccEEEEEEEEeccccceeecceEEEe----------cCeeeeecCcEEEeeCcEEEEEeCCCCC
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLGEVLIRCNNILYIRGAEEGD  151 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~----------~~~~~~~~g~~~iRG~~I~~i~~~~~~~  151 (158)
                      .+-++++.++.|.++|||+|.|++.+||.||||+|.||+|+.          ++++++.+|.+++||.||++.+..+-..
T Consensus         8 kml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp   87 (177)
T KOG3168|consen    8 KMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPP   87 (177)
T ss_pred             HHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCC
Confidence            355677899999999999999999999999999999999863          2346788999999999999987655433

>KOG3168|consensus

Probab=99.05  E-value=1.5e-11  Score=93.20  Aligned_cols=67  Identities=24%  Similarity=0.224  Sum_probs=58.4

Q ss_pred             HHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEE----------eccceecceeEEEEecCCCCCCCCC
Q psy9934          12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus        12 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~----------~~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      -|.+.+|.++.|.++|||.+.|++.+||.|||++|.||+|..          ++++.+.+|++++||.+|++.....
T Consensus         8 kml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg   84 (177)
T KOG3168|consen    8 KMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG   84 (177)
T ss_pred             HHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence            456779999999999999999999999999999999999973          2346789999999999999876433

>KOG1784|consensus

Probab=98.97  E-value=5.3e-10  Score=76.87  Aligned_cols=67  Identities=21%  Similarity=0.121  Sum_probs=59.6

Q ss_pred             HHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEE----eccceecceeEEEEecCCCCCCCCC
Q psy9934          12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----DGHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus        12 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~----~~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      -|.+|++++|.|-..|||.+.|.|.|||+..||.++++-|+.    .+.+...+|...|||+++..+.+.+
T Consensus         4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iD   74 (96)
T KOG1784|consen    4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEID   74 (96)
T ss_pred             hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecc
Confidence            478999999999999999999999999999999999999973    2334678999999999999988755

>KOG1782|consensus

Probab=98.96  E-value=9.3e-11  Score=84.63  Aligned_cols=79  Identities=24%  Similarity=0.209  Sum_probs=62.7

Q ss_pred             CCCCCCCCc-hHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEE-ecc--ceecceeEEEEecCCCCCCC
Q psy9934           1 MSTPLPCNP-KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGH--CTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         1 m~~~~~~~p-~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~--~~~~lg~~~iRG~~i~~I~p   76 (158)
                      |+.+.+..| ..-|-+++++++.|-|+|||++.|.|++||+|-|++|.+|.|.+ -++  .-...|...|||.||..+..
T Consensus         1 md~~~~~~~~t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGe   80 (129)
T KOG1782|consen    1 MDLADGDLPFTTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGE   80 (129)
T ss_pred             CCccccCCCchhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEec
Confidence            444443333 34488899999999999999999999999999999999999984 222  13567899999999999876


Q ss_pred             CCC
Q psy9934          77 CNP   79 (158)
Q Consensus        77 ~dP   79 (158)
                      .++
T Consensus        81 id~   83 (129)
T KOG1782|consen   81 IDL   83 (129)
T ss_pred             CCc
Confidence            554

>KOG3428|consensus

Probab=98.80  E-value=1.5e-08  Score=71.95  Aligned_cols=69  Identities=30%  Similarity=0.324  Sum_probs=62.1

Q ss_pred             CcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCC
Q psy9934          81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEG  150 (158)
Q Consensus        81 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~  150 (158)
                      .+|+.+.+.++.|.|++|...+|++.+.|.+||..|.+..-...| ...++....|||+||.|+-.||.-
T Consensus         5 r~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l   73 (109)
T KOG3428|consen    5 RFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSL   73 (109)
T ss_pred             HHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCc
Confidence            367888999999999999999999999999999999999977777 456889999999999999988864

>KOG3459|consensus

Probab=98.63  E-value=1.9e-09  Score=76.47  Aligned_cols=71  Identities=17%  Similarity=0.191  Sum_probs=58.5

Q ss_pred             CchHHHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEec-------c------ceecceeEEEEecCCC
Q psy9934           8 NPKPFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG-------H------CTGKLGEVLIRSLTMS   72 (158)
Q Consensus         8 ~p~~~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------~------~~~~lg~~~iRG~~i~   72 (158)
                      =|++.+...  -..+|.|.++|++.+.|.+.|||.|+|++|+|+.|.+..       .      ..+.++.+||||++|+
T Consensus        24 Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI  103 (114)
T KOG3459|consen   24 GPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVI  103 (114)
T ss_pred             CchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEE
Confidence            477777776  456799999999999999999999999999999998532       1      1467899999999998


Q ss_pred             CCCCCCC
Q psy9934          73 TPLPCNP   79 (158)
Q Consensus        73 ~I~p~dP   79 (158)
                      ... .+|
T Consensus       104 ~v~-r~p  109 (114)
T KOG3459|consen  104 LVL-RNP  109 (114)
T ss_pred             EEE-ecc
Confidence            754 444

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=98.17  E-value=3.4e-05  Score=58.91  Aligned_cols=119  Identities=18%  Similarity=0.081  Sum_probs=71.1

Q ss_pred             CCCCCCCCchHHHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEE---Eec----cceecceeEEEEecCC
Q psy9934           1 MSTPLPCNPKPFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI---IDG----HCTGKLGEVLIRSLTM   71 (158)
Q Consensus         1 m~~~~~~~p~~~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~---~~~----~~~~~lg~~~iRG~~i   71 (158)
                      |++...-..-.||..+  ...+|+|.|.+|-.++|.+.+||.|.=|.-.+....   ...    .+.+.....++--+..
T Consensus         5 m~~~~~nlQD~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~gkqqLIYKHAISTI~p~~~i~~~~~~~~~~   84 (165)
T PRK14091          5 MAEKVNNLQDIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDGQSQLVYKHAISTIMPAHPLDLSRFSKSLD   84 (165)
T ss_pred             ccccccchHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCCceEEEEeeeeeeecccCCcchhhhcchhh
Confidence            5554455566778777  455699999999999999999999984443343221   000    0011111111100000


Q ss_pred             CCCCCCCC-CCcccccc--cceeeEeeccccEEEEEEEEeccccceeecce
Q psy9934          72 STPLPCNP-KPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLAST  119 (158)
Q Consensus        72 ~~I~p~dP-~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~  119 (158)
                      ..-...+. ..||+.+.  +.+|.|-|.+|-.++|.+.|||+|.=|.-.+.
T Consensus        85 ~~~~~~nlQd~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g  135 (165)
T PRK14091         85 ANKKSRLLQDVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG  135 (165)
T ss_pred             hcccccccHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            00000111 13455543  44899999999999999999999987765554

>KOG3459|consensus

Probab=97.91  E-value=9.7e-07  Score=62.81  Aligned_cols=60  Identities=13%  Similarity=0.226  Sum_probs=50.6

Q ss_pred             cceeeEeeccccEEEEEEEEeccccceeecceEEEe-------cCee------eeecCcEEEeeCcEEEEEeC
Q psy9934          88 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-------DGHC------TGKLGEVLIRCNNILYIRGA  147 (158)
Q Consensus        88 ~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-------~~~~------~~~~g~~~iRG~~I~~i~~~  147 (158)
                      ..+|.+-.+|++..-|...+||-|+|++|+++.|.+       +|+.      .+.+|.+||||++|+.+.-.
T Consensus        36 ~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~r~  108 (114)
T KOG3459|consen   36 NTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVLRN  108 (114)
T ss_pred             CceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEEec
Confidence            448889999999999999999999999999998863       2322      46789999999999988643

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

Probab=97.85  E-value=1.4e-05  Score=52.07  Aligned_cols=36  Identities=22%  Similarity=0.236  Sum_probs=30.7

Q ss_pred             CCEEEEEEeCC----cEEEEEEeEecCcceeEEceeeEEE
Q psy9934          18 GKSVICKLKWG----HEYKGILVSTDGYMNCQLASTEEII   53 (158)
Q Consensus        18 ~k~V~V~l~~g----~~~~G~L~~~D~~mNlvL~~~~e~~   53 (158)
                      +++|.|.++.-    -.+.|.|.+||.|+||+|.||.|..
T Consensus         8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y   47 (66)
T cd01739           8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETY   47 (66)
T ss_pred             CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhh
Confidence            57788888764    3678899999999999999999984

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

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

Probab=97.76  E-value=8e-05  Score=49.94  Aligned_cols=62  Identities=19%  Similarity=0.275  Sum_probs=40.8

Q ss_pred             hHHHhhcCCCEEEEEEeCCcEEEEEEeEecC---cceeEEceeeEEEecc-------ceecceeEEEEecCC
Q psy9934          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDG---YMNCQLASTEEIIDGH-------CTGKLGEVLIRSLTM   71 (158)
Q Consensus        10 ~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~---~mNlvL~~~~e~~~~~-------~~~~lg~~~iRG~~i   71 (158)
                      ..++..++|++|.|.++||..|.|.|.+++.   -+-++|+-|.....+.       ......++.|.++.|
T Consensus         4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dv   75 (77)
T PF14438_consen    4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDV   75 (77)
T ss_dssp             HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE----
T ss_pred             HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEecccc
Confidence            3578889999999999999999999999998   8999999998763221       012334566666554

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

Probab=97.59  E-value=5.7e-05  Score=49.24  Aligned_cols=37  Identities=24%  Similarity=0.333  Sum_probs=29.7

Q ss_pred             cceeeEeecc--c--cEEEEEEEEeccccceeecceEEEec
Q psy9934          88 GKSVICKLKW--G--HEYKGILVSTDGYMNCQLASTEEIID  124 (158)
Q Consensus        88 ~k~V~V~L~~--g--~~~~G~L~~~D~~mNlvL~~~~e~~~  124 (158)
                      ..+|.|.++.  |  -.++|.|.+||+|+||+|.|+.|...
T Consensus         8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~   48 (66)
T cd01739           8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR   48 (66)
T ss_pred             CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence            3566666664  3  48899999999999999999999643

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

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

Probab=96.97  E-value=0.0013  Score=43.95  Aligned_cols=60  Identities=20%  Similarity=0.343  Sum_probs=38.2

Q ss_pred             ccccccceeeEeeccccEEEEEEEEecc---ccceeecceEEEecCe-------eeeecCcEEEeeCcEE
Q psy9934          83 LNLLTGKSVICKLKWGHEYKGILVSTDG---YMNCQLASTEEIIDGH-------CTGKLGEVLIRCNNIL  142 (158)
Q Consensus        83 L~~~~~k~V~V~L~~g~~~~G~L~~~D~---~mNlvL~~~~e~~~~~-------~~~~~g~~~iRG~~I~  142 (158)
                      +..++|++|.|.++||..|+|.|.+++.   -+.++|.-|.....+.       .......++|.++.|+
T Consensus         7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred             HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence            4568899999999999999999999998   8999998888653321       1123456666666554

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

Probab=96.62  E-value=0.0033  Score=44.27  Aligned_cols=62  Identities=18%  Similarity=0.218  Sum_probs=50.5

Q ss_pred             hhcCCCEEEEEEeCCcEEEEEEeEecC-cceeEEceeeEE-Eecc--------ceecceeEEEEecCCCCCC
Q psy9934          14 NLLTGKSVICKLKWGHEYKGILVSTDG-YMNCQLASTEEI-IDGH--------CTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus        14 ~~~~~k~V~V~l~~g~~~~G~L~~~D~-~mNlvL~~~~e~-~~~~--------~~~~lg~~~iRG~~i~~I~   75 (158)
                      .+++|++|.+..+.+-.|.|+|..+|. --.+.|.||..+ ..+.        .......+..||+.|.-+.
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~   75 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLK   75 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEE
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEE
Confidence            468999999999999999999999994 788999999876 2221        1235678999999998865

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

Probab=95.89  E-value=0.068  Score=37.60  Aligned_cols=68  Identities=19%  Similarity=0.228  Sum_probs=53.8

Q ss_pred             cccccceeeEeeccccEEEEEEEEecc-ccceeecceEEE-ecCe--------eeeecCcEEEeeCcEEEEEeCCCCC
Q psy9934          84 NLLTGKSVICKLKWGHEYKGILVSTDG-YMNCQLASTEEI-IDGH--------CTGKLGEVLIRCNNILYIRGAEEGD  151 (158)
Q Consensus        84 ~~~~~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~~~~e~-~~~~--------~~~~~g~~~iRG~~I~~i~~~~~~~  151 (158)
                      .+++|+.|.+..+.+-.|+|+|..+|. --.+.|.++..+ .+|.        ....+..+..||+.|.-+...+...
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~   81 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP   81 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence            468899999999999999999999995 789999998865 2221        1235789999999999988776554

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

Probab=95.87  E-value=0.027  Score=36.45  Aligned_cols=34  Identities=29%  Similarity=0.268  Sum_probs=27.9

Q ss_pred             HHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeE
Q psy9934          12 FLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQ   45 (158)
Q Consensus        12 ~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlv   45 (158)
                      ||+++  ...+|+|.|.||-.+.|.+.+||.|+=+.
T Consensus         3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll   38 (61)
T cd01716           3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLL   38 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEE
Confidence            45554  45679999999999999999999998444

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

>TIGR02383 Hfq RNA chaperone Hfq

Probab=95.73  E-value=0.033  Score=36.05  Aligned_cols=35  Identities=31%  Similarity=0.355  Sum_probs=28.9

Q ss_pred             HHHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeE
Q psy9934          11 PFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQ   45 (158)
Q Consensus        11 ~~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlv   45 (158)
                      .||+.+  ...+|+|.|.||-.+.|.+.+||.|+=+.
T Consensus         6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll   42 (61)
T TIGR02383         6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLL   42 (61)
T ss_pred             HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEE
Confidence            455555  56679999999999999999999998444

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

>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown

Probab=95.55  E-value=0.097  Score=31.83  Aligned_cols=47  Identities=23%  Similarity=0.198  Sum_probs=36.6

Q ss_pred             CCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEE
Q psy9934          17 TGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR   67 (158)
Q Consensus        17 ~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iR   67 (158)
                      +|++|.+.. ++..+.|+..++|+.-.|+++......   ..-..|.+++|
T Consensus         2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g~~---~~i~sGdv~~r   48 (48)
T PF02237_consen    2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDGSI---RTISSGDVSLR   48 (48)
T ss_dssp             TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTEEE---EEESSSEEEEE
T ss_pred             CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCCCE---EEEEEEEEEeC
Confidence            699999999 778889999999999999998766521   13345666665

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

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

Probab=95.55  E-value=0.096  Score=35.13  Aligned_cols=60  Identities=15%  Similarity=0.202  Sum_probs=44.9

Q ss_pred             hhcCCCEEEEEEeCCcEEEEEEeEec-CcceeEEceeeEEE-ecc---------ceecceeEEEEecCCCC
Q psy9934          14 NLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEII-DGH---------CTGKLGEVLIRSLTMST   73 (158)
Q Consensus        14 ~~~~~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~-~~~---------~~~~lg~~~iRG~~i~~   73 (158)
                      .+++|+++.+.-+.+-.|.|.|.++| .---+.|+||..+- .+.         .......+..||+.|.-
T Consensus         2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD   72 (74)
T cd01736           2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD   72 (74)
T ss_pred             ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence            46899999999999999999999999 44558899988762 111         11234567788887754

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

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

Probab=95.50  E-value=0.042  Score=41.60  Aligned_cols=93  Identities=17%  Similarity=0.148  Sum_probs=68.5

Q ss_pred             CCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEe---------------ccceecceeEEEEecCCCCCCCCCC--
Q psy9934          17 TGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID---------------GHCTGKLGEVLIRSLTMSTPLPCNP--   79 (158)
Q Consensus        17 ~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~---------------~~~~~~lg~~~iRG~~i~~I~p~dP--   79 (158)
                      -.-+|.|.+.||+.+.|.+-+|+.--|.+|.-+.-..+               .-.....|...|+.+.+-. ++..|  
T Consensus        28 ~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~~~~~nRi~~plE~I~t~Ee~~~~d~~g~~ti~~d~~~~-q~~~psr  106 (165)
T PF03614_consen   28 NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDPFKKENRIRLPLERISTIEELIVSDFKGRLTIHPDYFNN-QPYKPSR  106 (165)
T ss_pred             cCCceEEEecCCcEEEEEEeccCcccCEEeccCCCCCCceEEEEhHHhhhHhhhccccccccEEechhhccc-ccCCCcc
Confidence            46679999999999999999999999999977653210               0012346778888887765 33444  


Q ss_pred             CCcccc-----cccceeeEeeccccEEEEEEEEecc
Q psy9934          80 KPFLNL-----LTGKSVICKLKWGHEYKGILVSTDG  110 (158)
Q Consensus        80 ~~~L~~-----~~~k~V~V~L~~g~~~~G~L~~~D~  110 (158)
                      ..|++-     ..++.|.|-+.|||+++|+-.|.|.
T Consensus       107 rDFF~Icrka~qqg~sIrVyM~DgR~ieG~stGvna  142 (165)
T PF03614_consen  107 RDFFSICRKAHQQGKSIRVYMADGREIEGKSTGVNA  142 (165)
T ss_pred             chHHHHHHHHHHCCCeEEEEEcCCcEEEeeecccce
Confidence            234432     1367999999999999999999884

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

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=95.24  E-value=0.064  Score=36.40  Aligned_cols=39  Identities=28%  Similarity=0.308  Sum_probs=31.4

Q ss_pred             CCchHHHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeE
Q psy9934           7 CNPKPFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQ   45 (158)
Q Consensus         7 ~~p~~~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlv   45 (158)
                      -..-.||..+  .+.+|+|.|.||-.+.|.+.+||.|+=+.
T Consensus         6 nlQd~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll   46 (79)
T PRK00395          6 NLQDPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLL   46 (79)
T ss_pred             chHHHHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEE
Confidence            3445566666  56679999999999999999999998444

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

Probab=95.11  E-value=0.062  Score=36.14  Aligned_cols=39  Identities=31%  Similarity=0.413  Sum_probs=31.2

Q ss_pred             chHHHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeEEce
Q psy9934           9 PKPFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLAS   48 (158)
Q Consensus         9 p~~~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   48 (158)
                      .-.||.++  -+.+|.|.|.||-.+.|.+.+||.|. +.|++
T Consensus         8 QD~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~   48 (77)
T COG1923           8 QDPFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFV-VLLKN   48 (77)
T ss_pred             chHHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEE-EEEEc
Confidence            34566665  66779999999999999999999997 44444

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

Probab=94.73  E-value=0.061  Score=34.77  Aligned_cols=31  Identities=23%  Similarity=0.149  Sum_probs=26.8

Q ss_pred             cceeeEeeccccEEEEEEEEeccccceeecc
Q psy9934          88 GKSVICKLKWGHEYKGILVSTDGYMNCQLAS  118 (158)
Q Consensus        88 ~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~  118 (158)
                      +.+|.|-|.||-.++|.+.|||+|+=+.-.+
T Consensus        11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716          11 KIPVTIYLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence            4589999999999999999999998766443

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

>TIGR02383 Hfq RNA chaperone Hfq

Probab=94.59  E-value=0.068  Score=34.56  Aligned_cols=31  Identities=23%  Similarity=0.200  Sum_probs=26.7

Q ss_pred             cceeeEeeccccEEEEEEEEeccccceeecc
Q psy9934          88 GKSVICKLKWGHEYKGILVSTDGYMNCQLAS  118 (158)
Q Consensus        88 ~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~  118 (158)
                      +.+|.|-|.+|-.++|.+.|||+|+=|.-.+
T Consensus        15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383        15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            4589999999999999999999998766433

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

>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=94.23  E-value=0.24  Score=33.69  Aligned_cols=60  Identities=20%  Similarity=0.140  Sum_probs=44.9

Q ss_pred             hHHHhhcCCCEEEEEEeCCcEEEEEEeEec-CcceeEEceeeEEEeccceecceeEEEEecCCCCC
Q psy9934          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTP   74 (158)
Q Consensus        10 ~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I   74 (158)
                      |.+|..+.|++|.+.|.++.++.|+..++| ...|+..+|-.     .+-...+...+|.+.|+.+
T Consensus        16 Lr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-----TPlGv~~eAlLR~~DVi~~   76 (80)
T PF11095_consen   16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-----TPLGVQPEALLRCSDVISI   76 (80)
T ss_dssp             HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-----TTTTEEEEEEEEGGGEEEE
T ss_pred             HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-----CCcccChhheeecCCEEEE
Confidence            567888899999999999999999999999 67777766532     1233457889999988754

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.

>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown

Probab=94.19  E-value=0.16  Score=30.90  Aligned_cols=47  Identities=21%  Similarity=0.155  Sum_probs=34.7

Q ss_pred             ccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEe
Q psy9934          87 TGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR  137 (158)
Q Consensus        87 ~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iR  137 (158)
                      ++++|.+.+ ++..++|+..++|+.-.|+++.....   .....-|.+++|
T Consensus         2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g~---~~~i~sGdv~~r   48 (48)
T PF02237_consen    2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDGS---IRTISSGDVSLR   48 (48)
T ss_dssp             TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTEE---EEEESSSEEEEE
T ss_pred             CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCCC---EEEEEEEEEEeC
Confidence            578999998 67778999999999999998765541   122344666655

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

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=93.76  E-value=0.12  Score=35.12  Aligned_cols=38  Identities=26%  Similarity=0.269  Sum_probs=30.1

Q ss_pred             cccccc--cceeeEeeccccEEEEEEEEeccccceeecce
Q psy9934          82 FLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLAST  119 (158)
Q Consensus        82 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~  119 (158)
                      +|+.+.  +.+|.|-|.||-.++|.+.|||+|+=|.-.+-
T Consensus        11 fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g   50 (79)
T PRK00395         11 FLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG   50 (79)
T ss_pred             HHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence            444443  45899999999999999999999987775443

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

Probab=93.24  E-value=0.25  Score=31.88  Aligned_cols=34  Identities=18%  Similarity=0.258  Sum_probs=28.7

Q ss_pred             cCCCEEEEEEeCCcEEEEEEeEecCcceeEEcee
Q psy9934          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLAST   49 (158)
Q Consensus        16 ~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~   49 (158)
                      .+|.+|.+++..|.+++|.+.+||...++..=.+
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~   37 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKC   37 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEEC
Confidence            4799999999999999999999997776664443

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.

