Citrus Sinensis ID: 011128

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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-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490---
Protein Sequence
MAAAATEAPRSSSSGSADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHNDPAIIQSHYSQAAIASTTLPSGTGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWGSSPMPTTNGAGLAMPMYWQGFYGSPNGLQGQQQPLLQPPPGLSMLPSMQQSMQYPAMNPSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLPAQSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPLNSGIDKTAVAPVSEPKSVPGPIMPFQSTVSESVSTVGMSSSILNDGIMPSLVTPGQLLQPGLPAVSSSQSSQAAQKDVEVVQLSSSESAAAPPPASDVQEPILPLPSTTERKPYGAPTSTQYGYRGGRGRGRGRGNEVCLSCCPNVIAAHVRLYFFFFHN
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEEEccccEEEEEEccccccccEEEEcccccccccccccccccccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHEEEEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccEEEEEEcccEEEEEEEEEEcccccEEEHHcEcccccccccccccccccccEEEEEEEEccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccEEEEEEEEEEEEEcc
Coil and Loop (DISEMBL)
maaaateaprssssgsadsYIGSLISltskseiryeGVLFNinteessiglrndrleqkgeekigpqvppsdkiyEYILFRGSDIKHCLLTItgdaisgprlsqtrdWTLRSVIRKDiqdlqvkssppvqtttsihndpaiiqSHYSQAAiasttlpsgtgslpdptsqtsqlglsrppfqgnpplyqpggslgawgsspmpttngaglampmywqgfygspnglqgqqqpllqpppglsmlpsmqqsmqypamnpslptgvsnlpasqlaehrpplmppistgtlnllspmlpaqssamisdsstnlipdkastqtlptaapstslplvpplnsgidktavapvsepksvpgpimpfqstvsesvstvgmsssilndgimpslvtpgqllqpglpavsssqssqaaqKDVEVVqlsssesaaapppasdvqepilplpstterkpygaptstqygyrggrgrgrgrgnevclsccpnvIAAHVRLYFFFFHN
Flexible Loop (DISEMBL)
maaaateaprssssgsadsyIGSLISLTSKSEIRYEGVLfninteessiGLRNdrleqkgeekigpqvppsdKIYEYILFRGSDIKHCLLTItgdaisgprlsqtrdWTLRSVIRkdiqdlqvkssppvqtttsiHNDPAIIQSHYSQAAIASTTLPSGTGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWGSSPMPTTNGAGLAMPMYWQGFYGSPNGLQGQQQPLLQPPPGLSMLPSMQQSMQYPAMNPSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLPAQSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPLNSGIDKTAVAPVSEPKSVPGPIMPFQSTVSESVSTVGMSSSILNDGIMPSLVTPGQLLQPGLPAVSSSQSSQAAQKDVEVVQLSSSesaaapppasdvqepilplpstterkpygaptstqygyrggrgrGRGRGNEVCLSCCPNVIAAHVRLYFFFFHN
Low Complexity Region (SEG)
MAAAATEAPRssssgsadsyigsLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHNDPAIIQSHYSQAAIASTTLPSGTGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWGSSPMPTTNGAGLAMPMYWQGFYGSPNGlqgqqqpllqpppglsmlpsmqQSMQYPAMNPSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLPAQSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPLNSGIDKTAVAPVSEPKSVPGPIMPFQstvsesvstvgmsssILNDGIMPSLVTPGQLLQPGLPavsssqssqaaqKDVEVVQLsssesaaapppasDVQEPILPLPSTTERKPYGAPTSTQygyrggrgrgrgrgNEVCLSCCPNVIAAHVRLYFFFFHN
Disordered region (IsUnstruct)
*******************YIGSLISLTSKSEIRYEGVLFNINT****************************KIYEYILFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQ***************************************************************************************AGLAMPMYWQGFYG*********************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
***********************LISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQ*********VPPSDKIYEYILFRGSDIKH*************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************LSCCPNVIAAHVRLYFFFFHN
Disordered Region (DISEMBL)
******************SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQ*********TTSIHNDPAIIQSHYSQAAIASTTLPSG**************GLSRPPFQGNPPLYQPGGSLGAWGSSPMPTTNGAGLAMPMYWQGFYGSPNGLQGQQQPLLQPPPGLSMLPSMQQSMQYPAMNPSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLPAQSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPLNSGIDKTAVAPVSEPKSVPGPIMPFQSTVSESVSTVGMSSSILNDGIMPSLVTPGQLLQP*************************************VQEPILPLPSTTERKPYGAPTSTQYGYRGGRGRGRGRGNEVCLSCCPNVIAAHVRLYFFFFHN
Disordered Region (DISPRO)
******************SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITG*******LS*******************************************************************************************************AGLAMPMYWQG*YGSP********PLLQPPPGLSMLPSMQQSMQYPAMNPSL*****************************************************************************************************************************************************************************************RK*********************RGNEVCLSCCPNVIAAHVRLYFFFFHN
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAAATEAPRSSSSGSADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHNDPAIIQSHYSQAAIASTTLPSGTGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWGSSPMPTTNGAGLAMPMYWQGFYGSPNGLQGQQQPLLQPPPGLSMLPSMQQSMQYPAMNPSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLPAQSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPLNSGIDKTAVAPVSEPKSVPGPIMPFQSTVSESVSTVGMSSSILNDGIMPSLVTPGQLLQPGLPAVSSSQSSQAAQKDVEVVQLSSSESAAAPPPASDVQEPILPLPSTTERKPYGAPTSTQYGYRGGRGRGRGRGNEVCLSCCPNVIAAHVRLYFFFFHN
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	493	2.2.26 [Sep-21-2011]
Q9C658	611	Protein decapping 5 OS=Ar	yes	no	0.825	0.666	0.443	2e-71
Q9FH77	571	Decapping 5-like protein	no	no	0.229	0.197	0.387	4e-20
Q9HGL3	426	Protein sum2 OS=Schizosac	yes	no	0.551	0.638	0.286	1e-13
Q8ND56	463	Protein LSM14 homolog A O	yes	no	0.135	0.144	0.522	8e-13
Q5R4R4	463	Protein LSM14 homolog A O	yes	no	0.135	0.144	0.522	9e-13
A0A8M2	471	Protein LSM14 homolog A-A	N/A	no	0.135	0.142	0.537	1e-12
Q8K2F8	462	Protein LSM14 homolog A O	yes	no	0.144	0.153	0.492	1e-12
Q8AVJ2	471	Protein LSM14 homolog A-B	N/A	no	0.135	0.142	0.522	1e-12
Q3MHF8	463	Protein LSM14 homolog A O	yes	no	0.135	0.144	0.522	1e-12
Q6NVR8	469	Protein LSM14 homolog A O	yes	no	0.135	0.142	0.522	2e-12

>sp|Q9C658|DCP5_ARATH Protein decapping 5 OS=Arabidopsis thaliana GN=DCP5 PE=1 SV=1

 Score =  270 bits (689), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 218/491 (44%), Positives = 262/491 (53%), Gaps = 84/491 (17%)

Query: 1   MAAAATEAPRSSSSGSADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQK 59
           MAA  T    S SS +ADSY+GSLISLTSKSEIRYEG+L+NINT+ESSIGL+N R    +
Sbjct: 1   MAADNT---GSKSSSAADSYVGSLISLTSKSEIRYEGILYNINTDESSIGLQNVRSFGTE 57

Query: 60  GEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQ 119
           G +K GPQVPPSDK+YEYILFRG+DIK                                 
Sbjct: 58  GRKKDGPQVPPSDKVYEYILFRGTDIK--------------------------------- 84

Query: 120 DLQVKSSPPVQ-TTTSIHNDPAIIQSHYSQAAIASTTLPS-GTGSLPDPTSQTSQLGLSR 177
           DLQVK+SPPVQ   ++I+NDPAIIQSHY      S +LPS  +GSLPD +S   Q G   
Sbjct: 85  DLQVKASPPVQPPASTINNDPAIIQSHYPSPMPTSGSLPSTASGSLPDISSHNGQPGQHG 144