>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=92.70  E-value=0.42  Score=32.55  Aligned_cols=60  Identities=23%  Similarity=0.256  Sum_probs=44.3

Q ss_pred             cccccccceeeEeeccccEEEEEEEEec-cccceeecceEEEecCeeeeecCcEEEeeCcEEEEEe
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      +|..+.+++|.+.|.++.+..|++.++| ...|+..++=. +.=|    .....++|++-|+.++-
T Consensus        18 ~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-TPlG----v~~eAlLR~~DVi~~~f   78 (80)
T PF11095_consen   18 SLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-TPLG----VQPEALLRCSDVISISF   78 (80)
T ss_dssp             HHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-TTTT----EEEEEEEEGGGEEEEEE
T ss_pred             HHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-CCcc----cChhheeecCCEEEEEe
Confidence            4566789999999999999999999999 55677655544 2223    34688999999999874

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.

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

Probab=92.65  E-value=0.48  Score=31.79  Aligned_cols=61  Identities=16%  Similarity=0.210  Sum_probs=45.5

Q ss_pred             cccccceeeEeeccccEEEEEEEEec-cccceeecceEEEe-cCe---------eeeecCcEEEeeCcEEEE
Q psy9934          84 NLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEII-DGH---------CTGKLGEVLIRCNNILYI  144 (158)
Q Consensus        84 ~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~-~~~---------~~~~~g~~~iRG~~I~~i  144 (158)
                      .+++++++.+..+.+-.|.|+|.++| +---+.|.++..+- +|.         ...-++.++.||+.|.-+
T Consensus         2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkDL   73 (74)
T cd01736           2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKDL   73 (74)
T ss_pred             ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccccc
Confidence            35789999999999999999999999 44667788877551 111         123467889999887543

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

>PRK14638 hypothetical protein; Provisional

Probab=92.47  E-value=0.24  Score=37.46  Aligned_cols=45  Identities=22%  Similarity=0.102  Sum_probs=34.1

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEc
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA   47 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~   47 (158)
                      |+|.-.-|+   ..+..+.|++|.|++++++.+.|+|.++|.- ++.|.
T Consensus        81 SSPGldRpL~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         81 SSPGLDRPLRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            455444444   4566779999999999999999999999963 35443

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=91.49  E-value=0.56  Score=36.04  Aligned_cols=64  Identities=20%  Similarity=0.185  Sum_probs=42.0

Q ss_pred             CCchHHHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCCCCCc
Q psy9934           7 CNPKPFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNPKPF   82 (158)
Q Consensus         7 ~~p~~~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~dP~~~   82 (158)
                      -..-.||..+  ...+|+|.|.||-.+.|.+.+||.|.=|...+..            .-+|-=.-|+.+.|..|..+
T Consensus        91 nlQd~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~gk------------qqLIYKHAISTI~P~~~v~~  156 (165)
T PRK14091         91 LLQDVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDGY------------VQLVYKHAVSTVQPAGPVDL  156 (165)
T ss_pred             ccHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCCc------------EEEEEEeEEEEEccCCCccc
Confidence            3444566666  5566999999999999999999999844432322            12444445566666555443

>PRK14639 hypothetical protein; Provisional

Probab=91.45  E-value=0.37  Score=36.00  Aligned_cols=45  Identities=22%  Similarity=0.189  Sum_probs=34.4

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEc
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA   47 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~   47 (158)
                      |+|.-.-|+   ..+..++|++|.|++.+++.+.|+|.++|+- ++.|.
T Consensus        69 SSPGl~RpL~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~  116 (140)
T PRK14639         69 SSPGLERKLSKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE  116 (140)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            455444444   5566779999999999999999999999973 45553

>PRK02001 hypothetical protein; Validated

Probab=91.36  E-value=0.39  Score=36.48  Aligned_cols=44  Identities=20%  Similarity=0.179  Sum_probs=34.0

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEE
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL   46 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL   46 (158)
                      |+|.-.-|+   ..+..++|+.|.|.+.+++.+.|+|.++|+- +++|
T Consensus        71 SSPGldRpL~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l  117 (152)
T PRK02001         71 GSAGLTSPLKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL  117 (152)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence            555544454   4566679999999999999999999999964 3444

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

Probab=90.92  E-value=0.5  Score=36.45  Aligned_cols=61  Identities=23%  Similarity=0.177  Sum_probs=40.0

Q ss_pred             CCchHHHhhcCCCEEEEEEeCCcEEEEEEeEec-CcceeEEceeeEEEeccceecceeEEEEecCCCCCC
Q psy9934           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus         7 ~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~   75 (158)
                      .+|+ .+..|++|.|.|.+.| +++.|.|..+| -.-|+||-+-.|-  +  .  ..--+|-|.+|..+.
T Consensus         7 ~~p~-~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e~--~--~--~sv~~I~ghaVk~ve   68 (166)
T PF06372_consen    7 KSPL-EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQED--G--K--RSVKVIMGHAVKSVE   68 (166)
T ss_dssp             S-HH-HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-TT--S-----EEEEEE-GGGEEEEE
T ss_pred             CCHH-HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcccC--C--c--eeEEEEEccceEEEE
Confidence            4555 4578999999999999 99999999999 5788898865541  1  1  123566777777654

The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.

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

Probab=90.65  E-value=0.38  Score=37.08  Aligned_cols=61  Identities=26%  Similarity=0.287  Sum_probs=43.8

Q ss_pred             ccccccceeeEeeccccEEEEEEEEec-cccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCC
Q psy9934          83 LNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEG  150 (158)
Q Consensus        83 L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~  150 (158)
                      +..|++|+|.|.+.+ +++.|.|..+| -.-|++|-+..|  +++  .  ..-+|-|..|..|...++.
T Consensus        12 ~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e--~~~--~--sv~~I~ghaVk~vevl~~~   73 (166)
T PF06372_consen   12 WQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE--DGK--R--SVKVIMGHAVKSVEVLSEG   73 (166)
T ss_dssp             HHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T--TS---E--EEEEE-GGGEEEEEEEE--
T ss_pred             HHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc--CCc--e--eEEEEEccceEEEEEccCC
Confidence            567899999999999 99999999999 578999987665  332  2  3478899999999888764

The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.

>PRK14644 hypothetical protein; Provisional

Probab=89.95  E-value=0.73  Score=34.30  Aligned_cols=45  Identities=18%  Similarity=0.025  Sum_probs=34.4

Q ss_pred             CCCCCCCchH--HHhhcCCCEEEEEEeCC----cEEEEEEeEecCcceeEEc
Q psy9934           2 STPLPCNPKP--FLNLLTGKSVICKLKWG----HEYKGILVSTDGYMNCQLA   47 (158)
Q Consensus         2 ~~~~~~~p~~--~L~~~~~k~V~V~l~~g----~~~~G~L~~~D~~mNlvL~   47 (158)
                      |+|.-.-|+.  .+..++|+.|.|++++.    +.+.|.|.++|+. ++.|.
T Consensus        67 SSPGldRpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         67 SSPGFDMDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             ECCCCCCCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            4554444544  47788999999999987    9999999999973 45554

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

Probab=89.93  E-value=0.55  Score=31.63  Aligned_cols=37  Identities=27%  Similarity=0.283  Sum_probs=28.9

Q ss_pred             ccccc--ccceeeEeeccccEEEEEEEEeccccceeecc
Q psy9934          82 FLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLAS  118 (158)
Q Consensus        82 ~L~~~--~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~  118 (158)
                      ||..+  .+.+|.|-|.||-..+|.+.|||+|.=|.=++
T Consensus        11 fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~VlL~~~   49 (77)
T COG1923          11 FLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVLLKNT   49 (77)
T ss_pred             HHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEEEEcC
Confidence            44443  35589999999999999999999997655333

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

Probab=89.42  E-value=0.84  Score=30.78  Aligned_cols=40  Identities=33%  Similarity=0.381  Sum_probs=30.5

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEEe---CC-cEEEEEEeEecCc
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKLK---WG-HEYKGILVSTDGY   41 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l~---~g-~~~~G~L~~~D~~   41 (158)
                      |+|.-.-||   ..+..++|+.|.|+++   +| +.+.|.|.++|+-
T Consensus         6 SSPGl~RpL~~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~   52 (83)
T cd01734           6 SSPGAERPLKKEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD   52 (83)
T ss_pred             cCCCCCCcCCCHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence            555555555   4556669999999998   56 6899999999973

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

>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes []

Probab=88.50  E-value=0.57  Score=34.66  Aligned_cols=39  Identities=31%  Similarity=0.382  Sum_probs=26.9

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEEe----CCcEEEEEEeEecC
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKLK----WGHEYKGILVSTDG   40 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l~----~g~~~~G~L~~~D~   40 (158)
                      |+|.-.-|+   ..+..++|+.|.|+++    +.+++.|+|.++|+
T Consensus        68 SSPG~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~  113 (141)
T PF02576_consen   68 SSPGIDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE  113 (141)
T ss_dssp             E--SSSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred             eCCCCCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence            566666666   5778889999999994    55799999999997

; PDB: 1IB8_A.

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

Probab=87.49  E-value=1.2  Score=28.70  Aligned_cols=35  Identities=17%  Similarity=0.267  Sum_probs=30.0

Q ss_pred             ccceeeEeeccccEEEEEEEEeccccceeecceEE
Q psy9934          87 TGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEE  121 (158)
Q Consensus        87 ~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e  121 (158)
                      +|..|.+++..|.+++|.+.+||.-.++..-.|.+
T Consensus         5 iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s   39 (61)
T cd01735           5 VGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS   39 (61)
T ss_pred             cccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence            58899999999999999999999888877665544

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.

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

Probab=87.35  E-value=1.3  Score=29.07  Aligned_cols=57  Identities=26%  Similarity=0.450  Sum_probs=41.1

Q ss_pred             CCCC--CCcccccccceeeEeeccccEEEEEEEEec-cccceeecceEEEecCeeeeecCcEEEeeCcEEEEEe
Q psy9934          76 PCNP--KPFLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        76 p~dP--~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      ..||  ...|++++|+++.|.+..|.. +|+|.+.. +|.  +|+.+     +      ..+|||=..|++|.|
T Consensus         7 ~vdpyvyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~~-----~------~~~~IR~~~IV~v~p   66 (66)
T PF10842_consen    7 LVDPYVYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEEN-----G------TPFFIRIAQIVWVMP   66 (66)
T ss_pred             ccCHHHHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEeC-----C------cEEEEEeeeEEEEcC
Confidence            3455  356889999999999977765 99999886 333  33222     1      467899999988754

>PRK14642 hypothetical protein; Provisional

Probab=86.90  E-value=1.2  Score=35.23  Aligned_cols=44  Identities=20%  Similarity=0.297  Sum_probs=32.9

Q ss_pred             CCCCCCCchHH---HhhcCCCEEEEEEe-------------CCcEEEEEEeEecCcceeEE
Q psy9934           2 STPLPCNPKPF---LNLLTGKSVICKLK-------------WGHEYKGILVSTDGYMNCQL   46 (158)
Q Consensus         2 ~~~~~~~p~~~---L~~~~~k~V~V~l~-------------~g~~~~G~L~~~D~~mNlvL   46 (158)
                      |+|.-.-||..   +..++|+.|.|+|+             +.+.++|+|.++|+. ++.|
T Consensus        81 SSPGldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         81 SSPGIDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            45555555544   55569999999998             779999999999964 3444

>PRK14640 hypothetical protein; Provisional

Probab=86.86  E-value=1.2  Score=33.57  Aligned_cols=45  Identities=20%  Similarity=0.310  Sum_probs=33.3

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEE----eCCcEEEEEEeEecCcceeEEc
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKL----KWGHEYKGILVSTDGYMNCQLA   47 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~mNlvL~   47 (158)
                      |+|.-.-|+   ..+..++|+.|.|++    .+.+.+.|+|.++|+. ++.|.
T Consensus        78 SSPGl~RpL~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~  129 (152)
T PRK14640         78 SSPGLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT  129 (152)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence            555444454   456677999999999    5679999999999974 35543

>PRK14633 hypothetical protein; Provisional

Probab=86.78  E-value=1.3  Score=33.46  Aligned_cols=45  Identities=24%  Similarity=0.214  Sum_probs=33.0

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEEe----CCcEEEEEEeEecCcceeEEc
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKLK----WGHEYKGILVSTDGYMNCQLA   47 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l~----~g~~~~G~L~~~D~~mNlvL~   47 (158)
                      |+|.-.-||   ..+..++|++|.|+++    +.+++.|+|.++++. ++.|.
T Consensus        75 SSPGldRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~  126 (150)
T PRK14633         75 SSPGMNRQIFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN  126 (150)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence            555555555   4556669999999994    679999999999974 45553

>PRK14645 hypothetical protein; Provisional

Probab=86.74  E-value=1.2  Score=33.91  Aligned_cols=43  Identities=16%  Similarity=0.277  Sum_probs=32.0

Q ss_pred             CCCCCCCchH---HHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEE
Q psy9934           2 STPLPCNPKP---FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL   46 (158)
Q Consensus         2 ~~~~~~~p~~---~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL   46 (158)
                      |+|...-||.   .+..++|++|.|.+ +++++.|+|.++|+.. +.|
T Consensus        83 SSPGldRpL~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~~-i~l  128 (154)
T PRK14645         83 ESPGPKRPLFTARHFERFAGLKAKVRG-PGENFTGRIKAVSGDQ-VTF  128 (154)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCCE-EEE
Confidence            5565555554   55666999999986 7899999999999743 444

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

Probab=86.68  E-value=3.1  Score=27.27  Aligned_cols=51  Identities=24%  Similarity=0.311  Sum_probs=36.8

Q ss_pred             HHHhhcCCCEEEEEEeCCcEEEEEEeEec-CcceeEEceeeEEEeccceecceeEEEEecCCCCCC
Q psy9934          11 PFLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus        11 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~   75 (158)
                      ..|++++|++|.|++..|.. +|+|.++- +|.  +|+..           -...|||=..|..+.
T Consensus        14 q~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~~-----------~~~~~IR~~~IV~v~   65 (66)
T PF10842_consen   14 QTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEEN-----------GTPFFIRIAQIVWVM   65 (66)
T ss_pred             HHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEeC-----------CcEEEEEeeeEEEEc
Confidence            56899999999999987765 99999987 443  44432           134677777666554

>PRK14638 hypothetical protein; Provisional

Probab=84.43  E-value=1.2  Score=33.72  Aligned_cols=35  Identities=20%  Similarity=0.068  Sum_probs=28.5

Q ss_pred             cccccccceeeEeeccccEEEEEEEEeccccceeec
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA  117 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~  117 (158)
                      -+..++|+.|.|++++++.++|+|.++|+- ++.|.
T Consensus        94 ~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         94 DYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             HHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            455788999999999999999999999963 34443

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.34  E-value=2.7  Score=31.99  Aligned_cols=44  Identities=27%  Similarity=0.443  Sum_probs=34.5

Q ss_pred             CCCC---CCCchHHHhhcCCCEEEEEE----eCCcEEEEEEeEecCcceeEE
Q psy9934           2 STPL---PCNPKPFLNLLTGKSVICKL----KWGHEYKGILVSTDGYMNCQL   46 (158)
Q Consensus         2 ~~~~---~~~p~~~L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~mNlvL   46 (158)
                      |+|.   |-.-.+.+..++|+.|.|+|    .+.+.+.|+|.++|+-. +++
T Consensus        80 SSPGldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~  130 (153)
T COG0779          80 SSPGLDRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL  130 (153)
T ss_pred             eCCCCCCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence            4554   33445677778999999999    78999999999999776 444

>PRK14634 hypothetical protein; Provisional

Probab=83.19  E-value=2.4  Score=32.18  Aligned_cols=44  Identities=16%  Similarity=0.169  Sum_probs=32.2

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEEeCC----cEEEEEEeEecCcceeEE
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKLKWG----HEYKGILVSTDGYMNCQL   46 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l~~g----~~~~G~L~~~D~~mNlvL   46 (158)
                      |+|...-||   ..+..++|++|.|++++.    +.+.|+|.++|+- ++.|
T Consensus        81 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l  131 (155)
T PRK14634         81 SSPGIGDQLSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI  131 (155)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence            555444454   456667999999999743    8999999999963 3544

>PRK14636 hypothetical protein; Provisional

Probab=82.82  E-value=2.4  Score=32.91  Aligned_cols=44  Identities=23%  Similarity=0.277  Sum_probs=32.1

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEEe---CC-cEEEEEEeEecCcceeEE
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKLK---WG-HEYKGILVSTDGYMNCQL   46 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l~---~g-~~~~G~L~~~D~~mNlvL   46 (158)
                      |+|.-.-|+   ..+..++|++|.|+++   +| +++.|+|.++|+- ++.|
T Consensus        79 SSPGldRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         79 SSPGIDRPLTRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            455444444   4566779999999998   55 7999999999863 3444

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=82.15  E-value=2.6  Score=31.72  Aligned_cols=39  Identities=31%  Similarity=0.462  Sum_probs=31.0

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEE----eCCcEEEEEEeEecC
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKL----KWGHEYKGILVSTDG   40 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l----~~g~~~~G~L~~~D~   40 (158)
                      |+|.-.-|+   ..+..++|+.|.|++    .+++.+.|+|.++|+
T Consensus        79 SSPGi~RpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         79 SSPGLDRPLKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence            556555554   557777999999997    567999999999997

>PRK14632 hypothetical protein; Provisional

Probab=81.87  E-value=2.8  Score=32.32  Aligned_cols=45  Identities=20%  Similarity=0.283  Sum_probs=33.0

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEEeC-------CcEEEEEEeEecCcceeEEc
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKLKW-------GHEYKGILVSTDGYMNCQLA   47 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l~~-------g~~~~G~L~~~D~~mNlvL~   47 (158)
                      |+|.-.-||   ..+..++|+.|.|++++       .+++.|+|.++|+- ++.|.
T Consensus        79 SSPGldRpL~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         79 SSPGLERPFFRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            455444444   45667799999999986       58999999999953 45543

>PRK14647 hypothetical protein; Provisional

Probab=81.57  E-value=3.1  Score=31.64  Aligned_cols=39  Identities=18%  Similarity=0.112  Sum_probs=30.1

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEEe---------CCcEEEEEEeEecC
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKLK---------WGHEYKGILVSTDG   40 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l~---------~g~~~~G~L~~~D~   40 (158)
                      |+|.-.-||   ..+..++|++|.|+++         +.+++.|+|.++|.
T Consensus        80 SSPG~~RpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~  130 (159)
T PRK14647         80 SSPGLDRPLKKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD  130 (159)
T ss_pred             cCCCCCCcCCCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence            556545554   4566679999999996         35999999999995

>PRK02001 hypothetical protein; Validated

Probab=80.95  E-value=1.9  Score=32.72  Aligned_cols=35  Identities=23%  Similarity=0.211  Sum_probs=28.5

Q ss_pred             CcccccccceeeEeeccccEEEEEEEEeccccceee
Q psy9934          81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL  116 (158)
Q Consensus        81 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL  116 (158)
                      .-+..++|+.|.|++.+++.+.|+|.++|+- ++.|
T Consensus        83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l  117 (152)
T PRK02001         83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL  117 (152)
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence            3456788999999999999999999999964 3444

>PRK14639 hypothetical protein; Provisional

Probab=80.78  E-value=2  Score=32.09  Aligned_cols=35  Identities=23%  Similarity=0.256  Sum_probs=28.8

Q ss_pred             CcccccccceeeEeeccccEEEEEEEEeccccceee
Q psy9934          81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL  116 (158)
Q Consensus        81 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL  116 (158)
                      .-+....|+.|.|++.+++.+.|+|.++|+ -++.|
T Consensus        81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~-~~i~l  115 (140)
T PRK14639         81 EHFAKSIGELVKITTNEKEKFEGKIVSVDD-ENITL  115 (140)
T ss_pred             HHHHHhCCCEEEEEECCCcEEEEEEEEEeC-CEEEE
Confidence            345678899999999999999999999997 34444

>PRK14646 hypothetical protein; Provisional

Probab=80.01  E-value=3.8  Score=31.08  Aligned_cols=45  Identities=13%  Similarity=0.060  Sum_probs=32.9

Q ss_pred             CCCCCCCch---HHHhhcCCCEEEEEEeCC----cEEEEEEeEecCcceeEEc
Q psy9934           2 STPLPCNPK---PFLNLLTGKSVICKLKWG----HEYKGILVSTDGYMNCQLA   47 (158)
Q Consensus         2 ~~~~~~~p~---~~L~~~~~k~V~V~l~~g----~~~~G~L~~~D~~mNlvL~   47 (158)
                      |+|.-.-||   ..+..++|++|.|++++.    +.+.|+|.++|+- ++.|.
T Consensus        81 SSPGldRpL~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~  132 (155)
T PRK14646         81 SSQGVSDELTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN  132 (155)
T ss_pred             cCCCCCCcCCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            555444454   456677999999999753    7889999999974 45553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	158
3cw1_F	86	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		9e-27
1n9r_A	93	Crystal Structure Of A Heptameric Ring Complex Of Y		6e-17
1n9s_A	93	Crystal Structure Of Yeast Smf In Spacegroup P43212		3e-16
3swn_B	77	Structure Of The Lsm657 Complex: An Assembly Interm		9e-13
4emk_B	75	Crystal Structure Of Splsm567 Length = 75		1e-11
1loj_A	87	Crystal Structure Of A Methanobacterial Sm-Like Arc		2e-09
1jbm_A	86	Heptameric Crystal Structure Of Mth649, An Sm-Like		2e-09
1jri_A	85	The Crystal Structure Of An Sm-Like Archaeal Protei		2e-09
1i81_A	83	Crystal Structure Of A Heptameric Lsm Protein From		2e-09
1i8f_A	81	The Crystal Structure Of A Heptameric Archaeal Sm P		1e-07
1i5l_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm1) Fr		1e-07
1h64_1	75	Crystal Structure Of The Sm-Related Protein Of P. A		3e-06
1m8v_A	77	Structure Of Pyrococcus Abyssii Sm Protein In Compl		3e-06
1th7_A	81	Crystal Structure Of An Archaeal Sm Protein From Su		3e-05

>pdb|3CW1|F Chain F, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 86

Iteration: 1
 Score =  115 bits (288), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 55/71 (77%), Positives = 59/71 (83%)
Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct: 3   LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62
Query: 135 LIRCNNILYIR 145
           LIRCNN+LYIR
Sbjct: 63  LIRCNNVLYIR 73

>pdb|1N9R|A Chain A, Crystal Structure Of A Heptameric Ring Complex Of Yeast Smf In Spacegroup P4122 Length = 93

Iteration: 1
 Score = 83.2 bits (204), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 42/80 (52%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 67  RSLTMSTPLPCNPKPFLNLLTGKSVICKLKWGH-EYKGILVSTDGYMNCQLASTEEIIDG 125
            S  +S   P NPKPFL  L    V  KLK+   EY+G LVSTD Y N QL   EE + G
Sbjct: 10  ESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG 69
Query: 126 HCTGKLGEVLIRCNNILYIR 145
              G LGE+ IRCNN+LYIR
Sbjct: 70  VSHGTLGEIFIRCNNVLYIR 89

>pdb|1N9S|A Chain A, Crystal Structure Of Yeast Smf In Spacegroup P43212 Length = 93

Iteration: 1
 Score = 80.9 bits (198), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 41/79 (51%), Positives = 47/79 (59%), Gaps = 1/79 (1%)
Query: 68  SLTMSTPLPCNPKPFLNLLTGKSVICKLKWGH-EYKGILVSTDGYMNCQLASTEEIIDGH 126
           S  +S   P NPKPFL  L    V  KLK+   EY+G LVSTD Y N QL   EE + G 
Sbjct: 11  SSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGV 70
Query: 127 CTGKLGEVLIRCNNILYIR 145
             G LGE+ IR NN+LYIR
Sbjct: 71  SHGTLGEIFIRSNNVLYIR 89

>pdb|3SWN|B Chain B, Structure Of The Lsm657 Complex: An Assembly Intermediate Of The Lsm1 7 And Lsm2 8 Rings Length = 77

Iteration: 1
 Score = 69.3 bits (168), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 32/70 (45%), Positives = 43/70 (61%)
Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           +  +P  FLN + GK V+ +L  G +YKGIL   DGYMN  L  TEE ++G  T   G+ 
Sbjct: 3   MDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDA 62
Query: 135 LIRCNNILYI 144
            IR NN+LY+
Sbjct: 63  FIRGNNVLYV 72

>pdb|4EMK|B Chain B, Crystal Structure Of Splsm567 Length = 75

Iteration: 1
 Score = 65.9 bits (159), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/69 (44%), Positives = 41/69 (59%)
Query: 76  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 135
             +P  FLN + GK V+ +L  G +YKGIL   DGY N  L  TEE ++G  T   G+  
Sbjct: 2   DSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYXNLALERTEEYVNGKKTNVYGDAF 61
Query: 136 IRCNNILYI 144
           IR NN+LY+
Sbjct: 62  IRGNNVLYV 70

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)
Query: 91  VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
           VI KLK   E++G+L S D +MN  L   EE+ DG  T +LG VLIR +NI+YI
Sbjct: 26  VIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYI 79

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)
Query: 91  VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
           VI KLK   E++G+L S D +MN  L   EE+ DG  T +LG VLIR +NI+YI
Sbjct: 26  VIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYI 79

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)
Query: 91  VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
           VI KLK   E++G+L S D +MN  L   EE+ DG  T +LG VLIR +NI+YI
Sbjct: 26  VIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYI 79

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)
Query: 91  VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
           VI KLK   E++G+L S D +MN  L   EE+ DG  T +LG VLIR +NI+YI
Sbjct: 28  VIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYI 81

>pdb|1I8F|A Chain A, The Crystal Structure Of A Heptameric Archaeal Sm Protein: Implications For The Eukaryotic Snrnp Core Length = 81

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 88  GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
           GK V+ KL+  HE +GIL S D ++N  L   EEIIDG+   K G +++R  N+L+I
Sbjct: 21  GKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVY-KRGTMVVRGENVLFI 76

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 38/70 (54%)
Query: 75  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 134
           +P  P   LN      VI +LK G E++G L   D +MN  L   EEI +G    K+G V
Sbjct: 1   MPPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSV 60
Query: 135 LIRCNNILYI 144
           +IR + ++++
Sbjct: 61  VIRGDTVVFV 70

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 34/56 (60%)
Query: 89  KSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
           K V+  LK G E++G L+  D ++N  LA  E I DG    + G+++IR +N+L I
Sbjct: 15  KDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAI 70

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 34/56 (60%)
Query: 89  KSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
           K V+  LK G E++G L+  D ++N  LA  E I DG    + G+++IR +N+L I
Sbjct: 17  KDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAI 72

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 33/54 (61%)
Query: 91  VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
           V+ KLK   E +G+L S D +MN  L+ +EEI       KLG ++IR +N++ I
Sbjct: 22  VLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILI 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	158
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	5e-36
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	9e-25
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	1e-33
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	4e-25
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	3e-32
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	3e-24
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	1e-29
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	3e-22
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	3e-29
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	8e-23
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	4e-28
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	5e-21
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	6e-28
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	2e-22
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	1e-26
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	8e-21
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	1e-26
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	5e-19
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	3e-26
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	3e-20
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	4e-20
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	5e-15
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	5e-20
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	2e-15
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	5e-20
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	2e-14
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	2e-17
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	3e-13
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	6e-11
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	2e-07
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	6e-11
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	8e-06
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	5e-10
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	4e-07
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	1e-08
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	1e-05
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	3e-08
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	5e-05
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	1e-06
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	7e-05
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	6e-05

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Length = 86

 Score =  119 bits (299), Expect = 5e-36
 Identities = 66/88 (75%), Positives = 72/88 (81%), Gaps = 2/88 (2%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           MS PL  NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G 
Sbjct: 1   MSLPL--NPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGH 58

Query: 131 LGEVLIRCNNILYIRGAEEGDEEGEMRE 158
           LGEVLIRCNN+LYIRG EE +E+GEMRE
Sbjct: 59  LGEVLIRCNNVLYIRGVEEEEEDGEMRE 86

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Length = 86

 Score = 90.2 bits (224), Expect = 9e-25
 Identities = 50/67 (74%), Positives = 53/67 (79%), Gaps = 2/67 (2%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          MS PL  NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G 
Sbjct: 1  MSLPL--NPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGH 58

Query: 61 LGEVLIR 67
          LGEVLIR
Sbjct: 59 LGEVLIR 65

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Length = 93

 Score =  113 bits (284), Expect = 1e-33
 Identities = 42/83 (50%), Positives = 48/83 (57%), Gaps = 1/83 (1%)

Query: 68  SLTMSTPLPCNPKPFLNLLTGKSVICKLKW-GHEYKGILVSTDGYMNCQLASTEEIIDGH 126
           S  +S   P NPKPFL  L    V  KLK+   EY+G LVSTD Y N QL   EE + G 
Sbjct: 11  SSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGV 70

Query: 127 CTGKLGEVLIRCNNILYIRGAEE 149
             G LGE+ IRCNN+LYIR    
Sbjct: 71  SHGTLGEIFIRCNNVLYIRELPN 93

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Length = 93

 Score = 91.4 bits (227), Expect = 4e-25
 Identities = 34/68 (50%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKW-GHEYKGILVSTDGYMNCQLASTEEIIDGHCTG 59
          +S   P NPKPFL  L    V  KLK+   EY+G LVSTD Y N QL   EE + G   G
Sbjct: 14 ISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHG 73

Query: 60 KLGEVLIR 67
           LGE+ IR
Sbjct: 74 TLGEIFIR 81

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Length = 75

 Score =  108 bits (273), Expect = 3e-32
 Identities = 32/74 (43%), Positives = 44/74 (59%)

Query: 76  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 135
             +P  FLN + GK V+ +L  G +YKGIL   DGYMN  L  TEE ++G  T   G+  
Sbjct: 2   DSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAF 61

Query: 136 IRCNNILYIRGAEE 149
           IR NN+LY+   ++
Sbjct: 62  IRGNNVLYVSALDD 75

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Length = 75

 Score = 88.5 bits (220), Expect = 3e-24
 Identities = 28/62 (45%), Positives = 36/62 (58%)

Query: 6  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 65
            +P  FLN + GK V+ +L  G +YKGIL   DGYMN  L  TEE ++G  T   G+  
Sbjct: 2  DSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAF 61

Query: 66 IR 67
          IR
Sbjct: 62 IR 63

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

 Score =  102 bits (256), Expect = 1e-29
 Identities = 25/72 (34%), Positives = 39/72 (54%)

Query: 78  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 137
            P   ++    K V+  LK G E++G L+  D ++N  LA  E I DG    + G+++IR
Sbjct: 4   RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIR 63

Query: 138 CNNILYIRGAEE 149
            +N+L I   EE
Sbjct: 64  GDNVLAISPTEE 75

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

 Score = 83.5 bits (207), Expect = 3e-22
 Identities = 20/60 (33%), Positives = 32/60 (53%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
           P   ++    K V+  LK G E++G L+  D ++N  LA  E I DG    + G+++IR
Sbjct: 4  RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIR 63

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Length = 77

 Score =  101 bits (254), Expect = 3e-29
 Identities = 27/75 (36%), Positives = 39/75 (52%)

Query: 76  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 135
           P  P   LN      VI +LK G E++G L   D +MN  L   EEI +G    K+G V+
Sbjct: 2   PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVV 61

Query: 136 IRCNNILYIRGAEEG 150
           IR + ++++  A  G
Sbjct: 62  IRGDTVVFVSPAPGG 76

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Length = 77

 Score = 85.0 bits (211), Expect = 8e-23
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 6  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 65
          P  P   LN      VI +LK G E++G L   D +MN  L   EEI +G    K+G V+
Sbjct: 2  PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVV 61

Query: 66 IR--SLTMSTPLP 76
          IR  ++   +P P
Sbjct: 62 IRGDTVVFVSPAP 74

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Length = 105

 Score = 99.4 bits (248), Expect = 4e-28
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 1/79 (1%)

Query: 72  STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLAS-TEEIIDGHCTGK 130
            +  P  P   LN   G+ ++ +LK G  + G L + D YMN  L      + DG    +
Sbjct: 10  HSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFR 69

Query: 131 LGEVLIRCNNILYIRGAEE 149
           L E  IR NNI Y+R  +E
Sbjct: 70  LPECYIRGNNIKYLRIQDE 88

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Length = 105

 Score = 81.3 bits (201), Expect = 5e-21
 Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 2  STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLAS-TEEIIDGHCTGK 60
           +  P  P   LN   G+ ++ +LK G  + G L + D YMN  L      + DG    +
Sbjct: 10 HSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFR 69

Query: 61 LGEVLIR 67
          L E  IR
Sbjct: 70 LPECYIR 76

>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Length = 83

 Score = 98.2 bits (245), Expect = 6e-28
 Identities = 30/77 (38%), Positives = 40/77 (51%)

Query: 68  SLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHC 127
            ++        P   L       VI KLK   E++G+L S D +MN  L   EE+ DG  
Sbjct: 5   DVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEV 64

Query: 128 TGKLGEVLIRCNNILYI 144
           T +LG VLIR +NI+YI
Sbjct: 65  TRRLGTVLIRGDNIVYI 81

>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Length = 83

 Score = 83.9 bits (208), Expect = 2e-22
 Identities = 26/66 (39%), Positives = 32/66 (48%)

Query: 2  STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKL 61
                 P   L       VI KLK   E++G+L S D +MN  L   EE+ DG  T +L
Sbjct: 9  QRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRL 68

Query: 62 GEVLIR 67
          G VLIR
Sbjct: 69 GTVLIR 74

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Length = 81

 Score = 94.7 bits (236), Expect = 1e-26
 Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 70  TMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTG 129
            M+          L       V+ KLK   E +G+L S D +MN  L+ +EEI       
Sbjct: 2   AMNFL-AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGK 60

Query: 130 KLGEVLIRCNNILYIRGAE 148
           KLG ++IR +N++ I   +
Sbjct: 61  KLGTIVIRGDNVILISPLQ 79

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Length = 81

 Score = 80.0 bits (198), Expect = 8e-21
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          M+          L       V+ KLK   E +G+L S D +MN  L+ +EEI       K
Sbjct: 3  MNFL-AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKK 61

Query: 61 LGEVLIR--SLTMSTPL 75
          LG ++IR  ++ + +PL
Sbjct: 62 LGTIVIRGDNVILISPL 78

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Length = 77

 Score = 94.7 bits (236), Expect = 1e-26
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 78  NPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLI 136
            P   +  + GK +  ++K   ++  G L   D YMN  L +  E         LGE+++
Sbjct: 5   LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVL 64

Query: 137 RCNNILYIRGAEE 149
           R NN++ I+  EE
Sbjct: 65  RGNNVVLIQPQEE 77

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Length = 77

 Score = 75.4 bits (186), Expect = 5e-19
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 8  NPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLI 66
           P   +  + GK +  ++K   ++  G L   D YMN  L +  E         LGE+++
Sbjct: 5  LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVL 64

Query: 67 R 67
          R
Sbjct: 65 R 65

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Length = 81

 Score = 94.0 bits (234), Expect = 3e-26
 Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 4/81 (4%)

Query: 71  MST---PLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHC 127
           M++            L    GK V+ KL+  HE +GIL S D ++N  L   EEIIDG+ 
Sbjct: 1   MASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNV 60

Query: 128 TGKLGEVLIRCNNILYIRGAE 148
             K G +++R  N+L+I    
Sbjct: 61  Y-KRGTMVVRGENVLFISPVP 80

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Length = 81

 Score = 78.6 bits (194), Expect = 3e-20
 Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 1  MST---PLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHC 57
          M++            L    GK V+ KL+  HE +GIL S D ++N  L   EEIIDG+ 
Sbjct: 1  MASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNV 60

Query: 58 TGKLGEVLIR 67
            K G +++R
Sbjct: 61 Y-KRGTMVVR 69

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

 Score = 79.6 bits (196), Expect = 4e-20
 Identities = 19/64 (29%), Positives = 30/64 (46%)

Query: 82  FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 141
           FL  L+ ++V  +LK G +  G +   D  MN  L + +  +      +L  + IR NNI
Sbjct: 6   FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65

Query: 142 LYIR 145
            Y  
Sbjct: 66  RYFI 69

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

 Score = 66.2 bits (161), Expect = 5e-15
 Identities = 15/56 (26%), Positives = 26/56 (46%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
          FL  L+ ++V  +LK G +  G +   D  MN  L + +  +      +L  + IR
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIR 61

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Length = 126

 Score = 79.3 bits (195), Expect = 5e-20
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           MS  +P      L+   G  V C+   G  Y+G L+  +  MNCQ+++           +
Sbjct: 1   MSIGVP---IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ 57

Query: 131 LGEVLIRCNNILYIRGAEE 149
           L +V IR + I ++   + 
Sbjct: 58  LEQVYIRGSKIRFLILPDM 76

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Length = 126

 Score = 67.4 bits (164), Expect = 2e-15
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          MS  +P      L+   G  V C+   G  Y+G L+  +  MNCQ+++           +
Sbjct: 1  MSIGVP---IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ 57

Query: 61 LGEVLIR 67
          L +V IR
Sbjct: 58 LEQVYIR 64

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Length = 75

 Score = 77.8 bits (192), Expect = 5e-20
 Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           MS  +P      L+   G  V C+   G  Y+G L+  +  MNCQ+++           +
Sbjct: 1   MSIGVP---IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ 57

Query: 131 LGEVLIRCNNILYIR 145
           L +V IR   I ++ 
Sbjct: 58  LEQVYIRGCKIRFLI 72

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Length = 75

 Score = 63.6 bits (155), Expect = 2e-14
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          MS  +P      L+   G  V C+   G  Y+G L+  +  MNCQ+++           +
Sbjct: 1  MSIGVP---IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ 57

Query: 61 LGEVLIR 67
          L +V IR
Sbjct: 58 LEQVYIR 64

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Length = 76

 Score = 71.2 bits (175), Expect = 2e-17
 Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 71  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
           MS   P    P L     K +  KL  G   +GIL   D +MN  +    E+        
Sbjct: 1   MSKAHP----PELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNN 56

Query: 131 LGEVLIRCNNILYIRGAE 148
           +G V+IR N+I+ +   E
Sbjct: 57  IGMVVIRGNSIIMLEALE 74

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Length = 76

 Score = 60.0 bits (146), Expect = 3e-13
 Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 4/67 (5%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          MS   P    P L     K +  KL  G   +GIL   D +MN  +    E+        
Sbjct: 1  MSKAHP----PELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNN 56

Query: 61 LGEVLIR 67
          +G V+IR
Sbjct: 57 IGMVVIR 63

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

 Score = 54.9 bits (132), Expect = 6e-11
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 3/76 (3%)

Query: 70  TMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCT 128
            MS  +   P   ++   G ++   +K   E+ G LV  D Y+N  L    E       T
Sbjct: 14  PMSMTIL--PLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVT 71

Query: 129 GKLGEVLIRCNNILYI 144
            K  E+L+  N +  +
Sbjct: 72  EKHSEMLLNGNGMCML 87

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

 Score = 45.2 bits (107), Expect = 2e-07
 Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 5/77 (6%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCTG 59
          MS  +   P   ++   G ++   +K   E+ G LV  D Y+N  L    E       T 
Sbjct: 15 MSMTIL--PLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTE 72

Query: 60 KLGEVLIR--SLTMSTP 74
          K  E+L+    + M  P
Sbjct: 73 KHSEMLLNGNGMCMLIP 89

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

 Score = 55.3 bits (133), Expect = 6e-11
 Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 8/78 (10%)

Query: 83  LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-------CTGKLGEVL 135
           L+    + +      G +  GIL   D  MN  L   EE +             KLG V+
Sbjct: 28  LSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVV 87

Query: 136 IRCNNILYIRGAEEGDEE 153
           +R   ++ I    +G EE
Sbjct: 88  VRGTTLVLI-APMDGSEE 104

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

 Score = 41.9 bits (98), Expect = 8e-06
 Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 7/62 (11%)

Query: 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-------CTGKLGEVL 65
          L+    + +      G +  GIL   D  MN  L   EE +             KLG V+
Sbjct: 28 LSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVV 87

Query: 66 IR 67
          +R
Sbjct: 88 VR 89

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

 Score = 52.5 bits (126), Expect = 5e-10
 Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 13/86 (15%)

Query: 72  STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTG-- 129
           S      P   + L   + V  KL+   E  G L + D ++N  L   EEI+        
Sbjct: 3   SAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEET 62

Query: 130 -----------KLGEVLIRCNNILYI 144
                          + +R ++++ I
Sbjct: 63  DKDKALKTIRKHYEMLFVRGDSVILI 88

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

 Score = 44.8 bits (106), Expect = 4e-07
 Identities = 15/62 (24%), Positives = 24/62 (38%)

Query: 2  STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKL 61
          S      P   + L   + V  KL+   E  G L + D ++N  L   EEI+      + 
Sbjct: 3  SAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEET 62

Query: 62 GE 63
           +
Sbjct: 63 DK 64

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96

 Score = 49.0 bits (117), Expect = 1e-08
 Identities = 18/88 (20%), Positives = 28/88 (31%), Gaps = 10/88 (11%)

Query: 78  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-------DGHCTGK 130
            P   L L   + V  KL+      G L + D + N  L+   E I             +
Sbjct: 10  TPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERR 69

Query: 131 LGEVLIRCNNILYIRGAEEGDEEGEMRE 158
              V IR + +  I       E+ +   
Sbjct: 70  CEMVFIRGDTVTLI---STPSEDDDGAV 94

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 16/67 (23%), Positives = 22/67 (32%), Gaps = 7/67 (10%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-------DGHCTGK 60
           P   L L   + V  KL+      G L + D + N  L+   E I             +
Sbjct: 10 TPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERR 69

Query: 61 LGEVLIR 67
             V IR
Sbjct: 70 CEMVFIR 76

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

 Score = 47.9 bits (114), Expect = 3e-08
 Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 82  FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCTGKLGEVLIRCNN 140
           +L   +   V    +     +G ++  D YMN  L   EEI        +LG ++++ +N
Sbjct: 24  YLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDN 83

Query: 141 ILYI 144
           I  +
Sbjct: 84  ITLL 87

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

 Score = 39.0 bits (91), Expect = 5e-05
 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 3/68 (4%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCTGKLGEVLIR--S 68
          +L   +   V    +     +G ++  D YMN  L   EEI        +LG ++++  +
Sbjct: 24 YLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDN 83