Query: 178 PPFQGNPPLYQPGGSLGAWGSSPMPTTNGAGLAMPMYWQGFYG-SPNGL-QGQQQPLLQP 235
             FQ   PLYQPGG+LG+WG+SP P         PMYWQGFY   PNGL Q  QQ L++P
Sbjct: 145 MGFQNAMPLYQPGGNLGSWGASPQP---------PMYWQGFYTPPPNGLPQLHQQSLIRP 195

Query: 236 PPGLSMLPSMQQSMQYPAMNPSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLP- 294
           P GL M  S+QQ +QYP  N   P   S+          P  + P ST +  L    LP 
Sbjct: 196 PHGLPMPNSLQQPLQYPNFNTPPPPTGSSSLQGSSLPEAPSSLFPFSTSSQMLAPSSLPF 255

Query: 295 ------------------AQSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPLNSG 336
                             A S ++ S+ +  L+ +KA     PT    T+L     L+  
Sbjct: 256 PGLPPVTLSSSLQSTLQSAPSPSLASEMAPPLLSNKAPITAPPTLPQDTNL-----LSFS 310

Query: 337 IDKTAVAPVS-------EPKSVPGPIMPFQSTVSESVSTVGMSSSILNDGIMPSLVTPGQ 389
           +  T     S       +P  V GPI P Q+T   S    G+SSSI  D   P LVTPGQ
Sbjct: 311 LSTTRATEASTGLPLSNKPSVVTGPISPPQTTPLTSAPVAGVSSSISQDKPKPLLVTPGQ 370

Query: 390 LLQPGLPAVSSSQSSQAAQKDVEVVQLSSSES-AAAPPPASDVQEPILPLPSTTE--RKP 446
           LLQ G  AVS S  S  A KDVEVVQ+SSS     + P  S+ Q PILPLPS+    +KP
Sbjct: 371 LLQSGSSAVSLSPPSTNADKDVEVVQVSSSAGLEQSVPVTSEAQPPILPLPSSARPTQKP 430

Query: 447 YGAPTSTQYGY 457
            G       GY
Sbjct: 431 NGHSFPNHNGY 441

As a component of the decapping complex, involved in the degradation of mRNAs. Promotes P-body formation. Translational repressor.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FH77|DCP5L_ARATH Decapping 5-like protein OS=Arabidopsis thaliana GN=DCP5-L PE=2 SV=1

 Score = 99.8 bits (247), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 57/147 (38%), Positives = 82/147 (55%), Gaps = 34/147 (23%)

Query: 17  ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIY 75
            D++IGS ISL SK EIRYEG+L+++N ++S++GL+N R    +G +K GPQ+PP DK+Y
Sbjct: 30  GDTFIGSFISLISKYEIRYEGILYHLNVQDSTLGLKNVRSCGTEGRKKDGPQIPPCDKVY 89

Query: 76  EYILFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSI 135
           +YILFRGSDIK                                 DLQV  SP  Q+   I
Sbjct: 90  DYILFRGSDIK---------------------------------DLQVNPSPSAQSRQEI 116

Query: 136 HNDPAIIQSHYSQAAIASTTLPSGTGS 162
            ++  + QS +S+ A+  ++  SG  S
Sbjct: 117 QSEQDVNQSPHSRPAMTMSSPISGYDS 143

As a component of the decapping complex, involved in the degradation of mRNAs. Promotes P-body formation. Translational repressor (By similarity).

Arabidopsis thaliana (taxid: 3702)

>sp|Q9HGL3|SUM2_SCHPO Protein sum2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=sum2 PE=2 SV=1

 Score = 78.6 bits (192), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 103/360 (28%), Positives = 154/360 (42%), Gaps = 88/360 (24%)

Query: 20  YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGP--QVPPSDKIYEY 77
           +IGS ISL SKS+IRY G+L +IN+++S++ L++ R       K  P  ++PPSD +++Y
Sbjct: 4   FIGSRISLISKSDIRYVGILQDINSQDSTLALKHVRWCGTEGRKQDPSQEIPPSDNVFDY 63

Query: 78  ILFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHN 137
           I+FRGSD+K   +                            +     S+PPVQ      N
Sbjct: 64  IVFRGSDVKDLRIE---------------------------EPATTPSAPPVQPP----N 92

Query: 138 DPAII-----QSHYSQAAIASTTLPSGTGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGS 192
           DPAII     Q +++QA  A    P        P  Q    G     +   P  + P G 
Sbjct: 93  DPAIIGSNSGQYNWNQAQTAQPPQPVQPNPYGAPYQQAPPAGAPYYMYPNAPAQFVPPGG 152

Query: 193 LGAWGSSPMPT-TNGAGLAMPMYWQGFYGSPNGLQGQQQPLL----------QPP----P 237
           L      P+ T  + +  A+P     +YG+P+  Q  Q+P            Q P    P
Sbjct: 153 L------PLGTPLDASTPAVP-----YYGAPDQQQMGQRPEFAQNVSQGFAGQAPYNVRP 201

Query: 238 GLSMLPSMQQSMQY-PAMNPSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLPA- 295
           G  M PS Q+   + P M    PT VS  P+ Q        MPP + G +    P + A 
Sbjct: 202 GYGM-PSNQKPPNFAPGMPAPGPTAVSASPSLQ-------SMPP-TNGVIPGAQPSIEAS 252

Query: 296 --------QSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPLNSGIDKTAVAPVSE 347
                   ++S + +D   N   D + +QT+ T+ PS  +P   P     D +A  P +E
Sbjct: 253 IEKESTSIRNSTVTNDRVVNTTVDVSQSQTVETSGPSKEVPTTQP-----DASAAKPRTE 307

Required for G2/M phase checkpoint control.

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

>sp|Q8ND56|LS14A_HUMAN Protein LSM14 homolog A OS=Homo sapiens GN=LSM14A PE=1 SV=3

 Score = 75.5 bits (184), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 47/67 (70%)

Query: 20 YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYIL 79
          YIGS ISL SK+EIRYEG+L+ I+TE S++ L   R     +      +PP D+++EYI+
Sbjct: 7  YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYII 66

Query: 80 FRGSDIK 86
          FRGSDIK
Sbjct: 67 FRGSDIK 73

Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for non-translating mRNAs.

Homo sapiens (taxid: 9606)

>sp|Q5R4R4|LS14A_PONAB Protein LSM14 homolog A OS=Pongo abelii GN=LSM14A PE=2 SV=1

 Score = 75.5 bits (184), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 47/67 (70%)

Query: 20 YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYIL 79
          YIGS ISL SK+EIRYEG+L+ I+TE S++ L   R     +      +PP D+++EYI+
Sbjct: 7  YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYII 66

Query: 80 FRGSDIK 86
          FRGSDIK
Sbjct: 67 FRGSDIK 73

Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for non-translating mRNAs.

Pongo abelii (taxid: 9601)

>sp|A0A8M2|L14AA_XENLA Protein LSM14 homolog A-A OS=Xenopus laevis GN=lsm14a-a PE=1 SV=1

 Score = 75.5 bits (184), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 36/67 (53%), Positives = 47/67 (70%)

Query: 20 YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYIL 79
          YIGS ISL SK+EIRYEG+L+ I+TE S++ L   R     +      +PP D+I+EYI+
Sbjct: 7  YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEIFEYII 66

Query: 80 FRGSDIK 86
          FRGSDIK
Sbjct: 67 FRGSDIK 73

RNA-binding component of messenger ribonucleoprotein complexes (mRNPs), storage particles that mask maternal mRNAs from the translational apparatus during oocyte maturation. Acts as a repressor of mRNA translation.

Xenopus laevis (taxid: 8355)

>sp|Q8K2F8|LS14A_MOUSE Protein LSM14 homolog A OS=Mus musculus GN=Lsm14a PE=1 SV=1

 Score = 75.5 bits (184), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/71 (49%), Positives = 48/71 (67%)

Query: 20 YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYIL 79
          YIGS ISL SK+EIRYEG+L+ I+TE S++ L   R     +      +PP D+++EYI+
Sbjct: 7  YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYII 66

Query: 80 FRGSDIKHCLL 90
          FRGSDIK   +
Sbjct: 67 FRGSDIKDLTV 77

Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for non-translating mRNAs.