Query: 69 LTMSTPLP 76
          +T+   + 
Sbjct: 84 ITLLQSVS 91

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121

 Score = 44.2 bits (104), Expect = 1e-06
 Identities = 15/81 (18%), Positives = 28/81 (34%), Gaps = 15/81 (18%)

Query: 79  PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTG--------- 129
           P   ++   G  +   +K   E+ G+L   D Y+N  L   +E                 
Sbjct: 29  PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKL 88

Query: 130 ------KLGEVLIRCNNILYI 144
                 +L  +L+  NN+  +
Sbjct: 89  KRVMVNRLETILLSGNNVAML 109

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121

 Score = 39.2 bits (91), Expect = 7e-05
 Identities = 17/91 (18%), Positives = 31/91 (34%), Gaps = 18/91 (19%)

Query: 9   PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTG--------- 59
           P   ++   G  +   +K   E+ G+L   D Y+N  L   +E                 
Sbjct: 29  PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKL 88

Query: 60  ------KLGEVLIR--SLTMSTPLPCNPKPF 82
                 +L  +L+   ++ M  P   +P  F
Sbjct: 89  KRVMVNRLETILLSGNNVAMLVP-GGDPDSF 118

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

 Score = 39.1 bits (91), Expect = 6e-05
 Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 10/72 (13%)

Query: 83  LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLG 132
           +       + C L+ G  + G   + D +MN  L   +E            +      LG
Sbjct: 9   MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 68

Query: 133 EVLIRCNNILYI 144
            VL+R  N++ +
Sbjct: 69  LVLLRGENLVSM 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	158
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.94
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.9
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.89
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.89
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.88
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.88
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.88
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.88
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.88
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.88
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.88
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.88
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.87
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.87
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.87
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.87
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.87
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.87
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.87
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.87
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.87
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.87
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.87
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.86
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.86
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.86
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.86
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.85
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.85
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.84
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.84
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.84
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.84
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.83
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.83
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.83
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.83
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.83
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.83
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.82
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.81
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.79
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.78
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.78
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.77
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.75
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.75
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.72
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	98.83
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	98.68
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	97.14
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	96.96
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	96.9
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.86
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	96.78
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	96.64
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	96.61
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	95.75
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	95.74
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	95.63
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	95.51
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	95.26
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	95.17
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	94.97
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	94.92
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	94.89
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	94.76
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	94.59
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	94.27
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	93.86
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	93.8
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	92.32
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	91.69
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	91.48
1ycy_A	71	Conserved hypothetical protein; structural genomic	91.39
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	90.44
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	89.99
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	88.65
2qqr_A	118	JMJC domain-containing histone demethylation prote	87.97
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	84.88
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	83.91

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

Probab=99.94  E-value=2.5e-27  Score=162.89  Aligned_cols=84  Identities=76%  Similarity=1.229  Sum_probs=70.9

Q ss_pred             CCCCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCCCccc
Q psy9934          75 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDEEG  154 (158)
Q Consensus        75 ~p~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~~~~~  154 (158)
                      .|..|.++|+++++++|.|+|++|++|+|+|.|||+|||++|+||+|+.+++..+++|.++|||+||++|+++|++++.+
T Consensus         3 ~~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~IRG~nI~~i~~~d~~~~~~   82 (86)
T 3s6n_F            3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEEEEDG   82 (86)
T ss_dssp             CCCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEEECGGGEEEEEECC------
T ss_pred             cCcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEEEeCCeEEEEEeCCcccccc
Confidence            36789999999999999999999999999999999999999999999988877789999999999999999999999999


Q ss_pred             cccC
Q psy9934         155 EMRE  158 (158)
Q Consensus       155 ~~~~  158 (158)
                      ||||
T Consensus        83 ~~~~   86 (86)
T 3s6n_F           83 EMRE   86 (86)
T ss_dssp             ----
T ss_pred             cccC
Confidence            9997

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

Probab=99.90  E-value=2.5e-24  Score=147.85  Aligned_cols=77  Identities=65%  Similarity=0.944  Sum_probs=69.6

Q ss_pred             CCCCCCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCCC
Q psy9934           1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNP   79 (158)
Q Consensus         1 m~~~~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~dP   79 (158)
                      ||  +|..|+++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+|+.+++..+.+|.++|||++|.++.+.+.
T Consensus         1 ms--~~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~IRG~nI~~i~~~d~   77 (86)
T 3s6n_F            1 MS--LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEE   77 (86)
T ss_dssp             ----CCCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEEECGGGEEEEEECC-
T ss_pred             CC--cCcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEEEeCCeEEEEEeCCc
Confidence            77  589999999999999999999999999999999999999999999998877667899999999999999886553

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B

Probab=99.89  E-value=9.6e-24  Score=141.35  Aligned_cols=71  Identities=39%  Similarity=0.619  Sum_probs=67.0

Q ss_pred             CCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCC
Q psy9934           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPC   77 (158)
Q Consensus         7 ~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~   77 (158)
                      ..|+++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+|+.+++..+++|.++|||++|.++.+.
T Consensus         3 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~   73 (75)
T 4emk_B            3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVLYVSAL   73 (75)
T ss_dssp             SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEEEEGGGSSEEEEC
T ss_pred             CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEEEcCCeEEEEEec
Confidence            68999999999999999999999999999999999999999999998776778999999999999998754

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

Probab=99.89  E-value=1.3e-23  Score=143.22  Aligned_cols=76  Identities=37%  Similarity=0.412  Sum_probs=67.9

Q ss_pred             CCCC--CCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           1 MSTP--LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         1 m~~~--~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      ||+.  .+..|+++|.+++|++|+|+|+||++|.|+|.+||+|||++|+||+|++.++..+.+|.++|||++|.++.|
T Consensus         6 ms~~~~~~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A            6 VSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             ----CCCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             cccccccCcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEEECCCEEEEEEC
Confidence            5544  688999999999999999999999999999999999999999999999877678899999999999998754

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1

Probab=99.88  E-value=1.2e-23  Score=142.72  Aligned_cols=78  Identities=31%  Similarity=0.330  Sum_probs=70.0

Q ss_pred             CCCCCCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCCC
Q psy9934           1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNP   79 (158)
Q Consensus         1 m~~~~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~dP   79 (158)
                      ||+ .+..|+++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+|++.+...+.+|.++|||++|.++.+.++
T Consensus         3 m~~-~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   80 (81)
T 1th7_A            3 MNF-LAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             CCT-TCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEEC--
T ss_pred             ccc-cccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEEECCCEEEEEEecCC
Confidence            454 467899999999999999999999999999999999999999999999777678899999999999999876553

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B

Probab=99.88  E-value=1.1e-23  Score=141.11  Aligned_cols=73  Identities=44%  Similarity=0.773  Sum_probs=67.9

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      ..|.++|+++++++|.|+|+||++|+|+|.|||+|||++|+||+|+.+++..+++|.++|||+||++|++.|+
T Consensus         3 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   75 (75)
T 4emk_B            3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVLYVSALDD   75 (75)
T ss_dssp             SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEEEEGGGSSEEEEC--
T ss_pred             CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEEEcCCeEEEEEecCC
Confidence            4688999999999999999999999999999999999999999999888878899999999999999999864

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A*

Probab=99.88  E-value=3.6e-23  Score=138.97  Aligned_cols=74  Identities=35%  Similarity=0.501  Sum_probs=68.7

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCC
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEG  150 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~  150 (158)
                      ..|.++|+++++++|.|+|++|++|+|+|.|||+|||++|+||+|+..+...+++|.++|||+||++|+++++.
T Consensus         3 ~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~~   76 (77)
T 1i4k_A            3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSPAPGG   76 (77)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEECC--
T ss_pred             ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCcEeECCEEEECCCEEEEEEeCCCC
Confidence            36888999999999999999999999999999999999999999998887788999999999999999999875

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

Probab=99.88  E-value=3.5e-23  Score=138.48  Aligned_cols=73  Identities=34%  Similarity=0.493  Sum_probs=67.7

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      ..|.++|.++++++|.|+|+||++|+|+|.|||+|||++|+||+|+..+...+++|.++|||+||++|+++++
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~e   75 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTEE   75 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEEECCCEEEEEEeCCC
Confidence            3688899999999999999999999999999999999999999999888778899999999999999999874

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

Probab=99.88  E-value=9.5e-23  Score=141.89  Aligned_cols=75  Identities=53%  Similarity=0.877  Sum_probs=63.8

Q ss_pred             CCCCCCCCcccccccceeeEeeccc-cEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCC
Q psy9934          74 PLPCNPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE  148 (158)
Q Consensus        74 I~p~dP~~~L~~~~~k~V~V~L~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~  148 (158)
                      ..+..|.++|+++++++|.|+|++| ++|+|+|.|||+|||++|+||+|+.+++..+++|.++|||+||++|.+++
T Consensus        17 ~~~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~IRG~nI~~I~~~~   92 (93)
T 1n9r_A           17 MQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELP   92 (93)
T ss_dssp             ---------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECC
T ss_pred             cccCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEEEcCCeEEEEEeCC
Confidence            4467899999999999999999999 99999999999999999999999988888889999999999999999876

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

Probab=99.88  E-value=3.7e-23  Score=138.33  Aligned_cols=72  Identities=29%  Similarity=0.414  Sum_probs=66.8

Q ss_pred             CCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCC
Q psy9934           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus         7 ~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      ..|+++|++++|++|+|+|+||++|.|+|.|||+|||++|+||+|++.+...+.+|.++|||++|.++.+.+
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTE   74 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC-
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEEECCCEEEEEEeCC
Confidence            489999999999999999999999999999999999999999999977766889999999999999987543

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1

Probab=99.88  E-value=5.4e-23  Score=138.23  Aligned_cols=72  Identities=29%  Similarity=0.443  Sum_probs=67.3

Q ss_pred             CCCCcccccccceeeEeeccc-cEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          78 NPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        78 dP~~~L~~~~~k~V~V~L~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      .|.++|.++++++|.|+|++| ++|+|+|.|||+|||++|+||+|+..++..+++|.++|||+||++|+++|+
T Consensus         5 ~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~nI~~i~~~de   77 (77)
T 1ljo_A            5 LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQEE   77 (77)
T ss_dssp             CHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             chHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEEEeCCeEEEEEeCCC
Confidence            578899999999999999999 999999999999999999999999888888899999999999999999875

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1

Probab=99.88  E-value=6.8e-23  Score=137.29  Aligned_cols=71  Identities=24%  Similarity=0.383  Sum_probs=64.8

Q ss_pred             CCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         6 ~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      ...|++||+++.|++|+|+|++|++|+|+|.+||+|||++|+||+|+..+...+++|.++|||++|.++..
T Consensus         3 ~~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~IRG~nI~~i~l   73 (75)
T 1d3b_A            3 IGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLIL   73 (75)
T ss_dssp             -CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEE
T ss_pred             ccCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEEEeCCEEEEEEc
Confidence            46899999999999999999999999999999999999999999999644457899999999999998764

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A*

Probab=99.87  E-value=7.5e-23  Score=137.43  Aligned_cols=72  Identities=36%  Similarity=0.427  Sum_probs=67.3

Q ss_pred             CCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCC
Q psy9934           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus         7 ~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      ..|+++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+|++.+...+.+|.++|||++|.++.+.+
T Consensus         3 ~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d   74 (77)
T 1i4k_A            3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSPAP   74 (77)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEECC
T ss_pred             ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCcEeECCEEEECCCEEEEEEeCC
Confidence            479999999999999999999999999999999999999999999987766889999999999999987644

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A*

Probab=99.87  E-value=8.7e-23  Score=138.55  Aligned_cols=72  Identities=31%  Similarity=0.280  Sum_probs=66.1

Q ss_pred             CCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCC
Q psy9934           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPC   77 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~   77 (158)
                      .+..|+++|.++++++|+|+|+||++|.|+|.+||+|||++|+||+|+ +++..+.+|.++|||++|.++.+.
T Consensus         8 ~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~~~~lg~v~iRG~~I~~i~~~   79 (81)
T 1i8f_A            8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTMVVRGENVLFISPV   79 (81)
T ss_dssp             --CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETTEEEEEEEEEECGGGEEEEEEC
T ss_pred             cccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCCcccCCCEEEECCCEEEEEEeC
Confidence            468999999999999999999999999999999999999999999999 666688999999999999988754

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

Probab=99.87  E-value=4.8e-23  Score=138.29  Aligned_cols=72  Identities=24%  Similarity=0.285  Sum_probs=53.1

Q ss_pred             CchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCCC
Q psy9934           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNP   79 (158)
Q Consensus         8 ~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~dP   79 (158)
                      .|.++|++++|++|+|+|+||++|.|+|.|||+|||++|+||+|+..++..+.+|.++|||++|.++.|.++
T Consensus         4 ~~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            4 AHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             ----------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEEECSSSEEEEEC---
T ss_pred             cchHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEEECCCeEEEEEeccC
Confidence            377999999999999999999999999999999999999999999665567899999999999999987664

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1

Probab=99.87  E-value=1.1e-22  Score=136.77  Aligned_cols=72  Identities=24%  Similarity=0.340  Sum_probs=66.8

Q ss_pred             CCchHHHhhcCCCEEEEEEeCC-cEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCC
Q psy9934           7 CNPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus         7 ~~p~~~L~~~~~k~V~V~l~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      ..|+++|.++++++|+|+|+|| ++|.|+|.|||+|||++|+||+|+..++..+.+|.++|||++|.++.+.+
T Consensus         4 ~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~nI~~i~~~d   76 (77)
T 1ljo_A            4 VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQE   76 (77)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC-
T ss_pred             cchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEEEeCCeEEEEEeCC
Confidence            4799999999999999999999 99999999999999999999999987767889999999999999987643

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

Probab=99.87  E-value=1.7e-22  Score=135.62  Aligned_cols=72  Identities=28%  Similarity=0.391  Sum_probs=53.7

Q ss_pred             CCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        78 dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      .+.++|+++++++|.|+|+||++|+|+|.|||+|||++|+||+|+..+...+.+|.++|||+||++|++.|.
T Consensus         4 ~~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            4 AHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             ----------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEEECSSSEEEEEC---
T ss_pred             cchHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEEECCCeEEEEEeccC
Confidence            356899999999999999999999999999999999999999998766667899999999999999999874

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae}

Probab=99.87  E-value=1.4e-22  Score=141.77  Aligned_cols=76  Identities=25%  Similarity=0.286  Sum_probs=66.3

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEec-------CeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID-------GHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~-------~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      ..|.++|.++++++|.|+|++||+|.|+|.|||+||||+|+||+|+..       +...+.+|.++|||+||++|+++++
T Consensus         9 ~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d~   88 (96)
T 3bw1_A            9 ETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPSE   88 (96)
T ss_dssp             CCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC-
T ss_pred             hhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecCc
Confidence            357889999999999999999999999999999999999999999853       3456789999999999999999998


Q ss_pred             CCc
Q psy9934         150 GDE  152 (158)
Q Consensus       150 ~~~  152 (158)
                      +++
T Consensus        89 ~~d   91 (96)
T 3bw1_A           89 DDD   91 (96)
T ss_dssp             ---
T ss_pred             ccc
Confidence            865

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1

Probab=99.87  E-value=1.1e-22  Score=136.38  Aligned_cols=72  Identities=25%  Similarity=0.416  Sum_probs=66.8

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCC
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE  148 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~  148 (158)
                      ..|.++|+++.+++|.|+|++|++|+|+|.|||+|||++|+||+|+..+...+++|.++|||+||.+|..||
T Consensus         4 ~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            4 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             cCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEEEeCCEEEEEEcCC
Confidence            368889999999999999999999999999999999999999999965545789999999999999999986

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

Probab=99.87  E-value=1.4e-22  Score=141.26  Aligned_cols=74  Identities=23%  Similarity=0.279  Sum_probs=66.9

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEe-cCeeeeecCcEEEeeCcEEEEEeCCCC
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAEEG  150 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~~g~~~iRG~~I~~i~~~~~~  150 (158)
                      ..|.++|.++++++|+|+|++|++|+|+|.|||+||||+|+||+|+. +++..+++|.++|||+||++|++..+.
T Consensus        19 ~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG~nI~~i~p~~~p   93 (94)
T 4emk_A           19 ILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGNGMCMLIPGGKP   93 (94)
T ss_dssp             -CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECSTTEEEEEECC--
T ss_pred             ccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcCCEEEEEEeCCCC
Confidence            46788999999999999999999999999999999999999999997 666678999999999999999987553

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1

Probab=99.87  E-value=7.4e-23  Score=138.86  Aligned_cols=74  Identities=31%  Similarity=0.384  Sum_probs=68.2

Q ss_pred             CCCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          76 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        76 p~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      +..|.++|.++++++|.|+|+||++|+|+|.|||+|||++|+||+|+..+...+++|.++|||++|++|+++++
T Consensus         7 ~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   80 (81)
T 1th7_A            7 AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             CHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEEC--
T ss_pred             ccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEEECCCEEEEEEecCC
Confidence            45788999999999999999999999999999999999999999999877777899999999999999999875

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

Probab=99.87  E-value=2e-22  Score=140.50  Aligned_cols=73  Identities=25%  Similarity=0.319  Sum_probs=66.2

Q ss_pred             CCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEE-eccceecceeEEEEecCCCCCCCC
Q psy9934           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRSLTMSTPLPC   77 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~~~iRG~~i~~I~p~   77 (158)
                      ....|+++|.++++++|+|+|++|++|.|+|.|||+||||+|+||+|+. +++..+.+|.++|||++|.++.|.
T Consensus        17 ~~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG~nI~~i~p~   90 (94)
T 4emk_A           17 MTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGNGMCMLIPG   90 (94)
T ss_dssp             ---CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECSTTEEEEEEC
T ss_pred             ccccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcCCEEEEEEeC
Confidence            4678999999999999999999999999999999999999999999997 666688999999999999998864

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

Probab=99.87  E-value=9.1e-23  Score=141.98  Aligned_cols=74  Identities=45%  Similarity=0.657  Sum_probs=61.3

Q ss_pred             CCCCCchHHHhhcCCCEEEEEEeCC-cEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCC
Q psy9934           4 PLPCNPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPC   77 (158)
Q Consensus         4 ~~~~~p~~~L~~~~~k~V~V~l~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~   77 (158)
                      ..+..|+++|++++|++|+|+|+|| ++|.|+|.+||+|||++|+||+|+++++..+.+|.++|||++|.++.+.
T Consensus        17 ~~~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~IRG~nI~~I~~~   91 (93)
T 1n9r_A           17 MQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIREL   91 (93)
T ss_dssp             ---------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEEC
T ss_pred             cccCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEEEcCCeEEEEEeC
Confidence            3678999999999999999999999 9999999999999999999999998776778999999999999987643

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe}

Probab=99.86  E-value=3.8e-22  Score=141.65  Aligned_cols=77  Identities=35%  Similarity=0.501  Sum_probs=55.9

Q ss_pred             CCCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEe-cCeeeeecCcEEEeeCcEEEEEeCCCCCc
Q psy9934          76 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAEEGDE  152 (158)
Q Consensus        76 p~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~~g~~~iRG~~I~~i~~~~~~~~  152 (158)
                      |-.|.++|+++++++|.|+|++|++|+|+|.|||+||||+|+||+|+. +|+..+++|.++|||+||++|.++|+..+
T Consensus        14 ~~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG~nI~~I~~pd~l~d   91 (105)
T 4emh_A           14 PMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNIKYLRIQDEVLS   91 (105)
T ss_dssp             ------------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECGGGEEEEEC------
T ss_pred             CCcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeCCeEEEEecCHHHhh
Confidence            567899999999999999999999999999999999999999999984 56567899999999999999999998764

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

Probab=99.86  E-value=5.1e-22  Score=135.37  Aligned_cols=71  Identities=42%  Similarity=0.526  Sum_probs=67.7

Q ss_pred             CCCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEe
Q psy9934          76 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        76 p~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      +..|.++|.++++++|.|+|+||++|+|+|.|||+|||++|+||+|+..+...+.+|.++|||+||++|+|
T Consensus        13 ~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           13 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             TTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             CcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEEECCCEEEEEEC
Confidence            56889999999999999999999999999999999999999999999888788899999999999999975

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A*

Probab=99.86  E-value=2.7e-22  Score=136.12  Aligned_cols=73  Identities=33%  Similarity=0.363  Sum_probs=67.3

Q ss_pred             CCCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          76 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        76 p~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      +..|.++|.++++++|.|+|++|++|+|+|.|||+|||++|+||+|+ ++...+.+|.++|||+||++|+++++
T Consensus         9 ~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~~~~lg~v~iRG~~I~~i~~~dg   81 (81)
T 1i8f_A            9 FATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTMVVRGENVLFISPVPG   81 (81)
T ss_dssp             -CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETTEEEEEEEEEECGGGEEEEEECC-
T ss_pred             ccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCCcccCCCEEEECCCEEEEEEeCCC
Confidence            45788999999999999999999999999999999999999999999 66677899999999999999999874

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

Probab=99.86  E-value=5.7e-22  Score=137.11  Aligned_cols=77  Identities=19%  Similarity=0.214  Sum_probs=65.3

Q ss_pred             CCCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEe----------cCeeeeecCcEEEeeCcEEEEE
Q psy9934          76 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLGEVLIRCNNILYIR  145 (158)
Q Consensus        76 p~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~----------~~~~~~~~g~~~iRG~~I~~i~  145 (158)
                      +.+|.++|.++++++|.|+|++||+|.|+|.|||+||||+|+||+|+.          .+...+.+|.++|||+||++|+
T Consensus         2 ~~~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~   81 (91)
T 1d3b_B            2 TVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMT   81 (91)
T ss_dssp             -----CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEE
T ss_pred             CCChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEE
Confidence            457889999999999999999999999999999999999999999964          2345688999999999999999