Mus musculus (taxid: 10090)

>sp|Q8AVJ2|L14AB_XENLA Protein LSM14 homolog A-B OS=Xenopus laevis GN=lsm14a-b PE=2 SV=1

 Score = 75.1 bits (183), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 47/67 (70%)

Query: 20 YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYIL 79
          YIGS ISL SK+EIRYEG+L+ I+TE S++ L   R     +      +PP D+++EYI+
Sbjct: 7  YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYII 66

Query: 80 FRGSDIK 86
          FRGSDIK
Sbjct: 67 FRGSDIK 73

RNA-binding component of messenger ribonucleoprotein complexes (mRNPs), storage particles that mask maternal mRNAs from the translational apparatus during oocyte maturation. Acts as a repressor of mRNA translation.

Xenopus laevis (taxid: 8355)

>sp|Q3MHF8|LS14A_BOVIN Protein LSM14 homolog A OS=Bos taurus GN=LSM14A PE=2 SV=1

 Score = 75.1 bits (183), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 47/67 (70%)

Query: 20 YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYIL 79
          YIGS ISL SK+EIRYEG+L+ I+TE S++ L   R     +      +PP D+++EYI+
Sbjct: 7  YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYII 66

Query: 80 FRGSDIK 86
          FRGSDIK
Sbjct: 67 FRGSDIK 73

Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for non-translating mRNAs.

Bos taurus (taxid: 9913)

>sp|Q6NVR8|LS14A_XENTR Protein LSM14 homolog A OS=Xenopus tropicalis GN=lsm14a PE=2 SV=1

 Score = 74.3 bits (181), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 47/67 (70%)

Query: 20 YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYIL 79
          YIGS ISL SK+EIRYEG+L+ I+TE S++ L   R     +      +PP D+++EYI+
Sbjct: 7  YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYII 66

Query: 80 FRGSDIK 86
          FRGSDIK
Sbjct: 67 FRGSDIK 73

RNA-binding component of messenger ribonucleoprotein complexes (mRNPs), storage particles that mask maternal mRNAs from the translational apparatus during oocyte maturation. Acts as a repressor of mRNA translation.

Xenopus tropicalis (taxid: 8364)

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	493
224079874	579	predicted protein [Populus trichocarpa]	0.789	0.671	0.590	1e-116
255570007	576	conserved hypothetical protein [Ricinus	0.851	0.729	0.536	1e-108
224127400	564	predicted protein [Populus trichocarpa]	0.778	0.680	0.571	1e-106
147860146	665	hypothetical protein VITISV_020005 [Viti	0.819	0.607	0.506	1e-91
225423849	616	PREDICTED: uncharacterized protein LOC10	0.793	0.634	0.511	3e-91
356499741	616	PREDICTED: uncharacterized protein LOC10	0.809	0.647	0.483	4e-88
224111756	632	predicted protein [Populus trichocarpa]	0.799	0.623	0.481	4e-86
224099297	631	predicted protein [Populus trichocarpa]	0.825	0.645	0.475	5e-86
449503510	579	PREDICTED: protein decapping 5-like [Cuc	0.807	0.687	0.492	7e-86
297737880	564	unnamed protein product [Vitis vinifera]	0.750	0.656	0.518	2e-85

>gi|224079874|ref|XP_002305956.1| predicted protein [Populus trichocarpa] gi|222848920|gb|EEE86467.1| predicted protein [Populus trichocarpa]

 Score =  424 bits (1091), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 262/444 (59%), Positives = 303/444 (68%), Gaps = 55/444 (12%)

Query: 20  YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYI 78
           Y+GSLISLTSKSEIRYEGVLFNINT+ES+IGLRN R    +G +K G QVPPSDKIYE+I
Sbjct: 31  YVGSLISLTSKSEIRYEGVLFNINTQESTIGLRNVRSFGTEGRKKDGLQVPPSDKIYEFI 90

Query: 79  LFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHND 138
           LFRG+DIK                                 DLQVKSSPPVQT T +HND
Sbjct: 91  LFRGTDIK---------------------------------DLQVKSSPPVQTATPVHND 117

Query: 139 PAIIQSHYSQAAIASTTLP-SGTGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWG 197
           PAIIQS Y QAA AS  LP SG GSL DP+S  S  GL RP FQG+ P YQP  SL +WG
Sbjct: 118 PAIIQSQYPQAATASMNLPSSGNGSLTDPSSHASSNGLPRPTFQGSLPQYQPDASLESWG 177

Query: 198 -SSPMPTTNGAGLAMPMYWQGFYGSPNGLQGQQQPLLQPPPGLSMLPSMQQSMQYPAMNP 256
            S  +PTTNG+GLAMPMYWQG+YG  NG+Q  QQ LL+PPPGLSM PSM QS+QYPAMN 
Sbjct: 178 PSHLLPTTNGSGLAMPMYWQGYYGPSNGVQAPQQALLRPPPGLSMPPSMMQSVQYPAMN- 236

Query: 257 SLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLP-AQSSAMISDSSTNLIPDKAST 315
                 SN  AS L+E  PPL+PP ST TLNL +  +P ++SSAM+SD STNL PD+ ST
Sbjct: 237 -----ASNTSASPLSE-SPPLLPPFSTSTLNLQTSTIPSSRSSAMVSD-STNLTPDRVST 289

Query: 316 QTLPTAAPSTSLPLVPPLNSGIDKTAVA-PVSE-PKSVPGPIMPFQSTVSESVSTVGMSS 373
           QTLP     ++LPL  PL + +DK A+A P S  PK+VP PIMPF+       S +  SS
Sbjct: 290 QTLP-----SNLPLASPLTTAVDKIAIASPGSYLPKTVPDPIMPFKRMSEPPSSIMRTSS 344

Query: 374 SILNDGIMPSLVTPGQLLQPGLPAVSSSQSSQAAQKDVEVVQLSSSESAAAPP--PASDV 431
           S+L +G  P LVTPGQL QPG P V S QSSQ AQKDVEVVQ+SS E +A PP   A++V
Sbjct: 345 SVLKEGKTP-LVTPGQLSQPGPPIVPSLQSSQIAQKDVEVVQVSSPELSALPPTTAAAEV 403

Query: 432 QEPILPLPSTTERKPYGAPTSTQY 455
           Q+PILPLPS  E K YGAP  T +
Sbjct: 404 QKPILPLPSQPEHKIYGAPMYTYH 427

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255570007|ref|XP_002525966.1| conserved hypothetical protein [Ricinus communis] gi|223534698|gb|EEF36390.1| conserved hypothetical protein [Ricinus communis]

 Score =  397 bits (1020), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 258/481 (53%), Positives = 305/481 (63%), Gaps = 61/481 (12%)

Query: 2   AAAATEAPRSSSSGSADSYIGS--LISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQ 58
           A A  EAP+SSS G          LISLTSKSEIRYEGVL+NINT+ES+IGLRN R    
Sbjct: 4   ATATAEAPKSSSGGGGSGDSYIGSLISLTSKSEIRYEGVLYNINTQESTIGLRNVRSFGT 63

Query: 59  KGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDI 118
           +G ++ GPQVPPSDKIYE+ILFRGSDIK                                
Sbjct: 64  EGRKRDGPQVPPSDKIYEFILFRGSDIK-------------------------------- 91

Query: 119 QDLQVKSSPPVQTTTSIHNDPAIIQSHYSQAAIASTTLP-SGTGSLPDPTSQTSQLGLSR 177
            DLQVKSSPPVQTT  IH DPAIIQSHY Q A AS T+P S TGSL D +S  S   LS 
Sbjct: 92  -DLQVKSSPPVQTTKPIHTDPAIIQSHYPQTATASMTMPSSSTGSLKDSSSHASPHELSM 150