Q ss_pred             eCCCCCc
Q psy9934         146 GAEEGDE  152 (158)
Q Consensus       146 ~~~~~~~  152 (158)
                      +++...+
T Consensus        82 ~~~~~~~   88 (91)
T 1d3b_B           82 VEGPPPK   88 (91)
T ss_dssp             EEECCC-
T ss_pred             cCCCCCC
Confidence            9887654

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

Probab=99.85  E-value=9e-22  Score=136.93  Aligned_cols=76  Identities=22%  Similarity=0.285  Sum_probs=63.6

Q ss_pred             CCCC-CCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEe-----c--------cceecceeEEE
Q psy9934           1 MSTP-LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID-----G--------HCTGKLGEVLI   66 (158)
Q Consensus         1 m~~~-~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~-----~--------~~~~~lg~~~i   66 (158)
                      ||+. +...|+++|+.++|++|+|+|+||++|.|+|.|||+||||+|+||+|++.     +        +..+.+|.++|
T Consensus         1 m~~~~~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~i   80 (93)
T 4emg_A            1 MESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFV   80 (93)
T ss_dssp             --------CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEE
T ss_pred             CCcccccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEE
Confidence            5543 56899999999999999999999999999999999999999999999964     2        13688999999


Q ss_pred             EecCCCCCCC
Q psy9934          67 RSLTMSTPLP   76 (158)
Q Consensus        67 RG~~i~~I~p   76 (158)
                      ||++|.++.|
T Consensus        81 RG~nVv~I~p   90 (93)
T 4emg_A           81 RGDSVILIAP   90 (93)
T ss_dssp             CGGGEEEEEC
T ss_pred             CCCeEEEEEe
Confidence            9999999876

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe}

Probab=99.85  E-value=4.6e-22  Score=141.20  Aligned_cols=74  Identities=28%  Similarity=0.387  Sum_probs=55.1

Q ss_pred             CCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEE-eccceecceeEEEEecCCCCCCCCC
Q psy9934           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      .|-+|++||++++|++|+|+|+||++|.|+|.+||.|||++|+||+|+. +++..+.+|.++|||++|.++.+++
T Consensus        13 ~~~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG~nI~~I~~pd   87 (105)
T 4emh_A           13 DPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNIKYLRIQD   87 (105)
T ss_dssp             -------------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECGGGEEEEEC--
T ss_pred             CCCcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeCCeEEEEecCH
Confidence            5778999999999999999999999999999999999999999999984 5555789999999999999988644

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

Probab=99.84  E-value=5.4e-22  Score=137.23  Aligned_cols=74  Identities=20%  Similarity=0.217  Sum_probs=62.2

Q ss_pred             CCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEE----------eccceecceeEEEEecCCCCCC
Q psy9934           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus         6 ~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~----------~~~~~~~lg~~~iRG~~i~~I~   75 (158)
                      +.+|.++|.+++|++|+|+|+|||+|.|+|.|||+|||++|+||+|++          .+...+.+|.++|||++|.++.
T Consensus         2 ~~~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~   81 (91)
T 1d3b_B            2 TVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMT   81 (91)
T ss_dssp             -----CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEE
T ss_pred             CCChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEE
Confidence            467899999999999999999999999999999999999999999974          2334688999999999999987


Q ss_pred             CCCC
Q psy9934          76 PCNP   79 (158)
Q Consensus        76 p~dP   79 (158)
                      +..|
T Consensus        82 ~~~~   85 (91)
T 1d3b_B           82 VEGP   85 (91)
T ss_dssp             EEEC
T ss_pred             cCCC
Confidence            6444

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae}

Probab=99.84  E-value=2.6e-21  Score=135.30  Aligned_cols=73  Identities=23%  Similarity=0.183  Sum_probs=66.1

Q ss_pred             CCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEe-------ccceecceeEEEEecCCCCCCCCC
Q psy9934           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID-------GHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus         6 ~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~-------~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      -..|+++|++++|++|+|+|+|||+|.|+|.|||+|||++|+||+|++.       ++..+.+|.++|||++|.++.+.+
T Consensus         8 ~~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d   87 (96)
T 3bw1_A            8 METPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPS   87 (96)
T ss_dssp             CCCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC
T ss_pred             hhhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecC
Confidence            3679999999999999999999999999999999999999999999964       234678999999999999988654

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

Probab=99.84  E-value=3.4e-21  Score=138.39  Aligned_cols=76  Identities=24%  Similarity=0.305  Sum_probs=57.4

Q ss_pred             CCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecC-------eeeeecCcEEEeeCcEEEEEeCCCC
Q psy9934          78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG-------HCTGKLGEVLIRCNNILYIRGAEEG  150 (158)
Q Consensus        78 dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------~~~~~~g~~~iRG~~I~~i~~~~~~  150 (158)
                      .|...|.++++++|.|+|++||+|.|+|.|||+||||+|+||+|+..+       ...+.+|.++|||+||++|+++|+.
T Consensus        23 e~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~  102 (113)
T 4emk_C           23 ESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDGS  102 (113)
T ss_dssp             ---------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC--
T ss_pred             chHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCcc
Confidence            455678999999999999999999999999999999999999998643       3468999999999999999999988


Q ss_pred             Ccc
Q psy9934         151 DEE  153 (158)
Q Consensus       151 ~~~  153 (158)
                      +|+
T Consensus       103 ee~  105 (113)
T 4emk_C          103 EEI  105 (113)
T ss_dssp             ---
T ss_pred             ccc
Confidence            864

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

Probab=99.84  E-value=2.9e-21  Score=139.94  Aligned_cols=73  Identities=21%  Similarity=0.220  Sum_probs=67.2

Q ss_pred             CchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCCCC
Q psy9934           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNPK   80 (158)
Q Consensus         8 ~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~dP~   80 (158)
                      .|++||+++++++|+|+|+||++|.|+|.+||+|||++|+||+|+..+.....++.+||||++|.++.+++..
T Consensus         2 ~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~~lg~v~IRG~nI~~I~~pd~l   74 (119)
T 1b34_A            2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSL   74 (119)
T ss_dssp             CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTC
T ss_pred             ChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEEEcCCeEEEEEecccc
Confidence            5999999999999999999999999999999999999999999996555578999999999999999876553

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A

Probab=99.83  E-value=1.4e-21  Score=141.92  Aligned_cols=76  Identities=18%  Similarity=0.269  Sum_probs=67.0

Q ss_pred             CCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEe----------ccc-----eecceeEEEEec
Q psy9934           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----------GHC-----TGKLGEVLIRSL   69 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----------~~~-----~~~lg~~~iRG~   69 (158)
                      ....|+++|.++++++|+|+|+|||+|.|+|.|||+||||+|+||+|++.          ++.     .+.+|.++|||+
T Consensus        25 ~~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~  104 (121)
T 2fwk_A           25 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGN  104 (121)
T ss_dssp             CCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGG
T ss_pred             cccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCC
Confidence            56799999999999999999999999999999999999999999999862          323     678999999999


Q ss_pred             CCCCCCCCCCC
Q psy9934          70 TMSTPLPCNPK   80 (158)
Q Consensus        70 ~i~~I~p~dP~   80 (158)
                      +|.++.+..|.
T Consensus       105 nVv~I~~~~~~  115 (121)
T 2fwk_A          105 NVAMLVPGGDP  115 (121)
T ss_dssp             GEEEEESSSCC
T ss_pred             EEEEEEecCCC
Confidence            99998875543

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

Probab=99.83  E-value=1e-21  Score=136.34  Aligned_cols=73  Identities=16%  Similarity=0.272  Sum_probs=66.6

Q ss_pred             CCCCchHHHhhcCCCEEEEEE----eCCcEEEEEEeEecCcceeEEceeeEEE-eccceecceeEEEEecCCCCCCCC
Q psy9934           5 LPCNPKPFLNLLTGKSVICKL----KWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRSLTMSTPLPC   77 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~~~iRG~~i~~I~p~   77 (158)
                      ....|+++|.++++++|+|++    ++|++|.|+|.|||+|||++|+||+|+. +++..+.+|.++|||++|.++.|.
T Consensus        13 ~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~nV~~i~~~   90 (92)
T 3s6n_E           13 VMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSV   90 (92)
T ss_dssp             -CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGGGEEEEEEC
T ss_pred             eccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCCEEEEEEeC
Confidence            377899999999999999999    9999999999999999999999999995 455678999999999999998754

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

Probab=99.83  E-value=6.7e-21  Score=132.49  Aligned_cols=71  Identities=23%  Similarity=0.331  Sum_probs=64.1

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEec-----C--------eeeeecCcEEEeeCcEEE
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID-----G--------HCTGKLGEVLIRCNNILY  143 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~-----~--------~~~~~~g~~~iRG~~I~~  143 (158)
                      ..|.++|+.+++++|.|+|++|++|+|+|.|||+||||+|+||+|+..     +        ...+.+|.++|||+||++
T Consensus         8 ~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nVv~   87 (93)
T 4emg_A            8 AEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVIL   87 (93)
T ss_dssp             -CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGEEE
T ss_pred             CCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeEEE
Confidence            468899999999999999999999999999999999999999999864     3        236889999999999999


Q ss_pred             EEeC
Q psy9934         144 IRGA  147 (158)
Q Consensus       144 i~~~  147 (158)
                      |+++
T Consensus        88 I~p~   91 (93)
T 4emg_A           88 IAPP   91 (93)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9985

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

Probab=99.83  E-value=2e-21  Score=134.89  Aligned_cols=73  Identities=19%  Similarity=0.335  Sum_probs=66.6

Q ss_pred             CCCCCCcccccccceeeEee----ccccEEEEEEEEeccccceeecceEEEe-cCeeeeecCcEEEeeCcEEEEEeCC
Q psy9934          76 PCNPKPFLNLLTGKSVICKL----KWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAE  148 (158)
Q Consensus        76 p~dP~~~L~~~~~k~V~V~L----~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~~g~~~iRG~~I~~i~~~~  148 (158)
                      +..|.++|.+++++++.|++    ++|++|+|+|.|||+||||+|+||+|+. +++..+++|.++|||+||++|++.+
T Consensus        14 m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~nV~~i~~~~   91 (92)
T 3s6n_E           14 MVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSVS   91 (92)
T ss_dssp             CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGGGEEEEEEC-
T ss_pred             ccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCCEEEEEEeCC
Confidence            45788999999999999998    9999999999999999999999999986 4556789999999999999999875

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

Probab=99.83  E-value=3.2e-21  Score=139.69  Aligned_cols=71  Identities=27%  Similarity=0.317  Sum_probs=66.9

Q ss_pred             CCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        79 P~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      |.++|+++++++|.|+|++|++|+|+|.+||+||||+|+||+|+..+....++|.+||||+||++|.++|+
T Consensus         3 p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~~lg~v~IRG~nI~~I~~pd~   73 (119)
T 1b34_A            3 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDS   73 (119)
T ss_dssp             HHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTT
T ss_pred             hHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEEEcCCeEEEEEeccc
Confidence            66789999999999999999999999999999999999999999776667899999999999999999987

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D

Probab=99.83  E-value=5.8e-21  Score=139.52  Aligned_cols=73  Identities=23%  Similarity=0.366  Sum_probs=65.9

Q ss_pred             CCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCC
Q psy9934           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus         6 ~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      ...|++||++++|++|+|+|+||++|+|+|.+||.|||++|+||+|+..+....+++.+||||++|.++.+++
T Consensus         3 ~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd   75 (126)
T 2y9a_D            3 IGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPD   75 (126)
T ss_dssp             -CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCS
T ss_pred             cccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEccc
Confidence            4689999999999999999999999999999999999999999999853334789999999999999987544

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A

Probab=99.82  E-value=4.4e-21  Score=139.35  Aligned_cols=78  Identities=21%  Similarity=0.296  Sum_probs=67.6

Q ss_pred             CCCCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEec----------Cee-----eeecCcEEEeeC
Q psy9934          75 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----------GHC-----TGKLGEVLIRCN  139 (158)
Q Consensus        75 ~p~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----------~~~-----~~~~g~~~iRG~  139 (158)
                      ....|..+|.++++++|+|+|++||+|+|+|.|||+||||+|+||+|+..          |..     .+.+|.++|||+
T Consensus        25 ~~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~  104 (121)
T 2fwk_A           25 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGN  104 (121)
T ss_dssp             CCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGG
T ss_pred             cccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCC
Confidence            34578899999999999999999999999999999999999999999862          323     678999999999


Q ss_pred             cEEEEEeCCCCCc
Q psy9934         140 NILYIRGAEEGDE  152 (158)
Q Consensus       140 ~I~~i~~~~~~~~  152 (158)
                      +|++|++.++..+
T Consensus       105 nVv~I~~~~~~~~  117 (121)
T 2fwk_A          105 NVAMLVPGGDPDS  117 (121)
T ss_dssp             GEEEEESSSCC--
T ss_pred             EEEEEEecCCCCC
Confidence            9999999888764

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D

Probab=99.81  E-value=1.9e-20  Score=136.78  Aligned_cols=75  Identities=24%  Similarity=0.385  Sum_probs=68.0

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCCC
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD  151 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~~  151 (158)
                      ..|.++|+++++++|.|+|++|++|+|+|.+||+|||++|+||+|+..+.+..+++.+||||+||.||.++|.-.
T Consensus         4 ~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd~l~   78 (126)
T 2y9a_D            4 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLK   78 (126)
T ss_dssp             CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCSSCS
T ss_pred             ccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEcccccc
Confidence            368899999999999999999999999999999999999999999864434689999999999999999887654

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

Probab=99.79  E-value=6.5e-20  Score=131.70  Aligned_cols=73  Identities=25%  Similarity=0.281  Sum_probs=56.2

Q ss_pred             CCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEec-------cceecceeEEEEecCCCCCCCCCC
Q psy9934           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG-------HCTGKLGEVLIRSLTMSTPLPCNP   79 (158)
Q Consensus         7 ~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------~~~~~lg~~~iRG~~i~~I~p~dP   79 (158)
                      ..|...|.++++++|+|+|+|||+|.|+|.|||.||||+|+||+|++..       ...+.+|.++|||++|.++.+.+.
T Consensus        22 ke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~  101 (113)
T 4emk_C           22 KESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDG  101 (113)
T ss_dssp             ----------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC-
T ss_pred             cchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCc
Confidence            4678899999999999999999999999999999999999999999542       347899999999999999887653

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

Probab=99.78  E-value=1.3e-19  Score=131.07  Aligned_cols=75  Identities=12%  Similarity=0.139  Sum_probs=63.9

Q ss_pred             CCCCCcccccc--cceeeEeeccccEEEEEEEEeccccceeecceEEEecCe--------------eeeecCcEEEeeCc
Q psy9934          77 CNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH--------------CTGKLGEVLIRCNN  140 (158)
Q Consensus        77 ~dP~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~--------------~~~~~g~~~iRG~~  140 (158)
                      ..|..+|..++  +++|.|+|++|++|.|+|.|||+||||+|+||+|+....              ..+.+|.+||||+|
T Consensus        26 ~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~n  105 (118)
T 1b34_B           26 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDS  105 (118)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGG
T ss_pred             cChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCCE
Confidence            46788999998  599999999999999999999999999999999985221              13569999999999


Q ss_pred             EEEEEeCCCCC
Q psy9934         141 ILYIRGAEEGD  151 (158)
Q Consensus       141 I~~i~~~~~~~  151 (158)
                      |++|++++...
T Consensus       106 Vv~I~~~~~~~  116 (118)
T 1b34_B          106 VIVVLRNPLIA  116 (118)
T ss_dssp             EEEEEECCCCC
T ss_pred             EEEEEeCchhh
Confidence            99999987643

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

Probab=99.78  E-value=1.6e-19  Score=130.58  Aligned_cols=72  Identities=14%  Similarity=0.140  Sum_probs=61.5

Q ss_pred             CCCchHHHhhcC--CCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEecc--------------ceecceeEEEEec
Q psy9934           6 PCNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH--------------CTGKLGEVLIRSL   69 (158)
Q Consensus         6 ~~~p~~~L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~--------------~~~~lg~~~iRG~   69 (158)
                      ...|+++|..++  +++|.|+|+||++|.|+|.|||+||||+|+||+|++...              ..+.+|.+||||+
T Consensus        25 ~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~  104 (118)
T 1b34_B           25 NTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGD  104 (118)
T ss_dssp             -CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGG
T ss_pred             ccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCC
Confidence            468999999999  599999999999999999999999999999999985221              1346999999999


Q ss_pred             CCCCCCCC
Q psy9934          70 TMSTPLPC   77 (158)
Q Consensus        70 ~i~~I~p~   77 (158)
                      +|.++.+.
T Consensus       105 nVv~I~~~  112 (118)
T 1b34_B          105 SVIVVLRN  112 (118)
T ss_dssp             GEEEEEEC
T ss_pred             EEEEEEeC
Confidence            99998754

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

Probab=99.77  E-value=4.5e-19  Score=140.46  Aligned_cols=73  Identities=21%  Similarity=0.220  Sum_probs=65.5

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEec----------CeeeeecCcEEEeeCcEEEEEe
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----------GHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----------~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      .++...|.++++++|+|+|+|||+|+|+|++||+||||+|+||+|+..          +++.+++|.+||||+||++|+.
T Consensus         3 v~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isv   82 (231)
T 3pgw_B            3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTV   82 (231)
T ss_pred             cCchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEe
Confidence            356788999999999999999999999999999999999999999852          2357899999999999999996


Q ss_pred             CCC
Q psy9934         147 AEE  149 (158)
Q Consensus       147 ~~~  149 (158)
                      .+.
T Consensus        83 e~p   85 (231)
T 3pgw_B           83 EGP   85 (231)
T ss_pred             cCC
Confidence            654

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

Probab=99.75  E-value=1.3e-18  Score=137.77  Aligned_cols=72  Identities=19%  Similarity=0.177  Sum_probs=64.9

Q ss_pred             CCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEe----------ccceecceeEEEEecCCCCCCC
Q psy9934           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----------GHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         7 ~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----------~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      +++-.+|.+++||+|+|+|+|||+|.|+|++||+||||+|+||+|++.          +++.+.+|+++|||++|.++..
T Consensus         3 v~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isv   82 (231)
T 3pgw_B            3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTV   82 (231)
T ss_pred             cCchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEe
Confidence            578899999999999999999999999999999999999999999852          2357899999999999999874


Q ss_pred             CC
Q psy9934          77 CN   78 (158)
Q Consensus        77 ~d   78 (158)
                      ..
T Consensus        83 e~   84 (231)
T 3pgw_B           83 EG   84 (231)
T ss_pred             cC
Confidence            43

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

Probab=99.75  E-value=4e-19  Score=130.41  Aligned_cols=68  Identities=32%  Similarity=0.416  Sum_probs=62.7

Q ss_pred             CcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCCCc
Q psy9934          81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDE  152 (158)
Q Consensus        81 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~~~  152 (158)
                      ++|+++++++|.|+|++|++|+|+|.|||+|||++|+||+|+ .+   +++|.++|||+||++|+++++..+
T Consensus         3 ~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~-~~---~~lg~v~IRG~nI~~I~~~d~~~d   70 (130)
T 1m5q_A            3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK-AG---EKFNRVFIMYRYIVHIDSTERRID   70 (130)
T ss_dssp             HHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECT-TC---CEEEEEEECGGGEEEEEECCCCCC
T ss_pred             hHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEE-cC---CEeceEEEeCCeEEEEEcCCcccC
Confidence            478899999999999999999999999999999999999997 32   688999999999999999998754

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

Probab=99.72  E-value=3.4e-18  Score=125.42  Aligned_cols=66  Identities=27%  Similarity=0.278  Sum_probs=60.1

Q ss_pred             hHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCCC
Q psy9934          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNP   79 (158)
Q Consensus        10 ~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~dP   79 (158)
                      .++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+|+.    .+++|.++|||++|.++.+.++
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~----~~~lg~v~IRG~nI~~I~~~d~   67 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA----GEKFNRVFIMYRYIVHIDSTER   67 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT----CCEEEEEEECGGGEEEEEECCC
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc----CCEeceEEEeCCeEEEEEcCCc
Confidence            36899999999999999999999999999999999999999972    3689999999999999886544

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

Probab=98.83  E-value=5.6e-09  Score=71.03  Aligned_cols=62  Identities=24%  Similarity=0.137  Sum_probs=54.7

Q ss_pred             CCchHHHhhcCCCEEEEEEeCCcEEEEEEeEec-CcceeEEceeeEEEeccceecceeEEEEecCCCCCC
Q psy9934           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus         7 ~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~   75 (158)
                      .+|+ .|++++||+|.|.|.||++|+|.|.++| ...|++|.||.+      ..+...++|.|+.|..+.
T Consensus         7 ~~p~-el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~~------~~~~~~~iI~G~aI~eI~   69 (86)
T 1y96_A            7 KGPL-EWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLE------DGSMSVTGIMGHAVQTVE   69 (86)
T ss_dssp             SCHH-HHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEECT------TSCEEEEEECGGGEEEEE
T ss_pred             CCHH-HHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeeccc------CCeEEEEEEecceEEEEE
Confidence            4666 7899999999999999999999999999 999999999922      346689999999998875

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

Probab=98.68  E-value=2.1e-08  Score=68.22  Aligned_cols=65  Identities=23%  Similarity=0.201  Sum_probs=57.6

Q ss_pred             cccccccceeeEeeccccEEEEEEEEec-cccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCCCc
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDE  152 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~~~  152 (158)
                      .++++++|+|.|.|.+|++|+|+|.+|| ..+|++|.+|.   ++   .++..++|.|..|..|...++.++
T Consensus        11 el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~---~~---~~~~~~iI~G~aI~eI~v~~~~~~   76 (86)
T 1y96_A           11 EWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFL---ED---GSMSVTGIMGHAVQTVETMNEGDH   76 (86)
T ss_dssp             HHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEEC---TT---SCEEEEEECGGGEEEEEEEECCCH
T ss_pred             HHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeecc---cC---CeEEEEEEecceEEEEEEecchhH
Confidence            5789999999999999999999999999 89999999992   23   355889999999999998887764

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

Probab=97.14  E-value=0.00088  Score=44.55  Aligned_cols=68  Identities=26%  Similarity=0.275  Sum_probs=45.3

Q ss_pred             CCCCCCCCchHHHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCC
Q psy9934           1 MSTPLPCNPKPFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCN   78 (158)
Q Consensus         1 m~~~~~~~p~~~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~d   78 (158)
                      |++...-..-.||+.+  -..+|.|.|.||..+.|++.+||.|+ +.|++      ++      ..+|-=..|+++.|..
T Consensus         1 m~~~~~nlQd~fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~-VlL~~------g~------~qLIYKhAISTI~P~~   67 (79)
T 3sb2_A            1 MSNKGQLLQDPFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYV-VLLRN------TV------TQMVYKHAISTVVPAR   67 (79)
T ss_dssp             -----CTTHHHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEES------SS------EEEEEGGGEEEEEESS
T ss_pred             CCccccchHHHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcE-EEEEC------Cc------eEEEEeeeEEEEeecC
Confidence            5554556677888888  45569999999999999999999999 44532      21      2355666666666655


Q ss_pred             CCC
Q psy9934          79 PKP   81 (158)
Q Consensus        79 P~~   81 (158)
                      |..
T Consensus        68 ~v~   70 (79)
T 3sb2_A           68 AVN   70 (79)
T ss_dssp             CCC
T ss_pred             cee
Confidence            433

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

Probab=96.96  E-value=0.0012  Score=43.40  Aligned_cols=43  Identities=28%  Similarity=0.292  Sum_probs=34.5

Q ss_pred             CCCCchHHHhhcC--CCEEEEEEeCCcEEEEEEeEecCcceeEEce
Q psy9934           5 LPCNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLAS   48 (158)
Q Consensus         5 ~~~~p~~~L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   48 (158)
                      ..-..-.||+++.  ..+|.|.|.||..+.|++.+||.|+ +.|++
T Consensus         6 ~~~lQd~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~-vlL~~   50 (74)
T 2ylb_A            6 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLKN   50 (74)
T ss_dssp             --CCHHHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSE-EEEES
T ss_pred             ccccHHHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEEC
Confidence            3445667888885  7889999999999999999999999 55543

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

Probab=96.90  E-value=0.0018  Score=43.25  Aligned_cols=41  Identities=27%  Similarity=0.312  Sum_probs=33.6

Q ss_pred             CCCchHHHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeEEc
Q psy9934           6 PCNPKPFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLA   47 (158)
Q Consensus         6 ~~~p~~~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~   47 (158)
                      .-..-.||+.+  ...+|+|.|.||..+.|++.+||.|+ +.|+
T Consensus         5 ~nlQd~fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ft-VlL~   47 (82)
T 1u1s_A            5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   47 (82)
T ss_dssp             -CCHHHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             cchHHHHHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceE-EEEe
Confidence            34566778877  47789999999999999999999999 5554

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

Probab=96.86  E-value=0.0016  Score=42.40  Aligned_cols=29  Identities=21%  Similarity=0.203  Sum_probs=25.7

Q ss_pred             CCCEEEEEEeCCcEEEEEEeEecCcceeE
Q psy9934          17 TGKSVICKLKWGHEYKGILVSTDGYMNCQ   45 (158)
Q Consensus        17 ~~k~V~V~l~~g~~~~G~L~~~D~~mNlv   45 (158)
                      .+.+|+|.|.||..+.|++.+||.|+=+.
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll   52 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSNYEIMV   52 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            56789999999999999999999999433

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

Probab=96.78  E-value=0.0015  Score=43.27  Aligned_cols=45  Identities=20%  Similarity=0.139  Sum_probs=33.2

Q ss_pred             CCCCCCCCchHHHhhcC--CCEEEEEEeCCcEEEEEEeEecCcceeE
Q psy9934           1 MSTPLPCNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQ   45 (158)
Q Consensus         1 m~~~~~~~p~~~L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~mNlv   45 (158)
                      ||+...-..-.||+.+.  +.+|+|.|.||..+.|++.+||.|+=+.
T Consensus         4 ~~~~~~nlQd~fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL   50 (78)
T 3ahu_A            4 GSMKPINIQDQFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLL   50 (78)
T ss_dssp             ------CHHHHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             ccccccChHHHHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            44444455667888875  8889999999999999999999999433

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

Probab=96.64  E-value=0.0033  Score=41.57  Aligned_cols=61  Identities=23%  Similarity=0.221  Sum_probs=41.6

Q ss_pred             CCchHHHhhcC--CCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCCC
Q psy9934           7 CNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNP   79 (158)
Q Consensus         7 ~~p~~~L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~dP   79 (158)
                      -..-.||+.+.  ..+|.|.|.||..+.|++.+||.|+ +.|+.     ++      ...+|-=..|+++.|..|
T Consensus         6 ~lQd~fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~-VlL~~-----~g------~~qLIYKhAISTI~p~~~   68 (77)
T 1kq1_A            6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYV-VSLNS-----QG------KQHLIYKHAISTYTVETE   68 (77)
T ss_dssp             CHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE-EEEEE-----TT------EEEEEEGGGEEEEEC---
T ss_pred             ccHHHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcE-EEEEE-----CC------eeEEEEeeeEEEEeECcc
Confidence            44556788885  8889999999999999999999999 44442     11      123455555666555443

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

Probab=96.61  E-value=0.002  Score=44.90  Aligned_cols=42  Identities=29%  Similarity=0.315  Sum_probs=33.2

Q ss_pred             CCCCchHHHhhcCCC--EEEEEEeCCcEEEEEEeEecCcceeEEc
Q psy9934           5 LPCNPKPFLNLLTGK--SVICKLKWGHEYKGILVSTDGYMNCQLA   47 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k--~V~V~l~~g~~~~G~L~~~D~~mNlvL~   47 (158)
                      ..-..-.||+.+..+  +|.|.|.||..+.|++.+||.|+ +.|+
T Consensus         6 ~~nlQd~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~-VlL~   49 (104)
T 2y90_A            6 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   49 (104)
T ss_dssp             --CCHHHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             ccccHHHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEE
Confidence            344566788888444  79999999999999999999999 4554

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

Probab=95.75  E-value=0.017  Score=37.46  Aligned_cols=35  Identities=20%  Similarity=0.136  Sum_probs=28.9

Q ss_pred             cccccc--cceeeEeeccccEEEEEEEEeccccceee
Q psy9934          82 FLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQL  116 (158)
Q Consensus        82 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL  116 (158)
                      ||+.+.  +.+|.|-|.+|..++|.+.|||+|+=+.-
T Consensus        17 fLn~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~   53 (71)
T 2qtx_A           17 FEYARRLNGKKVKIFLRNGEVLDAEVTGVSNYEIMVK   53 (71)
T ss_dssp             CCGGGGGTTCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEEE
Confidence            655554  45889999999999999999999986664

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

Probab=95.74  E-value=0.023  Score=38.31  Aligned_cols=62  Identities=16%  Similarity=0.105  Sum_probs=48.5

Q ss_pred             hcCCCEEEEEEeCCcEEEEEEeEec-CcceeEEceeeEEE-ecc--------ceecceeEEEEecCCCCCCC
Q psy9934          15 LLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEII-DGH--------CTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus        15 ~~~~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~-~~~--------~~~~lg~~~iRG~~i~~I~p   76 (158)
                      .|+|+++.+..+.+-.|.|+|..+| +---+.|+||..+- .+.        ...-...+..||+.|..+..
T Consensus        10 ~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V   81 (88)
T 2vxe_A           10 PELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRV   81 (88)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEE
T ss_pred             cccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEE
Confidence            4799999999999999999999999 56679999998772 211        01245678889998887653

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

Probab=95.63  E-value=0.0067  Score=40.09  Aligned_cols=36  Identities=19%  Similarity=0.227  Sum_probs=29.8

Q ss_pred             cccccc--cceeeEeeccccEEEEEEEEeccccceeec
Q psy9934          82 FLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLA  117 (158)
Q Consensus        82 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~  117 (158)
                      ||+.+.  +.+|.|.|.+|-.++|.+.+||+|+=+.-.
T Consensus        11 fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~~   48 (77)
T 1kq1_A           11 ALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNS   48 (77)
T ss_dssp             HHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEE
T ss_pred             HHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEEE
Confidence            555555  569999999999999999999999866643

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

Probab=95.51  E-value=0.062  Score=35.84  Aligned_cols=59  Identities=17%  Similarity=0.115  Sum_probs=49.4

Q ss_pred             hhcCCCEEEEEEeCCc-EEEEEEeEecCc-ceeEEceeeEEEeccceecceeEEEEecCCCCCC
Q psy9934          14 NLLTGKSVICKLKWGH-EYKGILVSTDGY-MNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus        14 ~~~~~k~V~V~l~~g~-~~~G~L~~~D~~-mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~   75 (158)
                      .+++|+.|.+.++++- .|+|.|..+|+. -++.|.+|  +.+|- +.....+.+|+..|..+.
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~--f~NG~-~~~s~eVtls~~DI~~L~   65 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRP--FHNGV-KCLVPEVTFRAGDITELK   65 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEE--EETTE-ECSSSEEEEEGGGCSEEE
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehh--hhCCC-CCCCcEEEEEecChhheE
Confidence            4789999999999999 999999999954 57999999  45664 455678999999988754

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

Probab=95.26  E-value=0.017  Score=38.49  Aligned_cols=35  Identities=26%  Similarity=0.243  Sum_probs=29.1

Q ss_pred             cccccc--cceeeEeeccccEEEEEEEEeccccceee
Q psy9934          82 FLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQL  116 (158)
Q Consensus        82 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL  116 (158)
                      ||+.+.  +.+|.|-|.||-.++|.+.|||+|+=+.-
T Consensus        11 fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~   47 (82)
T 1u1s_A           11 YLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK   47 (82)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEe
Confidence            555544  56999999999999999999999986664

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

Probab=95.17  E-value=0.019  Score=37.54  Aligned_cols=36  Identities=31%  Similarity=0.325  Sum_probs=29.6

Q ss_pred             Ccccccc--cceeeEeeccccEEEEEEEEeccccceee
Q psy9934          81 PFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQL  116 (158)
Q Consensus        81 ~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL  116 (158)
                      .+|+.+.  +.+|.|.|.+|..++|.+.+||+|+=+.-
T Consensus        12 ~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL~   49 (74)
T 2ylb_A           12 PFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK   49 (74)
T ss_dssp             HHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE
Confidence            3566655  56999999999999999999999986553

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

Probab=94.97  E-value=0.041  Score=39.28  Aligned_cols=39  Identities=18%  Similarity=0.234  Sum_probs=33.0

Q ss_pred             HhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEE--ceeeEE
Q psy9934          13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL--ASTEEI   52 (158)
Q Consensus        13 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL--~~~~e~   52 (158)
                      ...++|.+|.|+|+||..++|++..+|. -+|+|  .+|...
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd~-k~LtL~~~~a~~s   47 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFDS-SNSILQLRLANDS   47 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEET-TTTEEEEEETTTE
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeecC-CeeEEeccccccc
Confidence            4678999999999999999999999993 34666  998643

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

Probab=94.92  E-value=0.025  Score=37.47  Aligned_cols=34  Identities=32%  Similarity=0.305  Sum_probs=28.2

Q ss_pred             cccccc--cceeeEeeccccEEEEEEEEecccccee
Q psy9934          82 FLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQ  115 (158)
Q Consensus        82 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlv  115 (158)
                      ||+.+.  +.+|.|.|.+|..++|.+.+||+|+=+.
T Consensus        12 fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL   47 (79)
T 3sb2_A           12 FLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL   47 (79)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            555554  3489999999999999999999998665

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

Probab=94.89  E-value=0.012  Score=40.98  Aligned_cols=38  Identities=29%  Similarity=0.343  Sum_probs=30.6

Q ss_pred             Ccccccccc--eeeEeeccccEEEEEEEEeccccceeecc
Q psy9934          81 PFLNLLTGK--SVICKLKWGHEYKGILVSTDGYMNCQLAS  118 (158)
Q Consensus        81 ~~L~~~~~k--~V~V~L~~g~~~~G~L~~~D~~mNlvL~~  118 (158)
                      .||+.+..+  +|.|.|.+|-.++|++.+||+|+=|.-++
T Consensus        12 ~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~~~   51 (104)
T 2y90_A           12 PFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNT   51 (104)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEESS
T ss_pred             HHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEECC
Confidence            356666544  99999999999999999999998666533

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

Probab=94.76  E-value=0.039  Score=36.43  Aligned_cols=35  Identities=23%  Similarity=0.264  Sum_probs=29.5

Q ss_pred             cccccc--cceeeEeeccccEEEEEEEEeccccceee
Q psy9934          82 FLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQL  116 (158)
Q Consensus        82 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL  116 (158)
                      ||+.+.  +.+|.|-|.||..++|.+.+||+|+=+.-
T Consensus        15 fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~   51 (78)
T 3ahu_A           15 FLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLE   51 (78)
T ss_dssp             HHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEEE
Confidence            555554  56999999999999999999999986664

>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387, stronGly BENT five-stranded antiparallel beta- sheet, structural genomics, PSI; NMR {Danio rerio} SCOP: b.38.1.5 PDB: 2vxf_A

Probab=94.59  E-value=0.029  Score=38.34  Aligned_cols=69  Identities=14%  Similarity=0.108  Sum_probs=48.7

Q ss_pred             CchHHHhhcCCCEEEEEEeCCcEEEEEEeEec-CcceeEEceeeEEE-ecc--------ceecceeEEEEecCCCCCCC
Q psy9934           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEII-DGH--------CTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         8 ~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~-~~~--------~~~~lg~~~iRG~~i~~I~p   76 (158)
                      .|-.--..++|+++.+..+.+-.|.|+|..+| +---+.|+||..+- .+.        ...-+..+..||+.|..+..
T Consensus         9 ~~~~~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V   87 (95)
T 2fb7_A            9 EDPSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTV   87 (95)
T ss_dssp             -------CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEE
T ss_pred             CCCCccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEE
Confidence            45556678999999999999999999999999 56668999988762 211        01235578889998887653

>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387, stronGly BENT five-stranded antiparallel beta- sheet, structural genomics, PSI; NMR {Danio rerio} SCOP: b.38.1.5 PDB: 2vxf_A

Probab=94.27  E-value=0.17  Score=34.53  Aligned_cols=74  Identities=16%  Similarity=0.148  Sum_probs=53.1

Q ss_pred             CCCCcccccccceeeEeeccccEEEEEEEEec-cccceeecceEEE-ecCe--------eeeecCcEEEeeCcEEEEEeC
Q psy9934          78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEI-IDGH--------CTGKLGEVLIRCNNILYIRGA  147 (158)
Q Consensus        78 dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~-~~~~--------~~~~~g~~~iRG~~I~~i~~~  147 (158)
                      .|..-..+++++++.+..+.+-.|.|+|..+| +---+.|.++..+ .+|.        ...-+..++.||+.|.-+...
T Consensus         9 ~~~~~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~   88 (95)
T 2fb7_A            9 EDPSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVC   88 (95)
T ss_dssp             -------CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEES
T ss_pred             CCCCccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEe
Confidence            34455667899999999999999999999999 5677888887654 1111        123568999999999999887


Q ss_pred             CCCC
Q psy9934         148 EEGD  151 (158)
Q Consensus       148 ~~~~  151 (158)
                      +...
T Consensus        89 e~p~   92 (95)
T 2fb7_A           89 EPPK   92 (95)
T ss_dssp             CCSC
T ss_pred             cCCC
Confidence            6543

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

Probab=93.86  E-value=0.16  Score=33.92  Aligned_cols=60  Identities=20%  Similarity=0.165  Sum_probs=48.2

Q ss_pred             hHHHhhcCCCEEEEEEeCCcEEEEEEeEec-CcceeEEceeeEEEeccceecceeEEEEecCCCCC
Q psy9934          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTP   74 (158)
Q Consensus        10 ~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I   74 (158)
                      |.+|..+.|++|.+.+.++-++.|+..++| ...|+..++-.     .+-...++..+|++.|..+
T Consensus        21 Lr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-----TPiGv~~eAlLR~~Dii~~   81 (85)
T 1y96_B           21 LRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQ-----TPIGVQAEALLRCSDIISY   81 (85)
T ss_dssp             HHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEC-----CTTCCEEEEEEEGGGEEEE
T ss_pred             HHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcC-----CCcccchhhhhhcCCEEEE
Confidence            567888899999999999999999999999 67777655532     1234567899999988754

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

Probab=93.80  E-value=0.35  Score=32.48  Aligned_cols=65  Identities=20%  Similarity=0.168  Sum_probs=51.7

Q ss_pred             ccccceeeEeeccccEEEEEEEEec-cccceeecceEEEe-cCe--------eeeecCcEEEeeCcEEEEEeCCC
Q psy9934          85 LLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEII-DGH--------CTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        85 ~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~-~~~--------~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      .++++++.+..+.+-.|.|+|..+| +---+.|.++..+- +|.        ...-+..++.||+.|.-+...+.
T Consensus        10 ~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~~~   84 (88)
T 2vxe_A           10 PELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVNN   84 (88)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEECCC
T ss_pred             cccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEEecc
Confidence            3679999999999999999999999 56778899988652 221        12346789999999999887654

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

Probab=92.32  E-value=0.21  Score=33.37  Aligned_cols=60  Identities=23%  Similarity=0.273  Sum_probs=46.9

Q ss_pred             cccccccceeeEeeccccEEEEEEEEec-cccceeecceEEEecCeeeeecCcEEEeeCcEEEEEe
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      +|..+.+++|.+.+..+.+..|+..++| ...|+..++=. +.    .......++|++-|++++-
T Consensus        23 ~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TP----iGv~~eAlLR~~Dii~~sF   83 (85)
T 1y96_B           23 SLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQ-TP----IGVQAEALLRCSDIISYTF   83 (85)
T ss_dssp             HHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEC-CT----TCCEEEEEEEGGGEEEEEE
T ss_pred             HHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcC-CC----cccchhhhhhcCCEEEEEe
Confidence            3556779999999999999999999999 56777655543 11    2245788999999999874

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

Probab=91.69  E-value=0.28  Score=34.96  Aligned_cols=59  Identities=17%  Similarity=0.157  Sum_probs=42.0

Q ss_pred             ccccccceeeEeeccccEEEEEEEEec-cccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCCC
Q psy9934          83 LNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD  151 (158)
Q Consensus        83 L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~~  151 (158)
                      ..++++..|.|.|++|..++|++..+| +.+=|.|++|...          ..-|+.+.|.-+...+-.+
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd~k~LtL~~~~a~~s----------~~~I~asdI~DLkVl~~~~   66 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFDSSNSILQLRLANDS----------TKSIVTKDIKDLRILPKNE   66 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEETTTTEEEEEETTTE----------EEEEEGGGEEEEEECCSCC
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeecCCeeEEeccccccc----------cceeecccccceeeeeccc
Confidence            356789999999999999999999998 3344444888421          1167777776666555443

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

Probab=91.48  E-value=0.32  Score=31.36  Aligned_cols=38  Identities=24%  Similarity=0.114  Sum_probs=30.4

Q ss_pred             hHHHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeEEce
Q psy9934          10 KPFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLAS   48 (158)
Q Consensus        10 ~~~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   48 (158)
                      ...|+++  -..+|.|+|.+|..+.|.+.-+|+|+ +.|.+
T Consensus        11 vR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~c-l~L~~   50 (70)
T 3hfo_A           11 VRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDG-LGLVD   50 (70)
T ss_dssp             HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE-EEEEC
T ss_pred             HHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCE-EEEEc
Confidence            3556666  35679999999999999999999998 44444

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

Probab=91.39  E-value=0.5  Score=29.89  Aligned_cols=41  Identities=20%  Similarity=0.275  Sum_probs=32.9

Q ss_pred             HHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEE
Q psy9934          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI   52 (158)
Q Consensus        11 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~   52 (158)
                      +-|....|++|-|-..+...+.|+|..||+-. +.|+|++..
T Consensus         9 ktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~   49 (71)
T 1ycy_A            9 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDV   49 (71)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEET
T ss_pred             HHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHH
Confidence            45788899999999999999999999999776 788999876

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

Probab=90.44  E-value=0.77  Score=29.68  Aligned_cols=39  Identities=23%  Similarity=0.139  Sum_probs=30.5

Q ss_pred             hHHHhhcC--CCEEEEEEeCCcEEEEEEeEecCcceeEEcee
Q psy9934          10 KPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLAST   49 (158)
Q Consensus        10 ~~~L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~   49 (158)
                      .+.|++++  ..+|.|+|.+|..+.|.+.-.|+++ +.|.+.
T Consensus        13 vR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~c-l~L~~~   53 (72)
T 3hfn_A           13 IRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTC-VCIADE   53 (72)
T ss_dssp             HHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSE-EEEEC-
T ss_pred             HHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCE-EEEEcC
Confidence            35677774  4569999999999999999999998 445443

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

Probab=89.99  E-value=1.2  Score=29.49  Aligned_cols=66  Identities=18%  Similarity=0.103  Sum_probs=51.6