Query: 178 PPFQGNPPLYQPGGSLGAWGS-SPMPTTNGAGLAMPMYWQGFYGSPNGLQGQQQPLLQPP 236
           P FQGN PLYQPGG LG+ GS S  PTT+G GLAMPMYWQG+Y   NGLQ  QQ LL PP
Sbjct: 151 PTFQGNLPLYQPGGKLGSQGSLSNPPTTSGTGLAMPMYWQGYYDPSNGLQPHQQTLLHPP 210

Query: 237 PGLSMLPSMQQSMQYPAMNPSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLPAQ 296
           PGLS+ PS+QQ +Q+PA      T  S L ASQ++E+ P   P  STGT N+ S +LP Q
Sbjct: 211 PGLSIPPSIQQYVQHPA------TDASKLSASQMSENPPLSFPSFSTGTQNMQSSILPVQ 264

Query: 297 SSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPLNSGIDKTAVAP--VSEPKSVPGP 354
           SS  + DS+ NLI +KAS Q LP A+ + +LP+  PL S +DK+ +A   + E ++V  P
Sbjct: 265 SSPTVPDSA-NLISNKASVQALPAASVNINLPMASPLTSALDKSFIASPVIIESRTVDDP 323

Query: 355 IMPFQSTVSESVSTVGMSSSILNDGIMPSLVTPGQLLQPGLPAVSSSQSSQAAQKDVEVV 414
           ++P +S      S      S+ N+G +PSLVTPG  LQPG   V S QSSQAAQKDVE V
Sbjct: 324 LVPSKSMSESLSSNTRALVSVSNEGAIPSLVTPGHFLQPG--TVPSLQSSQAAQKDVEAV 381

Query: 415 QLSSSESAAAPPPAS----DVQEPILPLPSTTERKPYGAPTSTQYGYRGGRGRGRGRGNE 470
           Q  SSES   PPP++    ++QEPILPLP   +R+ YGAP  T   Y G RG  RGRGN 
Sbjct: 382 Q--SSES---PPPSTVAVMEMQEPILPLPCPPDRRVYGAPMHT---YHGSRGHERGRGNR 433

Query: 471 V 471
           V
Sbjct: 434 V 434

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127400|ref|XP_002329268.1| predicted protein [Populus trichocarpa] gi|222870722|gb|EEF07853.1| predicted protein [Populus trichocarpa]

 Score =  390 bits (1002), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 252/441 (57%), Positives = 292/441 (66%), Gaps = 57/441 (12%)

Query: 20  YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYI 78
           Y+GSLISLTSKSEIRYEGVLFNI+T+ES+IGLRN R    +G +K G QVPPSDK+YE+I
Sbjct: 24  YVGSLISLTSKSEIRYEGVLFNIDTQESTIGLRNVRSFGTEGRKKDGLQVPPSDKVYEFI 83

Query: 79  LFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHND 138
           LFRG+DIK                                 DLQVKS PPVQT T +HND
Sbjct: 84  LFRGTDIK---------------------------------DLQVKSYPPVQTATPVHND 110

Query: 139 PAIIQSHYSQAAIASTTLP-SGTGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWG 197
           PAIIQS Y QA  AS  LP S  G L DP+S  S  GL R  FQG+ P YQPG SL  WG
Sbjct: 111 PAIIQSQYPQATTASMNLPSSANGPLTDPSSHASSNGLPRATFQGSLPQYQPGASLEPWG 170

Query: 198 SSPM-PTTNGAGLAMPMYWQGFYGSPNGLQGQQQPLLQPPPGLSMLPSMQQSMQYPAMNP 256
            S + PTTN +GLAMPMYWQG+YG  NG+Q  QQ LL+PPP LSM PSM Q +QYPAMN 
Sbjct: 171 LSHLPPTTNTSGLAMPMYWQGYYGPSNGVQAPQQALLRPPPNLSMPPSMLQYVQYPAMN- 229

Query: 257 SLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLPAQSSAMISDSSTNLIPDKASTQ 316
                 SN  AS L E+ PPL+PP++  T       LP++SSAM+SD STNLIPD+ STQ
Sbjct: 230 -----ASNTSASALLENPPPLLPPLNLQTST-----LPSRSSAMVSD-STNLIPDRVSTQ 278

Query: 317 TLPTAAPSTSLPLVPPLNSGIDKTAVAP-VSE-PKSVPGPIMPFQSTVSESVSTVGMSSS 374
           TLP     + LPL  PL + +DK AVAP VS+ PK+VP PIMPF+S      S +  SSS
Sbjct: 279 TLP-----SKLPLASPLTTAVDKIAVAPSVSDIPKTVPDPIMPFKSISEPPTSIMRASSS 333

Query: 375 ILNDGIMPSLVTPGQLLQPGLPAVSSSQSSQAAQKDVEVVQLSSSESAAAPPPA--SDVQ 432
           + N+G  PSLVTPGQLLQPG P + S QSS  AQKDVEVVQ+SS E +A PP    ++VQ
Sbjct: 334 VTNEGKTPSLVTPGQLLQPGPPIMPSLQSSHIAQKDVEVVQVSSPELSAPPPTTALTEVQ 393

Query: 433 EPILPLPSTTERKPYGAPTST 453
           E ILPLPS  E K YGAP  T
Sbjct: 394 ESILPLPSQPEHKVYGAPMYT 414

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860146|emb|CAN78722.1| hypothetical protein VITISV_020005 [Vitis vinifera]

 Score =  343 bits (880), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 243/480 (50%), Positives = 292/480 (60%), Gaps = 76/480 (15%)

Query: 20  YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYI 78
           YIGSLISLTSKSEIRYEGVL+NINTEESSIGLRN R    +G +K GPQVPPSDK+YEYI
Sbjct: 15  YIGSLISLTSKSEIRYEGVLYNINTEESSIGLRNVRSFGTEGRKKDGPQVPPSDKVYEYI 74

Query: 79  LFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHND 138
           LFRGSDIK     +             R W    +    + DLQVKSSPPVQ T  I+ND
Sbjct: 75  LFRGSDIKIFSFIV-------------RGW----LALDSLPDLQVKSSPPVQATPPINND 117

Query: 139 PAIIQSHYSQAAIASTTLPSG-TGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWG 197
           PAIIQSHY + A  S +LPS  +G LPD +S  +QLGL    FQG  PLYQPGG+LG+WG
Sbjct: 118 PAIIQSHYPRPATTSASLPSTVSGPLPDLSSHNAQLGLPGSTFQGGLPLYQPGGNLGSWG 177

Query: 198 -SSPMPTTNGAGLAMPMYWQGFYGSPNGL-QGQQQPLLQPPPGLSMLPSMQQSMQYPAMN 255
            + P PT NG+GL MPMYWQG+YG PNGL    QQ LL+PPP LSM P     MQYP  N
Sbjct: 178 PAPPPPTANGSGLTMPMYWQGYYGPPNGLPHLHQQSLLRPPPVLSMPP-----MQYPGFN 232

Query: 256 PSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPML---------------------- 293
            SL  G  NLP S L E+  PL+ P S+G+LNL S  L                      
Sbjct: 233 ASLQPGAPNLPGSNLPEYSSPLL-PTSSGSLNLTSTSLSPSTLPSNLPSSMPSILPSSMP 291

Query: 294 --------------------PAQSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPL 333
                               P  S+A+ S++ ++L+P+K    TLP+     SLPLV PL
Sbjct: 292 SILPSSMPSILPSTLPSALPPVPSAALASETLSSLMPNKVPNPTLPSVTLGISLPLVTPL 351

Query: 334 N-SGIDKTAVAP--VSEPKSVPGPIMPFQSTVSESVSTVGMSSSILNDGIMPSLVTPGQL 390
           N S  +  A+AP   ++P +V GP +P+Q T+S+S+ +VG SS    +   PSLVTPGQL
Sbjct: 352 NTSSSEINAIAPPISNKPNAVSGPTLPYQ-TISQSIPSVGTSSPNHPEIAAPSLVTPGQL 410