Q ss_pred             ccccccceeeEeecccc-EEEEEEEEeccc-cceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCCC
Q psy9934          83 LNLLTGKSVICKLKWGH-EYKGILVSTDGY-MNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD  151 (158)
Q Consensus        83 L~~~~~k~V~V~L~~g~-~~~G~L~~~D~~-mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~~  151 (158)
                      ..+++++.|.+.-+++- .|+|.+..+|+. -+|.|.+|.  .+|- +.....+.+|+.-|.-+...+..+
T Consensus         4 a~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f--~NG~-~~~s~eVtls~~DI~~L~ii~~~~   71 (84)
T 2vc8_A            4 ATDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF--HNGV-KCLVPEVTFRAGDITELKILEIPG   71 (84)
T ss_dssp             -CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE--ETTE-ECSSSEEEEEGGGCSEEEEEECCC
T ss_pred             cccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh--hCCC-CCCCcEEEEEecChhheEEEecCC
Confidence            45788999999999998 999999999965 579999995  4675 345577999999887665544433

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

Probab=88.65  E-value=0.5  Score=30.40  Aligned_cols=29  Identities=21%  Similarity=0.009  Sum_probs=24.9

Q ss_pred             cceeeEeeccccEEEEEEEEeccccceee
Q psy9934          88 GKSVICKLKWGHEYKGILVSTDGYMNCQL  116 (158)
Q Consensus        88 ~k~V~V~L~~g~~~~G~L~~~D~~mNlvL  116 (158)
                      ..+|.|+|.+|..++|.+..+|+|+=+..
T Consensus        21 k~~V~I~L~tG~~l~G~i~WQD~~cl~L~   49 (70)
T 3hfo_A           21 QTPVEIKLLTGDSLFGTIRWQDTDGLGLV   49 (70)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             CceEEEEecCCCEEEEEEEEeCCCEEEEE
Confidence            34899999999999999999999875543

>2qqr_A JMJC domain-containing histone demethylation protein 3A; histone lysine demethylase, tandem hybrid tudor domains, metal binding protein; 1.80A {Homo sapiens} SCOP: b.34.9.1 b.34.9.1 PDB: 2qqs_A* 2gfa_A* 2gf7_A*

Probab=87.97  E-value=1.1  Score=31.61  Aligned_cols=76  Identities=20%  Similarity=0.229  Sum_probs=51.4

Q ss_pred             CCCEEEEEEeCCcEEEEEEeEec--CcceeEEceeeEEEeccceecceeEEEEecCCCCCCC---CCCCCccccccccee
Q psy9934          17 TGKSVICKLKWGHEYKGILVSTD--GYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP---CNPKPFLNLLTGKSV   91 (158)
Q Consensus        17 ~~k~V~V~l~~g~~~~G~L~~~D--~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p---~dP~~~L~~~~~k~V   91 (158)
                      +|.+|..+-+||+.|.|++.+..  .|..+..+|-.-..+     ..++      .|..-..   ..|      ..+..|
T Consensus         8 vGq~V~akh~ngryy~~~V~~~~~~~~y~V~F~DgS~s~d-----l~pe------DIvs~dc~~~GpP------~~G~~V   70 (118)
T 2qqr_A            8 AGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDN-----LYPE------DIVSQDCLQFGPP------AEGEVV   70 (118)
T ss_dssp             TTCEEEEECTTSSEEEEEEEEEEEEEEEEEEETTSCEEEE-----ECGG------GBCSSCHHHHCCC------CTTCEE
T ss_pred             cCCEEEEECCCCCEEeEEEEEEeeEEEEEEEcCCCCccCC-----CCHh------hcccccccccCCC------CCCCEE
Confidence            79999999999999999999977  455555555443311     1111      2222110   112      238899


Q ss_pred             eEeeccccEEEEEEEEec
Q psy9934          92 ICKLKWGHEYKGILVSTD  109 (158)
Q Consensus        92 ~V~L~~g~~~~G~L~~~D  109 (158)
                      .|+-.+|..|.++..|.-
T Consensus        71 ~V~W~DG~~y~a~f~g~~   88 (118)
T 2qqr_A           71 QVRWTDGQVYGAKFVASH   88 (118)
T ss_dssp             EEECTTSCEEEEEEEEEE
T ss_pred             EEEcCCCCEeeeEEecee
Confidence            999999999999998854

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

Probab=84.88  E-value=1.1  Score=28.99  Aligned_cols=48  Identities=21%  Similarity=0.232  Sum_probs=32.9

Q ss_pred             cceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEe
Q psy9934          88 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        88 ~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      ..+|.|+|.+|..++|.+.-+|+++=+..++ .+          ..++|.-..|.+|.+
T Consensus        23 k~~V~I~L~tGd~l~G~i~WQD~~cl~L~~~-~~----------~~~LI~R~AI~~Ikp   70 (72)
T 3hfn_A           23 AAPVEIKLVTGDAITGRVLWQDPTCVCIADE-NS----------RQTTIWKQAIAYLQP   70 (72)
T ss_dssp             CCEEEEEETTSCEEEEEEEEECSSEEEEEC--------------CEEEEEGGGEEEEEE
T ss_pred             CceEEEEecCCCEEEEEEEEECCCEEEEEcC-CC----------CeEEEEeeeeEEEEe
Confidence            3489999999999999999999887444322 11          124555556666654

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

Probab=83.91  E-value=0.71  Score=34.19  Aligned_cols=40  Identities=18%  Similarity=0.187  Sum_probs=30.4

Q ss_pred             CCCCCCCchH---HHhhcCCCEEEEEE----eCCcEEEEEEeEecCc
Q psy9934           2 STPLPCNPKP---FLNLLTGKSVICKL----KWGHEYKGILVSTDGY   41 (158)
Q Consensus         2 ~~~~~~~p~~---~L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~   41 (158)
                      |+|.-.-||.   .+..+.|+.|.|++    .+.+.+.|+|.++|+-
T Consensus        85 SSPGldRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T 1ib8_A           85 TSPGLERPLKTKDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED  131 (164)
T ss_dssp             ECCSSSSCCSSHHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             eCCCCCCCCCCHHHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCC
Confidence            5555555554   45566999999999    4559999999999954

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	158
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	1e-23
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	6e-19
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-22
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	8e-18
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	2e-21
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	7e-17
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	2e-21
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	3e-15
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	5e-21
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	1e-15
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	4e-20
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	3e-15
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	9e-20
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	5e-15
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	9e-20
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	2e-15
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	4e-19
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	3e-14
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	1e-17
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	2e-12
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	3e-13
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	3e-09
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	3e-12
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	2e-08
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	2e-04
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	0.003

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

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

 Score = 85.9 bits (213), Expect = 1e-23
 Identities = 26/72 (36%), Positives = 38/72 (52%)

Query: 76  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 135
           P  P   LN      VI +LK G E++G L   D +MN  L   EEI +G    K+G V+
Sbjct: 1   PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVV 60

Query: 136 IRCNNILYIRGA 147
           IR + ++++  A
Sbjct: 61  IRGDTVVFVSPA 72

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

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

 Score = 74.0 bits (182), Expect = 6e-19
 Identities = 25/62 (40%), Positives = 32/62 (51%)

Query: 6  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 65
          P  P   LN      VI +LK G E++G L   D +MN  L   EEI +G    K+G V+
Sbjct: 1  PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVV 60

Query: 66 IR 67
          IR
Sbjct: 61 IR 62

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

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

 Score = 83.2 bits (206), Expect = 1e-22
 Identities = 30/67 (44%), Positives = 38/67 (56%)

Query: 78  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 137
            P   L       VI KLK   E++G+L S D +MN  L   EE+ DG  T +LG VLIR
Sbjct: 6   RPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIR 65

Query: 138 CNNILYI 144
            +NI+YI
Sbjct: 66  GDNIVYI 72

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

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

 Score = 70.9 bits (174), Expect = 8e-18
 Identities = 26/60 (43%), Positives = 32/60 (53%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
           P   L       VI KLK   E++G+L S D +MN  L   EE+ DG  T +LG VLIR
Sbjct: 6  RPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIR 65

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

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

 Score = 80.1 bits (198), Expect = 2e-21
 Identities = 23/67 (34%), Positives = 37/67 (55%)

Query: 78  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 137
            P   ++    K V+  LK G E++G L+  D ++N  LA  E I DG    + G+++IR
Sbjct: 2   RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIR 61

Query: 138 CNNILYI 144
            +N+L I
Sbjct: 62  GDNVLAI 68

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

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

 Score = 68.2 bits (167), Expect = 7e-17
 Identities = 20/60 (33%), Positives = 32/60 (53%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
           P   ++    K V+  LK G E++G L+  D ++N  LA  E I DG    + G+++IR
Sbjct: 2  RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIR 61

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 79.7 bits (197), Expect = 2e-21
 Identities = 34/68 (50%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 83  LNLLTGKSVICKLKWGH-EYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 141
           L  L    V  KLK+   EY+G LVSTD Y N QL   EE + G   G LGE+ IRCNN+
Sbjct: 1   LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNV 60

Query: 142 LYIRGAEE 149
           LYIR    
Sbjct: 61  LYIRELPN 68

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 64.0 bits (156), Expect = 3e-15
 Identities = 27/56 (48%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 13 LNLLTGKSVICKLKWGH-EYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
          L  L    V  KLK+   EY+G LVSTD Y N QL   EE + G   G LGE+ IR
Sbjct: 1  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIR 56

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72

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

 Score = 79.1 bits (195), Expect = 5e-21
 Identities = 18/67 (26%), Positives = 30/67 (44%)

Query: 79  PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRC 138
           P   L+   G  V C+   G  Y+G L+  +  MNCQ+++           +L +V IR 
Sbjct: 3   PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRG 62

Query: 139 NNILYIR 145
             I ++ 
Sbjct: 63  CKIRFLI 69

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72

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

 Score = 65.6 bits (160), Expect = 1e-15
 Identities = 17/59 (28%), Positives = 27/59 (45%)

Query: 9  PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
          P   L+   G  V C+   G  Y+G L+  +  MNCQ+++           +L +V IR
Sbjct: 3  PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIR 61

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.0 bits (190), Expect = 4e-20
 Identities = 19/64 (29%), Positives = 30/64 (46%)

Query: 82  FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 141
           FL  L+ ++V  +LK G +  G +   D  MN  L + +  +      +L  + IR NNI
Sbjct: 5   FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 64

Query: 142 LYIR 145
            Y  
Sbjct: 65  RYFI 68

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.3 bits (157), Expect = 3e-15
 Identities = 15/56 (26%), Positives = 26/56 (46%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
          FL  L+ ++V  +LK G +  G +   D  MN  L + +  +      +L  + IR
Sbjct: 5  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIR 60

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

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

 Score = 75.9 bits (187), Expect = 9e-20
 Identities = 27/64 (42%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 82  FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 141
            L    GK V+ KL+  HE +GIL S D ++N  L   EEIIDG+   K G +++R  N+
Sbjct: 6   TLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVY-KRGTMVVRGENV 64

Query: 142 LYIR 145
           L+I 
Sbjct: 65  LFIS 68

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

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

 Score = 63.6 bits (155), Expect = 5e-15
 Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 3/67 (4%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR--SL 69
           L    GK V+ KL+  HE +GIL S D ++N  L   EEIIDG+   K G +++R  ++
Sbjct: 6  TLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVY-KRGTMVVRGENV 64

Query: 70 TMSTPLP 76
             +P+P
Sbjct: 65 LFISPVP 71

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

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

 Score = 75.9 bits (187), Expect = 9e-20
 Identities = 23/67 (34%), Positives = 34/67 (50%)

Query: 78  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 137
                L       V+ KLK   E +G+L S D +MN  L+ +EEI       KLG ++IR
Sbjct: 7   TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIR 66

Query: 138 CNNILYI 144
            +N++ I
Sbjct: 67  GDNVILI 73

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

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

 Score = 64.7 bits (158), Expect = 2e-15
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
               L       V+ KLK   E +G+L S D +MN  L+ +EEI       KLG ++IR
Sbjct: 7  TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIR 66

Query: 68 --SLTMSTPL 75
            ++ + +PL
Sbjct: 67 GDNVILISPL 76

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

 Score = 74.4 bits (183), Expect = 4e-19
 Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 78  NPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLI 136
            P   +  + GK +  ++K   ++  G L   D YMN  L +  E         LGE+++
Sbjct: 5   LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVL 64

Query: 137 RCNNILYIR 145
           R NN++ I+
Sbjct: 65  RGNNVVLIQ 73

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

 Score = 61.7 bits (150), Expect = 3e-14
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 8  NPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLI 66
           P   +  + GK +  ++K   ++  G L   D YMN  L +  E         LGE+++
Sbjct: 5  LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVL 64

Query: 67 R 67
          R
Sbjct: 65 R 65

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

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

 Score = 72.1 bits (177), Expect = 1e-17
 Identities = 21/68 (30%), Positives = 28/68 (41%), Gaps = 4/68 (5%)

Query: 82  FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 141
            LN L G+ V   L  G  YKG+L + D  +N  LA+           K   V I    I
Sbjct: 4   ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAG----EKFNRVFIMYRYI 59

Query: 142 LYIRGAEE 149
           ++I   E 
Sbjct: 60  VHIDSTER 67

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

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

 Score = 58.2 bits (141), Expect = 2e-12
 Identities = 18/56 (32%), Positives = 23/56 (41%), Gaps = 4/56 (7%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
           LN L G+ V   L  G  YKG+L + D  +N  LA+           K   V I 
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAG----EKFNRVFIM 55

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

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

 Score = 59.9 bits (145), Expect = 3e-13
 Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 15/82 (18%)

Query: 78  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-------------- 123
            P   ++   G  +   +K   E+ G+L   D Y+N  L   +E                
Sbjct: 5   LPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKK 64

Query: 124 -DGHCTGKLGEVLIRCNNILYI 144
                  +L  +L+  NN+  +
Sbjct: 65  LKRVMVNRLETILLSGNNVAML 86

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

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

 Score = 49.1 bits (117), Expect = 3e-09
 Identities = 13/75 (17%), Positives = 24/75 (32%), Gaps = 15/75 (20%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-------------- 53
           P   ++   G  +   +K   E+ G+L   D Y+N  L   +E                
Sbjct: 5  LPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKK 64

Query: 54 -DGHCTGKLGEVLIR 67
                 +L  +L+ 
Sbjct: 65 LKRVMVNRLETILLS 79

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81

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

 Score = 56.7 bits (137), Expect = 3e-12
 Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 10/67 (14%)

Query: 88  GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLGEVLIR 137
              + C L+ G  + G   + D +MN  L   +E            +      LG VL+R
Sbjct: 8   DYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLR 67

Query: 138 CNNILYI 144
             N++ +
Sbjct: 68  GENLVSM 74

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81

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

 Score = 46.7 bits (111), Expect = 2e-08
 Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 10/60 (16%)

Query: 18 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLGEVLIR 67
             + C L+ G  + G   + D +MN  L   +E            +      LG VL+R
Sbjct: 8  DYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLR 67

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

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

 Score = 36.4 bits (84), Expect = 2e-04
 Identities = 7/77 (9%), Positives = 28/77 (36%), Gaps = 14/77 (18%)

Query: 82  FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII--------------DGHC 127
             ++     V+   +   +  G + + D + N  L + +E+                 + 
Sbjct: 8   TQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNK 67

Query: 128 TGKLGEVLIRCNNILYI 144
              + ++ +R ++++ +
Sbjct: 68  DRYISKMFLRGDSVIVV 84

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

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

 Score = 33.3 bits (76), Expect = 0.003
 Identities = 13/85 (15%), Positives = 29/85 (34%), Gaps = 6/85 (7%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTM 71
            ++     V+   +   +  G + + D + N  L + +E+         G+   + +  
Sbjct: 8  TQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNK 67

Query: 72 STPLPCNPKPFLNLLTGKSVICKLK 96
             +          L G SVI  L+
Sbjct: 68 DRYIS------KMFLRGDSVIVVLR 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	158
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.89
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.88
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.88
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.87
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.87
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.86
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.86
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.86
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.85
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.85
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.85
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.85
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.84
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.83
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.83
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.82
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.81
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.8
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.79
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.78
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.78
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.77
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.75
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.74
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.66
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.66
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	96.08
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	95.73
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	95.47
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	95.18
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	94.8
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	93.61
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	93.45
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	91.85
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	91.42
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	84.23

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

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

Probab=99.89  E-value=9.8e-24  Score=138.76  Aligned_cols=71  Identities=38%  Similarity=0.470  Sum_probs=66.8

Q ss_pred             CCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         6 ~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      |..|+++|++++|++|+|+|+||++|.|+|.+||.|||++|+||+|+..++..+.+|.++|||++|.++.|
T Consensus         1 p~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~Isp   71 (72)
T d1i4k1_           1 PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSP   71 (72)
T ss_dssp             CCCHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEEEEECGGGEEEEEC
T ss_pred             CCChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcceEEEeCCeEEEEEc
Confidence            56899999999999999999999999999999999999999999999777778899999999999998764

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

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

Probab=99.88  E-value=1.9e-23  Score=138.07  Aligned_cols=72  Identities=38%  Similarity=0.411  Sum_probs=67.6

Q ss_pred             CCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      ..+.|+++|++++|++|.|+|+||++|.|+|.+||+|||++|+||+|+.+++..+.+|.+||||++|.++.|
T Consensus         3 ~~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           3 NVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             CTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             cccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEEEeCCEEEEEeC
Confidence            467899999999999999999999999999999999999999999999877778899999999999998764

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

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

Probab=99.88  E-value=1.5e-23  Score=137.48  Aligned_cols=70  Identities=30%  Similarity=0.424  Sum_probs=66.0

Q ss_pred             CCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         7 ~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      +.|+++|++++|++|+|+|+||+.|+|+|.+||+|||++|+||+|..+++..+.+|.+||||++|.++.|
T Consensus         1 ~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           1 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             CCchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCcEeEcCcEEEECCeEEEEeC
Confidence            4699999999999999999999999999999999999999999999877778899999999999998764

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

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

Probab=99.87  E-value=4.2e-23  Score=135.71  Aligned_cols=71  Identities=35%  Similarity=0.522  Sum_probs=66.7

Q ss_pred             CCCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEe
Q psy9934          76 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        76 p~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      |.-|..+|+++++++|.|+|+||++|+|+|.+||+|||++|+||+|+..++..+++|.+||||++|++|++
T Consensus         1 p~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~Isp   71 (72)
T d1i4k1_           1 PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSP   71 (72)
T ss_dssp             CCCHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEEEEECGGGEEEEEC
T ss_pred             CCChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcceEEEeCCeEEEEEc
Confidence            45678899999999999999999999999999999999999999999887778899999999999999985

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

Probab=99.87  E-value=1e-22  Score=134.92  Aligned_cols=71  Identities=24%  Similarity=0.340  Sum_probs=65.8

Q ss_pred             CCCchHHHhhcCCCEEEEEEeCC-cEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           6 PCNPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         6 ~~~p~~~L~~~~~k~V~V~l~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      -..|+++|++++|++|+|+|++| +.|.|+|.+||+|||++|+||+|+..+...+++|++||||++|.++.|
T Consensus         3 ~~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           3 MVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             CCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             ccccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCcEeEcceEEEeCCEEEEEEC
Confidence            46899999999999999999976 899999999999999999999999777678899999999999998765

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

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

Probab=99.86  E-value=1.4e-22  Score=132.70  Aligned_cols=69  Identities=33%  Similarity=0.498  Sum_probs=65.7

Q ss_pred             CCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEe
Q psy9934          78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        78 dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      .|.++|+++++++|.|+|+||++|+|+|.+||+|||++|+||.|+.+++..+++|.+||||++|++|+|
T Consensus         2 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           2 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             CchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCcEeEcCcEEEECCeEEEEeC
Confidence            477889999999999999999999999999999999999999999888888899999999999999987

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=5.7e-22  Score=128.95  Aligned_cols=67  Identities=51%  Similarity=0.788  Sum_probs=61.5

Q ss_pred             ccccccceeeEeec-cccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCC
Q psy9934          83 LNLLTGKSVICKLK-WGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE  149 (158)
Q Consensus        83 L~~~~~k~V~V~L~-~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~  149 (158)
                      |+++++++|.|+|+ +|++|+|+|.+||+|||++|++|+|+.+++..+++|.+||||+||++|++.|+
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~IRG~nI~~I~~~pd   68 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN   68 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECCC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCcccCcCeEEEECCEEEEEEeCCC
Confidence            56789999999999 56889999999999999999999999888888899999999999999986653

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

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

Probab=99.86  E-value=3.3e-22  Score=132.01  Aligned_cols=70  Identities=43%  Similarity=0.542  Sum_probs=66.6

Q ss_pred             CCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEe
Q psy9934          77 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        77 ~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      ..|..+|+++++++|.|+|+||++|+|+|.+||+|||++|+||+|+.++...+++|.+||||++|.+|+|
T Consensus         5 ~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           5 QRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             TCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             cCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEEEeCCEEEEEeC
Confidence            4688999999999999999999999999999999999999999999888888899999999999999986

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

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

Probab=99.85  E-value=5.5e-22  Score=130.03  Aligned_cols=68  Identities=40%  Similarity=0.533  Sum_probs=62.8

Q ss_pred             CCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCC
Q psy9934          80 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE  148 (158)
Q Consensus        80 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~  148 (158)
                      .++|+++++++|.|+|+||++|+|+|.+||+|||++|+||+|+.+++ .+++|.++|||+||++|++++
T Consensus         4 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~~-~~~~g~v~iRG~~I~~I~~~P   71 (71)
T d1i8fa_           4 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN-VYKRGTMVVRGENVLFISPVP   71 (71)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETTE-EEEEEEEEECGGGEEEEEECC
T ss_pred             hHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECCC-EEEcceEEEeCCeEEEEeCCC
Confidence            35788999999999999999999999999999999999999998775 578999999999999999875

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

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

Probab=99.85  E-value=3.8e-22  Score=131.09  Aligned_cols=69  Identities=25%  Similarity=0.416  Sum_probs=64.1