Query: 391 LQPGLPAVSSSQSSQAAQKDVEVVQLSSSESAAAPPPAS-DVQEPILPL--PSTTERKPY 447
           LQ G   +SSS SSQ A KDVEVVQ+SSS S  +  P S + Q PILPL  PS T +K Y
Sbjct: 411 LQSGPTTISSSPSSQTAHKDVEVVQVSSSASQESSVPVSAEAQPPILPLPVPSRTVQKLY 470

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225423849|ref|XP_002281060.1| PREDICTED: uncharacterized protein LOC100242198 [Vitis vinifera]

 Score =  342 bits (876), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 243/475 (51%), Positives = 289/475 (60%), Gaps = 84/475 (17%)

Query: 20  YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYI 78
           YIGSLISLTSKSEIRYEGVL+NINTEESSIGLRN R    +G +K GPQVPPSDK+YEYI
Sbjct: 15  YIGSLISLTSKSEIRYEGVLYNINTEESSIGLRNVRSFGTEGRKKDGPQVPPSDKVYEYI 74

Query: 79  LFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHND 138
           LFRGSDIK                                 DLQVKSSPPVQ T  I+ND
Sbjct: 75  LFRGSDIK---------------------------------DLQVKSSPPVQATPPINND 101

Query: 139 PAIIQSHYSQAAIASTTLPSG-TGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWG 197
           PAIIQSHY + A  S +LPS  +G LPD +S  +QLGL    FQG  PLYQPGG+LG+WG
Sbjct: 102 PAIIQSHYPRPATTSASLPSTVSGPLPDLSSHNAQLGLPGSTFQGGLPLYQPGGNLGSWG 161

Query: 198 -SSPMPTTNGAGLAMPMYWQGFYGSPNGL-QGQQQPLLQPPPGLSMLPSMQQSMQYPAMN 255
            + P PT NG+GL MPMYWQG+YG PNGL    QQ LL+PPP LSM P     MQYP  N
Sbjct: 162 PAPPPPTANGSGLTMPMYWQGYYGPPNGLPHLHQQSLLRPPPVLSMPP-----MQYPGFN 216

Query: 256 PSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPML---------------------- 293
            SL  G  NLP S L E+  PL+ P S+G+LNL S  L                      
Sbjct: 217 ASLQPGAPNLPGSNLPEYSSPLL-PTSSGSLNLTSTSLSPSTLPSNLPSSMPSILPSSMP 275

Query: 294 ------------PAQSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPLN-SGIDKT 340
                       P  S+A+ S++ ++L+P+K    TLP+     SLPLV PLN S  +  
Sbjct: 276 SILPSTLPSALPPVPSAALASETLSSLMPNKVPNPTLPSVTLGISLPLVTPLNTSSSEIN 335

Query: 341 AVAP--VSEPKSVPGPIMPFQSTVSESVSTVGMSSSILNDGIMPSLVTPGQLLQPGLPAV 398
           A+AP   ++P +V GP +P+Q T+S+S+ +VG SS    +   PSLVTPGQLLQ G   +
Sbjct: 336 AIAPPISNKPNAVSGPTLPYQ-TISQSIPSVGTSSPNHPEIAAPSLVTPGQLLQSGPTTI 394

Query: 399 SSSQSSQAAQKDVEVVQLSSSESAAAPPPAS-DVQEPILPL--PSTTERKPYGAP 450
           SSS SSQ A KDVEVVQ+SSS S  +  P S + Q PILPL  PS T +K  GAP
Sbjct: 395 SSSPSSQTAHKDVEVVQVSSSASQESSVPVSAEAQPPILPLPVPSRTVQKLNGAP 449

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499741|ref|XP_003518695.1| PREDICTED: uncharacterized protein LOC100808030 [Glycine max]

 Score =  332 bits (850), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 230/476 (48%), Positives = 280/476 (58%), Gaps = 77/476 (16%)

Query: 20  YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYI 78
           YIGSLISLTSKSEIRYEG+L+NINTEESSIGLRN R    +G +K GPQ+PPSDK+YEYI
Sbjct: 16  YIGSLISLTSKSEIRYEGILYNINTEESSIGLRNVRSFGTEGRKKDGPQIPPSDKVYEYI 75

Query: 79  LFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHND 138
           LFRG+DIK                                 DLQVKSSPPVQ T  ++ND
Sbjct: 76  LFRGTDIK---------------------------------DLQVKSSPPVQPTPQVNND 102

Query: 139 PAIIQSHYSQAAIASTTLPSG-TGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWG 197
           PAIIQSHY      ST+LPS  +GSL DP+S T+QLGL    FQG  PLYQPGG++G+WG
Sbjct: 103 PAIIQSHYPFPVTTSTSLPSAVSGSLTDPSSHTTQLGLPGSNFQGPLPLYQPGGNIGSWG 162

Query: 198 SS-PMPTTNGAGLAM-PMYWQGFYGSPNGL-QGQQQPLLQPPPGLSMLPSMQQSMQYPAM 254
           +S P P  NG  LAM PMYWQG+YG+PNGL Q  QQ LLQPPPGLSM  SMQQ MQYP  
Sbjct: 163 ASPPAPNANGGRLAMPPMYWQGYYGAPNGLPQLHQQSLLQPPPGLSMPSSMQQPMQYPNF 222

Query: 255 NPSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLPAQ------------------ 296
            P LPT  SNLP        P  + P+S  T ++ S  LP                    
Sbjct: 223 TPPLPTVSSNLP------ELPSSLLPVSASTPSVTSASLPPNLPPAPSALPPAPSALPPA 276

Query: 297 --------SSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPL-NSGIDKTAVAP--V 345
                   S+ + S+     + +KA   +   A  +++LP +  L N   D  A+ P   
Sbjct: 277 PSALSPVPSATLASEIFPVSVANKAPNVSTSAAMLASNLPSLALLTNPARDINAIVPPIS 336

Query: 346 SEPKSVPGPIMPFQSTVSESVSTVGMSSSILNDGIMPSLVTPGQLLQPGLPAVSSSQSSQ 405
           S+  ++ G  +P+QS    S + V  S+SI  +   PSLVTPGQLL+PG   VSS+Q SQ
Sbjct: 337 SKSNAISGSSLPYQSVSQLSPAVVESSTSIHTETSAPSLVTPGQLLKPGPIIVSSAQPSQ 396

Query: 406 AAQKDVEVVQLSSSESAAAPPPAS-DVQEPILPLPSTTE--RKPYGAPTST-QYGY 457
           A  KDVEVVQ+SS+ S     P S + Q PILPLP T+    +P GAPT T  +GY
Sbjct: 397 APHKDVEVVQVSSTSSPEPSVPVSVETQPPILPLPVTSRPNHRPGGAPTQTHHHGY 452

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111756|ref|XP_002315966.1| predicted protein [Populus trichocarpa] gi|222865006|gb|EEF02137.1| predicted protein [Populus trichocarpa]

 Score =  325 bits (832), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 227/471 (48%), Positives = 273/471 (57%), Gaps = 77/471 (16%)

Query: 20  YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYI 78
           Y+GSLISLTSKSEIRYEG+L+NINT+ESSIGL+N R    +G +K GPQ+ PSDK+YEYI
Sbjct: 23  YVGSLISLTSKSEIRYEGILYNINTDESSIGLKNVRSFGTEGRKKDGPQILPSDKVYEYI 82

Query: 79  LFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHND 138
           LFRGSDIK                                 DLQVKSSPPVQ+   I+ND
Sbjct: 83  LFRGSDIK---------------------------------DLQVKSSPPVQSAPHINND 109

Query: 139 PAIIQSHYSQAAIASTTLPSG-TGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWG 197
           PAIIQSHY +    ST  PS  +GSL D  S     G     FQG  PLYQPGGSLG WG
Sbjct: 110 PAIIQSHYPRPFATSTGFPSAVSGSLTDLGSHNGPGGQPAMNFQGGMPLYQPGGSLGTWG 169

Query: 198 SS-PMPTTNGAGLAMPMYWQGFYGSPNGL-QGQQQPLLQPPPGLSMLPSMQQSMQYPAMN 255
           +S P P  NG+GLAMPMYWQGFY  PNGL    QQ LL+PPPGL+M  SMQQ MQYP  N
Sbjct: 170 ASPPPPNANGSGLAMPMYWQGFYAPPNGLPHLHQQSLLRPPPGLAMPSSMQQPMQYPNFN 229

Query: 256 PSLPTGVSNLPASQL-AEHRPPLMPPIST-----------------GTLNLLS------- 290
            SL TG+SNLP   L     P    PIST                  +LN  S       
Sbjct: 230 TSLLTGISNLPGPNLPVSTLPSSNLPISTLQASLPDVLPPLLPGIASSLNFTSHSAVPST 289

Query: 291 -----PMLPAQSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPL-NSGIDKTAVAP 344
                P++P  S+++ S++  +L+PDK  +  LPT     SLP++ PL  S  D   +AP
Sbjct: 290 LPSTVPLMP--SASLPSETLPSLMPDKIPSSALPTTNLGASLPVLSPLTTSSPDLNTIAP 347

Query: 345 VSEPK--SVPGPIMPFQSTVSESVSTVGMSSSILND--GIMPSLVTPGQLLQPGLPAVSS 400
               K  S+PGP MP+QST   + S V  S+S+  +    +PSLVTPGQLLQ G P V S
Sbjct: 348 PISNKLSSIPGPTMPYQSTAQSAPSGVLASNSLRTEIPTPIPSLVTPGQLLQSGSPIVPS 407

Query: 401 SQSSQAAQKDVEVVQLSSSESAAAPPPASDVQEPILPLPSTTE--RKPYGA 449
           +Q  Q A KDVEVV++S +   +  P  ++ Q PILPLP  T    KP GA
Sbjct: 408 TQPVQTAHKDVEVVKVSPAPEPSV-PATTEAQPPILPLPFPTRASHKPNGA 457

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224099297|ref|XP_002311428.1| predicted protein [Populus trichocarpa] gi|222851248|gb|EEE88795.1| predicted protein [Populus trichocarpa]

 Score =  325 bits (832), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 235/494 (47%), Positives = 282/494 (57%), Gaps = 87/494 (17%)

Query: 8   APRSSSSGSADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGP 66
           A  S S+ +ADSYIGSLISLTSKSEIRYEG+L+NINTEESSIGL+N R    +G +K GP
Sbjct: 4   ASTSRSNSTADSYIGSLISLTSKSEIRYEGILYNINTEESSIGLKNVRSFGTEGRKKDGP 63

Query: 67  QVPPSDKIYEYILFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSS 126
           Q+ PSDK+YEYILFRGSDIK                                 DLQVKSS
Sbjct: 64  QILPSDKVYEYILFRGSDIK---------------------------------DLQVKSS 90

Query: 127 PPVQTTTSIHNDPAIIQSHYSQAAIASTTLPSG-TGSLPDPTSQTSQLGLSRPPFQGNPP 185
           PPVQ+   I+NDPAIIQSHY +    ST+LPS  +GSL D  S     GL    FQG  P
Sbjct: 91  PPVQSFPPINNDPAIIQSHYPRPVATSTSLPSAVSGSLTDLGSNNGPGGLPGSNFQGGLP 150

Query: 186 LYQPGGSLGAWGSS-PMPTTNGAGLAMPMYWQGFYGSPNGLQGQQQPLLQPPPGLSMLPS 244
           LYQPGGSLGAWG S P P  NG GLAMPMYWQ +YG PNG+    Q LL+PPPGL+M PS
Sbjct: 151 LYQPGGSLGAWGVSPPPPNANGNGLAMPMYWQSYYGPPNGIPHLHQSLLRPPPGLAMPPS 210

Query: 245 MQQSMQYPAMNPSLPTGV----------SNLPASQL------AEHRPPLMPPIST----- 283
           MQQ MQYP  N SLPTG            NLPAS L      A + PP   P+ST     
Sbjct: 211 MQQPMQYPNFNTSLPTGALNLASSTLPPLNLPASTLPPFNLPASNLPPSNLPVSTLPASL 270

Query: 284 --------------GTLNLLSPMLPAQSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPL 329
                          TL    P++PA S  + S++  +LIP+K     LPT     + P+
Sbjct: 271 PDVPLPLLPGITMPSTLPSTVPLIPAAS--LPSETLPSLIPNKVPISALPTTNLGVTFPV 328

Query: 330 VPPLNSGID--KTAVAPVS-EPKSVPGPIMPFQSTVSESVSTVGMSSSILND--GIMPSL 384
           + P+++      T V P+S +P S+ GP MP+QS    + S V  S+S+  +     PSL
Sbjct: 329 LSPVSTSSSDLNTIVPPISNKPSSISGPTMPYQSVTQSASSAVLASNSLRTETPTPTPSL 388

Query: 385 VTPGQLLQPGLPAVSSSQSSQAAQKDVEVVQLSSSESAAAPPP-------ASDVQEPILP 437
           VTP QLLQ G   V S Q  Q A KDVEVV+ +++ +AAA P        A+  Q PILP
Sbjct: 389 VTPDQLLQSGPTIVPSPQPVQTAHKDVEVVKAAAAAAAAAAPSPEPSVPVATQAQPPILP 448

Query: 438 L--PSTTERKPYGA 449
           L  PS    KP GA
Sbjct: 449 LPVPSRASHKPNGA 462

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449503510|ref|XP_004162038.1| PREDICTED: protein decapping 5-like [Cucumis sativus]

 Score =  324 bits (830), Expect = 7e-86,   Method: Compositional matrix adjust.
 Identities = 230/467 (49%), Positives = 278/467 (59%), Gaps = 69/467 (14%)

Query: 1   MAAAATEAPRSSSSGSADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQK 59
           MA+     P S+    ADSYIGSLISLTSKSEIRYEGVL+NINTEESSIGLRN R    +
Sbjct: 1   MASDTASRPTSA----ADSYIGSLISLTSKSEIRYEGVLYNINTEESSIGLRNVRSFGTE 56

Query: 60  GEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQ 119
           G +K GP VPPSDK++EYILFRGSDIK                                 
Sbjct: 57  GRKKDGPHVPPSDKVFEYILFRGSDIK--------------------------------- 83

Query: 120 DLQVKSSPPVQTTTSIHNDPAIIQSHYSQAAIASTTLPSG-TGSLPDPTSQTSQLGLSRP 178
           DLQVKSSPPVQ    I+NDPAIIQSHY  +   ST + S  +GSLPD TS T+  G  + 
Sbjct: 84  DLQVKSSPPVQPAAPINNDPAIIQSHYPPSVSTSTNMHSAISGSLPDHTSNTA-FGFPQS 142

Query: 179 PFQGNPPLYQPGGSLGAWG--SSPMPTTNGAGLAMPMYWQGFYGSPNGL-QGQQQPLLQP 235
            FQG  P YQPG +LG WG    P P+ NG+GLAMPMYWQG+YG PNGL Q  QQ +++P
Sbjct: 143 NFQGGLPPYQPGANLGTWGASPPPPPSANGSGLAMPMYWQGYYGPPNGLPQLHQQSVVRP 202

Query: 236 PPGLSMLPSMQQSMQYPAMNPSLPTGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLPA 295
           PPGLSM PS+QQSMQYP +N SLPTG S  P     E   PL+  +         PM P 
Sbjct: 203 PPGLSMPPSLQQSMQYPNINVSLPTGASKQP-----EVPSPLLSAL---------PMFPF 248

Query: 296 QSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVPPLN--SGID-KTAVAPVS-EPKSV 351
            S   IS++  + + +K +  TL  A  S SLP  P L+  SG D  TA+ P+S EP +V
Sbjct: 249 TS---ISETLPSSVGNKTAVHTLSGAPVSVSLPGGPILSSFSGADVSTAIPPISNEPNAV 305