Q ss_pred             CchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         8 ~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      .|+.+|+++.|++|+|+|+||++|+|+|.+||.|||++|+||+++..+...+.++.+||||++|+++..
T Consensus         2 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~v~IRG~~I~~i~l   70 (72)
T d1d3ba_           2 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLIL   70 (72)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEE
T ss_pred             CchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCeEEEECCEEEEEEc
Confidence            699999999999999999999999999999999999999999998655557889999999999998764

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

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

Probab=99.85  E-value=2.4e-22  Score=133.36  Aligned_cols=72  Identities=32%  Similarity=0.347  Sum_probs=66.7

Q ss_pred             CCCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         5 ~~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      ....|.++|.+++|++|+|+|+||++|.|+|.+||+|||++|+||+|+..+...+.+|.++|||++|.++.|
T Consensus         4 ~~~~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~~~v~iRG~~I~~I~~   75 (76)
T d1th7a1           4 LAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISP   75 (76)
T ss_dssp             TCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEE
T ss_pred             ccccHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCcccCcceEEEECCEEEEEEe
Confidence            456799999999999999999999999999999999999999999999766668899999999999998764

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

Probab=99.85  E-value=6e-22  Score=131.14  Aligned_cols=69  Identities=28%  Similarity=0.428  Sum_probs=65.0

Q ss_pred             CCCCcccccccceeeEeeccc-cEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEe
Q psy9934          78 NPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG  146 (158)
Q Consensus        78 dP~~~L~~~~~k~V~V~L~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~  146 (158)
                      .|.++|+++++++|.|+|++| ++|.|+|.|||+|||++|+||+|+..+...+++|.+||||+||.+|+|
T Consensus         5 ~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           5 LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             CHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             ccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCcEeEcceEEEeCCEEEEEEC
Confidence            578899999999999999976 899999999999999999999999888788899999999999999987

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

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

Probab=99.84  E-value=1.3e-21  Score=128.17  Aligned_cols=68  Identities=37%  Similarity=0.434  Sum_probs=62.5

Q ss_pred             CchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCC
Q psy9934           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus         8 ~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      ++-++|++++|++|+|+|+||+.|.|+|.+||+|||++|+||+|+.+++ .+++|.++|||++|.++.|
T Consensus         2 t~~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~~-~~~~g~v~iRG~~I~~I~~   69 (71)
T d1i8fa_           2 TLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN-VYKRGTMVVRGENVLFISP   69 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETTE-EEEEEEEEECGGGEEEEEE
T ss_pred             cHhHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECCC-EEEcceEEEeCCeEEEEeC
Confidence            3567999999999999999999999999999999999999999997664 6789999999999998864

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

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

Probab=99.83  E-value=8e-22  Score=130.76  Aligned_cols=72  Identities=32%  Similarity=0.387  Sum_probs=66.3

Q ss_pred             CCCCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeC
Q psy9934          76 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGA  147 (158)
Q Consensus        76 p~dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~  147 (158)
                      +..|.++|.++++++|.|+|+||++|+|+|.+||+|||++|++|+|+..+.+.+.+|.++|||++|++|++.
T Consensus         5 ~~~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~~~v~iRG~~I~~I~~~   76 (76)
T d1th7a1           5 AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPL   76 (76)
T ss_dssp             CHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEEC
T ss_pred             cccHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCcccCcceEEEECCEEEEEEeC
Confidence            345778999999999999999999999999999999999999999987776778999999999999999974

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

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

Probab=99.83  E-value=1.5e-21  Score=128.21  Aligned_cols=71  Identities=25%  Similarity=0.431  Sum_probs=65.9

Q ss_pred             CCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCC
Q psy9934          78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE  148 (158)
Q Consensus        78 dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~  148 (158)
                      .|..+|+++.+++|.|+|+||++|+|+|.++|+|||++|+||+++..+.+..+++.+||||++|.+|..||
T Consensus         2 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           2 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             CchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCeEEEECCEEEEEEcCC
Confidence            46778999999999999999999999999999999999999999876656678999999999999999986

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.82  E-value=3.4e-21  Score=125.18  Aligned_cols=63  Identities=43%  Similarity=0.570  Sum_probs=58.5

Q ss_pred             HhhcCCCEEEEEEe-CCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCC
Q psy9934          13 LNLLTGKSVICKLK-WGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus        13 L~~~~~k~V~V~l~-~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~   75 (158)
                      |++++|++|.|+|+ +|++|+|+|.+||+|||++|+||+|+.+++..+++|.+||||++|.++.
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~IRG~nI~~I~   64 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIR   64 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEE
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCcccCcCeEEEECCEEEEEE
Confidence            57899999999999 5678999999999999999999999987777889999999999999985

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

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

Probab=99.81  E-value=4.9e-21  Score=131.14  Aligned_cols=71  Identities=20%  Similarity=0.305  Sum_probs=63.8

Q ss_pred             CCCchHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEec---------------cceecceeEEEEecC
Q psy9934           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG---------------HCTGKLGEVLIRSLT   70 (158)
Q Consensus         6 ~~~p~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~---------------~~~~~lg~~~iRG~~   70 (158)
                      -..|+++|++++|++|+|.|+||++|.|+|.|||.|||++|+||+|++..               ...+++|++||||++
T Consensus         3 ~~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~   82 (92)
T d2fwka1           3 IILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNN   82 (92)
T ss_dssp             CCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGG
T ss_pred             ccChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCE
Confidence            46899999999999999999999999999999999999999999998421               124689999999999


Q ss_pred             CCCCCC
Q psy9934          71 MSTPLP   76 (158)
Q Consensus        71 i~~I~p   76 (158)
                      |.++.|
T Consensus        83 Vv~I~p   88 (92)
T d2fwka1          83 VAMLVP   88 (92)
T ss_dssp             EEEEES
T ss_pred             EEEEEe
Confidence            999887

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

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

Probab=99.80  E-value=1e-20  Score=129.57  Aligned_cols=71  Identities=21%  Similarity=0.319  Sum_probs=63.1

Q ss_pred             CCCCcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEec---------------CeeeeecCcEEEeeCcEE
Q psy9934          78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID---------------GHCTGKLGEVLIRCNNIL  142 (158)
Q Consensus        78 dP~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~---------------~~~~~~~g~~~iRG~~I~  142 (158)
                      .|.++|+++++++|.|.|++|++|.|+|.+||+||||+|+||+|+..               ....+++|.+||||+||+
T Consensus         5 ~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~Vv   84 (92)
T d2fwka1           5 LPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVA   84 (92)
T ss_dssp             CHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEE
T ss_pred             ChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEEE
Confidence            57889999999999999999999999999999999999999999742               123468999999999999


Q ss_pred             EEEeCC
Q psy9934         143 YIRGAE  148 (158)
Q Consensus       143 ~i~~~~  148 (158)
                      +|+|..
T Consensus        85 ~I~p~~   90 (92)
T d2fwka1          85 MLVPGG   90 (92)
T ss_dssp             EEESSS
T ss_pred             EEEeCC
Confidence            999743

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=6.3e-20  Score=122.67  Aligned_cols=70  Identities=21%  Similarity=0.246  Sum_probs=63.4

Q ss_pred             hHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCCCCCC
Q psy9934          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPLPCNP   79 (158)
Q Consensus        10 ~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~p~dP   79 (158)
                      ..||+++.|++|.|+|+||.+|+|+|.++|+|||++|+||+++..+....+++.+||||++|+++..++.
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~lPd~   72 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDS   72 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTT
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEECCCC
Confidence            4689999999999999999999999999999999999999998655557889999999999999875443

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.78  E-value=1.7e-19  Score=120.71  Aligned_cols=66  Identities=23%  Similarity=0.248  Sum_probs=58.5

Q ss_pred             cccccccceeeEeeccccEEEEEEEEeccccceeecceEEEec----------CeeeeecCcEEEeeCcEEEEEeC
Q psy9934          82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----------GHCTGKLGEVLIRCNNILYIRGA  147 (158)
Q Consensus        82 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----------~~~~~~~g~~~iRG~~I~~i~~~  147 (158)
                      -|.++++++|.|+|+|||.|.|+|.|||+||||+|++|+|+..          ....+.+|.++|||++|++|+..
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEcc
Confidence            4778999999999999999999999999999999999999741          12357899999999999999854

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1.4e-19  Score=120.98  Aligned_cols=70  Identities=27%  Similarity=0.319  Sum_probs=64.4

Q ss_pred             CcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCC
Q psy9934          81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEG  150 (158)
Q Consensus        81 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~  150 (158)
                      .||+++.+++|.|+|++|.+|+|+|.++|+|||++|+||++...+....+++.+||||++|.+|..||.-
T Consensus         4 ~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~lPd~l   73 (80)
T d1b34a_           4 RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSL   73 (80)
T ss_dssp             HHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTC
T ss_pred             HHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEECCCCc
Confidence            3788999999999999999999999999999999999999987666668899999999999999998653

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.77  E-value=1.1e-19  Score=121.62  Aligned_cols=65  Identities=22%  Similarity=0.190  Sum_probs=57.4

Q ss_pred             HHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEec----------cceecceeEEEEecCCCCCCC
Q psy9934          12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG----------HCTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus        12 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----------~~~~~lg~~~iRG~~i~~I~p   76 (158)
                      .|.++++++|.|.|+|||.|.|+|.|||.|||++|+||+|++..          ...+.+|+++|||++|..+..
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~   76 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTV   76 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEc
Confidence            37899999999999999999999999999999999999998421          135789999999999998764

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

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

Probab=99.75  E-value=3.3e-19  Score=122.28  Aligned_cols=72  Identities=13%  Similarity=0.161  Sum_probs=59.0

Q ss_pred             CCCcccccc--cceeeEeeccccEEEEEEEEeccccceeecceEEEecC--------------eeeeecCcEEEeeCcEE
Q psy9934          79 PKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG--------------HCTGKLGEVLIRCNNIL  142 (158)
Q Consensus        79 P~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------------~~~~~~g~~~iRG~~I~  142 (158)
                      |..+|..+.  +++|.|++++|+.+.|+|.|||+||||+|+||+|++..              ...+.+|.+||||+||+
T Consensus         3 Pl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnVv   82 (93)
T d1b34b_           3 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVI   82 (93)
T ss_dssp             HHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEE
T ss_pred             cHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEEE
Confidence            445566665  78999999999999999999999999999999997421              12467999999999999


Q ss_pred             EEEeCCCC
Q psy9934         143 YIRGAEEG  150 (158)
Q Consensus       143 ~i~~~~~~  150 (158)
                      +|..++..
T Consensus        83 ~I~~~p~~   90 (93)
T d1b34b_          83 VVLRNPLI   90 (93)
T ss_dssp             EEEECCCC
T ss_pred             EEEcChhh
Confidence            99887753

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

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

Probab=99.74  E-value=7.6e-19  Score=120.44  Aligned_cols=67  Identities=15%  Similarity=0.184  Sum_probs=58.6

Q ss_pred             chHHHhhcC--CCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEec--------------cceecceeEEEEecCCC
Q psy9934           9 PKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG--------------HCTGKLGEVLIRSLTMS   72 (158)
Q Consensus         9 p~~~L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------------~~~~~lg~~~iRG~~i~   72 (158)
                      |+++|.+++  +++|.|.+++||.+.|+|.|||+||||+|+||+|++..              ...+.+|.++|||++|.
T Consensus         3 Pl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnVv   82 (93)
T d1b34b_           3 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVI   82 (93)
T ss_dssp             HHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEE
T ss_pred             cHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEEE
Confidence            899999998  99999999999999999999999999999999998421              12467999999999998


Q ss_pred             CCC
Q psy9934          73 TPL   75 (158)
Q Consensus        73 ~I~   75 (158)
                      .+.
T Consensus        83 ~I~   85 (93)
T d1b34b_          83 VVL   85 (93)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            875

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

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

Probab=99.66  E-value=3.1e-17  Score=117.93  Aligned_cols=62  Identities=29%  Similarity=0.296  Sum_probs=56.8

Q ss_pred             hHHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEEecCCCCCC
Q psy9934          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRSLTMSTPL   75 (158)
Q Consensus        10 ~~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~i~~I~   75 (158)
                      +++|++++|++|.|+|+||++|.|+|.+||+|||++|+||++..    ...++.++|||++|+++.
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~----~~k~~~v~IRG~~I~~I~   63 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA----GEKFNRVFIMYRYIVHID   63 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETT----CCEEEEEEECGGGEEEEE
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECC----CCcccEEEEeCCeEEEEE
Confidence            47899999999999999999999999999999999999999852    346899999999999986

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

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

Probab=99.66  E-value=6.3e-17  Score=116.30  Aligned_cols=68  Identities=32%  Similarity=0.414  Sum_probs=60.8

Q ss_pred             CcccccccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEeeCcEEEEEeCCCCCc
Q psy9934          81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDE  152 (158)
Q Consensus        81 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iRG~~I~~i~~~~~~~~  152 (158)
                      .+|+++++++|.|+|+||++|.|+|.+||+|||++|+||++.. +   .+++.++|||++|.+|..+++..+
T Consensus         3 ~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~-~---~k~~~v~IRG~~I~~I~~~e~~iD   70 (127)
T d1m5q1_           3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA-G---EKFNRVFIMYRYIVHIDSTERRID   70 (127)
T ss_dssp             HHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETT-C---CEEEEEEECGGGEEEEEECSCCCC
T ss_pred             hHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECC-C---CcccEEEEeCCeEEEEEcchhhcC
Confidence            3678899999999999999999999999999999999999852 2   257889999999999999998654

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

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

Probab=96.08  E-value=0.0056  Score=37.67  Aligned_cols=36  Identities=31%  Similarity=0.374  Sum_probs=29.3

Q ss_pred             HHHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeEEc
Q psy9934          11 PFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLA   47 (158)
Q Consensus        11 ~~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~   47 (158)
                      .||+.+  ....|+|.|.||-.+.|.+.+||.|.= .|+
T Consensus         5 ~fLn~~rk~~~~VtifL~nGvkl~G~I~~fD~ftv-LL~   42 (66)
T d1u1sa1           5 PYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVI-LLK   42 (66)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEE-EEE
T ss_pred             HHHHHHHHcCCcEEEEEEcCcEEEEEEEEEcceEE-EEE
Confidence            455555  567799999999999999999999984 454

>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: C-terminal domain of transcriptional repressors
family: Biotin repressor (BirA)
domain: Biotin repressor/biotin holoenzyme synthetase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.73  E-value=0.017  Score=32.91  Aligned_cols=47  Identities=21%  Similarity=0.101  Sum_probs=36.4

Q ss_pred             cCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEEEeccceecceeEEEE
Q psy9934          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR   67 (158)
Q Consensus        16 ~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iR   67 (158)
                      |+|++|.|.. +++++.|+..++|+.=.|.|+.....    ..-.-|++.+|
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t~~g~----~~~~sGEVSlR   47 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQDGII----KPWMGGEISLR   47 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEETTEE----EEESSCEEEEC
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEECCCE----EEEEEEEEEeC
Confidence            6899999975 56889999999999999999754432    23456777776

>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: LSM14 N-terminal domain-like
domain: LSM14 homolog A (Lsm14a)
species: Zebrafish (Danio rerio) [TaxId: 7955]

Probab=95.47  E-value=0.015  Score=36.97  Aligned_cols=61  Identities=16%  Similarity=0.184  Sum_probs=47.9

Q ss_pred             cCCCEEEEEEeCCcEEEEEEeEec-CcceeEEceeeEEE-ecc--------ceecceeEEEEecCCCCCCC
Q psy9934          16 LTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEII-DGH--------CTGKLGEVLIRSLTMSTPLP   76 (158)
Q Consensus        16 ~~~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~-~~~--------~~~~lg~~~iRG~~i~~I~p   76 (158)
                      |+|+++.+--+.+-.|.|.|..+| .---+.|+||..+- .+.        .....+.+..||+.|.-+..
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v   72 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTV   72 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEE
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEe
Confidence            789999999999999999999999 44558999998772 111        12345679999999987653

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

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

Probab=95.18  E-value=0.018  Score=34.62  Aligned_cols=37  Identities=19%  Similarity=0.226  Sum_probs=29.6

Q ss_pred             HHhhc--CCCEEEEEEeCCcEEEEEEeEecCcceeEEce
Q psy9934          12 FLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLAS   48 (158)
Q Consensus        12 ~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   48 (158)
                      ||..+  ...+|+|.|.||-.+.|.+.+||.|.=+...+
T Consensus         6 fln~lr~~~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~   44 (60)
T d1kq1a_           6 ALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQ   44 (60)
T ss_dssp             HHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             HHHHHHHcCCcEEEEEECCcEEEEEEEEEcceEEEEEeC
Confidence            44444  46789999999999999999999998555444

>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: LSM14 N-terminal domain-like
domain: LSM14 homolog A (Lsm14a)
species: Zebrafish (Danio rerio) [TaxId: 7955]

Probab=94.80  E-value=0.096  Score=33.06  Aligned_cols=66  Identities=18%  Similarity=0.201  Sum_probs=52.1

Q ss_pred             cccceeeEeeccccEEEEEEEEecc-ccceeecceEEEe-cCe--------eeeecCcEEEeeCcEEEEEeCCCCC
Q psy9934          86 LTGKSVICKLKWGHEYKGILVSTDG-YMNCQLASTEEII-DGH--------CTGKLGEVLIRCNNILYIRGAEEGD  151 (158)
Q Consensus        86 ~~~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~~~~e~~-~~~--------~~~~~g~~~iRG~~I~~i~~~~~~~  151 (158)
                      ++++++.+..+.+-.|.|+|..+|. ---+.|.++..+- +|.        ...-++.++.||+.|.-+...+..+
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e~p~   77 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEPPK   77 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESSCCC
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEeccCCC
Confidence            5789999999999999999999994 4568899988652 221        1235689999999999998877553

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

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

Probab=93.61  E-value=0.052  Score=32.56  Aligned_cols=33  Identities=18%  Similarity=0.233  Sum_probs=27.8

Q ss_pred             cceeeEeeccccEEEEEEEEeccccceeecceE
Q psy9934          88 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTE  120 (158)
Q Consensus        88 ~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~  120 (158)
                      +.+|.|-|.+|-.++|.+.|||+|.=|.-.+..
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~~~   46 (60)
T d1kq1a_          14 QTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGK   46 (60)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEEEETTE
T ss_pred             CCcEEEEEECCcEEEEEEEEEcceEEEEEeCCc
Confidence            458999999999999999999999877654433

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

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

Probab=93.45  E-value=0.039  Score=33.74  Aligned_cols=28  Identities=21%  Similarity=0.145  Sum_probs=24.7

Q ss_pred             cceeeEeeccccEEEEEEEEecccccee
Q psy9934          88 GKSVICKLKWGHEYKGILVSTDGYMNCQ  115 (158)
Q Consensus        88 ~k~V~V~L~~g~~~~G~L~~~D~~mNlv  115 (158)
                      +.+|.|-|.+|-.++|.+.|||+|.=|.
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvLL   41 (66)
T d1u1sa1          14 RVPVSIYLVNGIKLQGQIESFDQFVILL   41 (66)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             CCcEEEEEEcCcEEEEEEEEEcceEEEE
Confidence            4589999999999999999999997553

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

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

Probab=91.85  E-value=0.2  Score=29.78  Aligned_cols=41  Identities=20%  Similarity=0.275  Sum_probs=32.7

Q ss_pred             HHHhhcCCCEEEEEEeCCcEEEEEEeEecCcceeEEceeeEE
Q psy9934          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI   52 (158)
Q Consensus        11 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~   52 (158)
                      +-|....|++|-|-..+...+.|+|.-||+-. +.|+|++..
T Consensus         5 ktL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~   45 (66)
T d1ycya1           5 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDV   45 (66)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEET
T ss_pred             HHHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHH
Confidence            35778899999999999999999999999776 788999986

>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: C-terminal domain of transcriptional repressors
family: Biotin repressor (BirA)
domain: Biotin repressor/biotin holoenzyme synthetase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.42  E-value=0.24  Score=27.77  Aligned_cols=47  Identities=19%  Similarity=0.044  Sum_probs=33.3

Q ss_pred             cccceeeEeeccccEEEEEEEEeccccceeecceEEEecCeeeeecCcEEEe
Q psy9934          86 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR  137 (158)
Q Consensus        86 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~iR  137 (158)
                      +++++|.+.. ++++++|+..++|+.-.|.|+...    +.+...-|.+-+|
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t~~----g~~~~~sGEVSlR   47 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQDG----IIKPWMGGEISLR   47 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEETT----EEEEESSCEEEEC
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEECC----CEEEEEEEEEEeC
Confidence            4678999865 557899999999999999987433    2222344555554

>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]}

class: All beta proteins
fold: Sm-like fold
superfamily: YhbC-like, C-terminal domain
family: YhbC-like, C-terminal domain
domain: Hypothetical protein SP14.3 (SP0552)
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=84.23  E-value=0.67  Score=28.00  Aligned_cols=33  Identities=18%  Similarity=0.172  Sum_probs=27.6

Q ss_pred             chHHHhhcCCCEEEEEEeC---C-cEEEEEEeEecCc
Q psy9934           9 PKPFLNLLTGKSVICKLKW---G-HEYKGILVSTDGY   41 (158)
Q Consensus         9 p~~~L~~~~~k~V~V~l~~---g-~~~~G~L~~~D~~   41 (158)
                      -...+..++|+.|.|+|+.   | +.+.|.|.++|+-
T Consensus         5 ~~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~   41 (74)
T d1ib8a1           5 TKDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED   41 (74)
T ss_dssp             SHHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             CHHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCC
Confidence            3466788899999999863   4 8999999999964