Query: 352 PGPIMPFQSTVSESVSTVGMSSSILNDGIMPSLVTPGQLLQPGLPAVSSSQSSQAAQKDV 411
            G  + +Q+    + S VG+S+S     + PSLVTPGQLLQ G  AV SSQ   A  KDV
Sbjct: 306 SGSSLLYQTVSQSTSSVVGISNSRAESSV-PSLVTPGQLLQSGPVAVVSSQPLHAVHKDV 364

Query: 412 EVVQLSSSESAAAPPPASDVQEPILPLPSTTERKPYGAPTSTQYGYR 458
           EVVQ SS E +   P  ++ Q PILPLP  +  +P   P  + +  R
Sbjct: 365 EVVQSSSLEPSK--PVTTEAQPPILPLPVLS--RPIQKPNGSHFQAR 407

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737880|emb|CBI27081.3| unnamed protein product [Vitis vinifera]

 Score =  323 bits (827), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 230/444 (51%), Positives = 272/444 (61%), Gaps = 74/444 (16%)

Query: 20  YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYI 78
           YIGSLISLTSKSEIRYEGVL+NINTEESSIGLRN R    +G +K GPQVPPSDK+YEYI
Sbjct: 15  YIGSLISLTSKSEIRYEGVLYNINTEESSIGLRNVRSFGTEGRKKDGPQVPPSDKVYEYI 74

Query: 79  LFRGSDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHND 138
           LFRGSDIK                                 DLQVKSSPPVQ T  I+ND
Sbjct: 75  LFRGSDIK---------------------------------DLQVKSSPPVQATPPINND 101

Query: 139 PAIIQSHYSQAAIASTTLPSGTGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWGS 198
           PAIIQSHY + A  S +LPS    LP                     LYQPGG+LG+WG 
Sbjct: 102 PAIIQSHYPRPATTSASLPSTVSGLP---------------------LYQPGGNLGSWGP 140

Query: 199 SPMP-TTNGAGLAMPMYWQGFYGSPNGL-QGQQQPLLQPPPGLSMLPSMQQSMQYPAMNP 256
           +P P T NG+GL MPMYWQG+YG PNGL    QQ LL+PPP LSM P     MQYP  N 
Sbjct: 141 APPPPTANGSGLTMPMYWQGYYGPPNGLPHLHQQSLLRPPPVLSMPP-----MQYPGFNA 195

Query: 257 SLPTGVSNLPASQLAEHRPPLMPPISTGTLNL----LSPMLPAQSSAMISDSSTNLIPDK 312
           SL  G  NLP S L E+  PL+P  S+G+LNL    LSP     +    S++ ++L+P+K
Sbjct: 196 SLQPGAPNLPGSNLPEYSSPLLP-TSSGSLNLTSTSLSPSTLPSNLPSTSETLSSLMPNK 254

Query: 313 ASTQTLPTAAPSTSLPLVPPLN-SGIDKTAVAP--VSEPKSVPGPIMPFQSTVSESVSTV 369
               TLP+     SLPLV PLN S  +  A+AP   ++P +V GP +P+Q T+S+S+ +V
Sbjct: 255 VPNPTLPSVTLGISLPLVTPLNTSSSEINAIAPPISNKPNAVSGPTLPYQ-TISQSIPSV 313

Query: 370 GMSSSILNDGIMPSLVTPGQLLQPGLPAVSSSQSSQAAQKDVEVVQLSSSESAAAPPPAS 429
           G SS    +   PSLVTPGQLLQ G   +SSS SSQ A KDVEVVQ+SSS S  +  P S
Sbjct: 314 GTSSPNHPEIAAPSLVTPGQLLQSGPTTISSSPSSQTAHKDVEVVQVSSSASQESSVPVS 373

Query: 430 -DVQEPILPL--PSTTERKPYGAP 450
            + Q PILPL  PS T +K  GAP
Sbjct: 374 AEAQPPILPLPVPSRTVQKLNGAP 397

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	493
TAIR|locus:2011410	611	DCP5 "AT1G26110" [Arabidopsis	0.795	0.641	0.328	3.2e-33
TAIR|locus:2158470	571	DCP5-L "decapping 5-like" [Ara	0.168	0.145	0.488	9.9e-17
UNIPROTKB|A0A8M2	471	lsm14a-a "Protein LSM14 homolo	0.125	0.131	0.516	3.6e-12
ZFIN|ZDB-GENE-040426-2462	448	lsm14ab "LSM14 homolog Ab (SCD	0.125	0.138	0.5	1.6e-11
UNIPROTKB|F1NEM2	463	LSM14A "Uncharacterized protei	0.125	0.133	0.5	2e-11
UNIPROTKB|Q68FI1	422	lsm14b-a "Protein LSM14 homolo	0.125	0.146	0.483	5.5e-11
ASPGD|ASPL0000061577	552	AN1055 [Emericella nidulans (t	0.121	0.108	0.5	6.9e-11
UNIPROTKB|G4MRF0	542	MGG_02405 "Uncharacterized pro	0.125	0.114	0.507	9.7e-11
UNIPROTKB|F1MSA5	463	LSM14A "Protein LSM14 homolog	0.296	0.315	0.339	1.8e-10
UNIPROTKB|Q3MHF8	463	LSM14A "Protein LSM14 homolog	0.296	0.315	0.339	2.4e-10

TAIR|locus:2011410 DCP5 "AT1G26110" [Arabidopsis thaliana (taxid:3702)]

 Score = 367 (134.2 bits), Expect = 3.2e-33, P = 3.2e-33
 Identities = 146/445 (32%), Positives = 184/445 (41%)

Query:    24 LISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRG 82
             LISLTSKSEIRYEG+L+NINT+ESSIGL+N R    +G +K GPQVPPSDK+YEYILFRG
Sbjct:    21 LISLTSKSEIRYEGILYNINTDESSIGLQNVRSFGTEGRKKDGPQVPPSDKVYEYILFRG 80

Query:    83 SDIKHCLLTITGDAISGPRLSQTRDWTLRSVIRKDIQD-LQVKSSPPVQTTTSI-----H 136
             +DIK  L       +  P  +   D    ++I+      +    S P   + S+     H
Sbjct:    81 TDIKD-LQVKASPPVQPPASTINND---PAIIQSHYPSPMPTSGSLPSTASGSLPDISSH 136

Query:   137 NDPAIIQSHYSQAAIASTTLPSGT----GSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGS 192
             N          Q A+     P G     G+ P P       G   PP  G P L+Q    
Sbjct:   137 NGQPGQHGMGFQNAMPLYQ-PGGNLGSWGASPQPPMYWQ--GFYTPPPNGLPQLHQQSLI 193

Query:   193 LGAWGSSPMPTTNGAGLAMPMYWQGFYGSP--NGXXXXXXXXXXXXXXXXXXXXXXQSMQ 250
                 G  PMP +    L  P+ +  F   P   G                        M 
Sbjct:   194 RPPHGL-PMPNS----LQQPLQYPNFNTPPPPTGSSSLQGSSLPEAPSSLFPFSTSSQML 248

Query:   251 YPAMNP--SLP--TGVSNLPASQLAEHRPPLMPPISTGTLNLLSPMLPAQSSAMISDSST 306
              P+  P   LP  T  S+L ++  +   P L   ++     LLS   P  +   +    T
Sbjct:   249 APSSLPFPGLPPVTLSSSLQSTLQSAPSPSLASEMAPP---LLSNKAPITAPPTLPQD-T 304

Query:   307 NLIPDKASTQTLPTAAPSTSLPLVPPLNSGIDKTAVAPVSEPKSVPGPIMPFQXXXXXXX 366
             NL+    ST T  T A ST LPL                ++P  V GPI P Q       
Sbjct:   305 NLLSFSLST-TRATEA-STGLPLS---------------NKPSVVTGPISPPQTTPLTSA 347

Query:   367 XXXXXXXXILNDGIMPSLVTPGQLLQPGLPXXXXXXXXXXXXKDVEVVQLXXXXXXXXXX 426
                     I  D   P LVTPGQLLQ G              KDVEVVQ+          
Sbjct:   348 PVAGVSSSISQDKPKPLLVTPGQLLQSGSSAVSLSPPSTNADKDVEVVQVSSSAGLEQSV 407

Query:   427 -XXXDVQEPILPLPSTTE--RKPYG 448
                 + Q PILPLPS+    +KP G
Sbjct:   408 PVTSEAQPPILPLPSSARPTQKPNG 432

GO:0000932 "cytoplasmic mRNA processing body" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0010606 "positive regulation of cytoplasmic mRNA processing body assembly" evidence=IMP

GO:0017148 "negative regulation of translation" evidence=IMP

GO:0031087 "deadenylation-independent decapping of nuclear-transcribed mRNA" evidence=IMP

GO:0033962 "cytoplasmic mRNA processing body assembly" evidence=IMP

GO:0042803 "protein homodimerization activity" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006486 "protein glycosylation" evidence=RCA

GO:0006487 "protein N-linked glycosylation" evidence=RCA

TAIR|locus:2158470 DCP5-L "decapping 5-like" [Arabidopsis thaliana (taxid:3702)]

 Score = 208 (78.3 bits), Expect = 9.9e-17, Sum P(2) = 9.9e-17
 Identities = 41/84 (48%), Positives = 59/84 (70%)

Query:    25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGS 83
             ISL SK EIRYEG+L+++N ++S++GL+N R    +G +K GPQ+PP DK+Y+YILFRGS
Sbjct:    38 ISLISKYEIRYEGILYHLNVQDSTLGLKNVRSCGTEGRKKDGPQIPPCDKVYDYILFRGS 97

Query:    84 DIKHCLLTITGDAISGPRLSQTRD 107
             DIK   +  +  A S   +   +D
Sbjct:    98 DIKDLQVNPSPSAQSRQEIQSEQD 121

GO:0009507 "chloroplast" evidence=ISM

UNIPROTKB|A0A8M2 lsm14a-a "Protein LSM14 homolog A-A" [Xenopus laevis (taxid:8355)]

 Score = 161 (61.7 bits), Expect = 3.6e-12, Sum P(3) = 3.6e-12
 Identities = 32/62 (51%), Positives = 43/62 (69%)

Query:    25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSD 84
             ISL SK+EIRYEG+L+ I+TE S++ L   R     +      +PP D+I+EYI+FRGSD
Sbjct:    12 ISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEIFEYIIFRGSD 71

Query:    85 IK 86
             IK
Sbjct:    72 IK 73

GO:0003723 "RNA binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0017148 "negative regulation of translation" evidence=IMP

GO:0017151 "DEAD/H-box RNA helicase binding" evidence=IPI

GO:0030529 "ribonucleoprotein complex" evidence=IPI

GO:0043234 "protein complex" evidence=IPI

ZFIN|ZDB-GENE-040426-2462 lsm14ab "LSM14 homolog Ab (SCD6, S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 156 (60.0 bits), Expect = 1.6e-11, Sum P(2) = 1.6e-11
 Identities = 31/62 (50%), Positives = 42/62 (67%)

Query:    25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSD 84
             ISL SK+EIRYEGVL+ I+TE S++ L   +     +      +PP D ++EYI+FRGSD
Sbjct:    12 ISLISKAEIRYEGVLYTIDTENSTVALAKVKSFGTEDRPTDRPIPPRDDVFEYIIFRGSD 71

Query:    85 IK 86
             IK
Sbjct:    72 IK 73

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

UNIPROTKB|F1NEM2 LSM14A "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 160 (61.4 bits), Expect = 2.0e-11, Sum P(2) = 2.0e-11
 Identities = 31/62 (50%), Positives = 43/62 (69%)

Query:    25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSD 84
             ISL SK+EIRYEG+L+ I+TE S++ L   R     +      +PP D+++EYI+FRGSD
Sbjct:    12 ISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSD 71

Query:    85 IK 86
             IK
Sbjct:    72 IK 73

GO:0000932 "cytoplasmic mRNA processing body" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0033962 "cytoplasmic mRNA processing body assembly" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

UNIPROTKB|Q68FI1 lsm14b-a "Protein LSM14 homolog B-A" [Xenopus laevis (taxid:8355)]

 Score = 154 (59.3 bits), Expect = 5.5e-11, Sum P(2) = 5.5e-11
 Identities = 30/62 (48%), Positives = 42/62 (67%)

Query:    25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSD 84
             ISL SK++IRYEG+L+ I+TE S++ L   R     +       PP +++YEYI+FRGSD
Sbjct:    12 ISLISKAQIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPAPPREEVYEYIIFRGSD 71

Query:    85 IK 86
             IK
Sbjct:    72 IK 73

GO:0030529 "ribonucleoprotein complex" evidence=IPI

ASPGD|ASPL0000061577 AN1055 [Emericella nidulans (taxid:162425)]

 Score = 137 (53.3 bits), Expect = 6.9e-11, Sum P(3) = 6.9e-11
 Identities = 32/64 (50%), Positives = 43/64 (67%)

Query:    26 SLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIG-P--QVPPSDKIYEYILFRG 82
             +L SKS+IRY G L  IN E S+I L+N  +    E + G P  ++PPS  +YEYI+FRG
Sbjct:    12 NLISKSDIRYVGTLHEINPEASTIALQNV-VSYGTEGRRGNPDEELPPSSSVYEYIVFRG 70

Query:    83 SDIK 86
             SD+K
Sbjct:    71 SDVK 74

GO:0045947 "negative regulation of translational initiation" evidence=IEA

GO:0034063 "stress granule assembly" evidence=IEA

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IEA

GO:0071585 "detoxification of cadmium ion" evidence=IEA

GO:0033962 "cytoplasmic mRNA processing body assembly" evidence=IEA

GO:0071276 "cellular response to cadmium ion" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0000932 "cytoplasmic mRNA processing body" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0031370 "eukaryotic initiation factor 4G binding" evidence=IEA

UNIPROTKB|G4MRF0 MGG_02405 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 157 (60.3 bits), Expect = 9.7e-11, Sum P(2) = 9.7e-11
 Identities = 34/67 (50%), Positives = 47/67 (70%)

Query:    25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEE----KIGPQVPPSDKIYEYIL 79
             ISL SKS+IRY GVL  IN+EES++ L N +    +G +    K   ++ PSD++YEYI+
Sbjct:     9 ISLISKSDIRYVGVLHEINSEESTVSLENVKSFGTEGRKRDAGKPAEEIAPSDQVYEYIV 68

Query:    80 FRGSDIK 86
             FRGSD+K
Sbjct:    69 FRGSDVK 75

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|F1MSA5 LSM14A "Protein LSM14 homolog A" [Bos taurus (taxid:9913)]

 Score = 176 (67.0 bits), Expect = 1.8e-10, P = 1.8e-10
 Identities = 53/156 (33%), Positives = 81/156 (51%)

Query:    25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSD 84
             ISL SK+EIRYEG+L+ I+TE S++ L   R     +      +PP D+++EYI+FRGSD
Sbjct:    12 ISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSD 71

Query:    85 IKHCLLTITGDAISGPRLSQTRDWTL-RSVIRKDIQDLQ-VKSSPPV--QTTTSIHNDPA 140
             IK   LT+       P+ S  +D  + +S +       Q V S  P     T S  +  +
Sbjct:    72 IKD--LTVCEPP--KPQCSLPQDPAIVQSSLGSSTSSFQSVGSYGPFGRMPTYSQFSPSS 127

Query:   141 IIQSHYSQAAIASTTLPS-GT-GSLPDPTSQTSQLG 174
             ++   +    +A ++L S GT  S     SQ+S +G
Sbjct:   128 LVGQQFGAVGVAGSSLTSFGTEASSSSALSQSSAVG 163

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

GO:0033962 "cytoplasmic mRNA processing body assembly" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0000932 "cytoplasmic mRNA processing body" evidence=IEA

UNIPROTKB|Q3MHF8 LSM14A "Protein LSM14 homolog A" [Bos taurus (taxid:9913)]

 Score = 175 (66.7 bits), Expect = 2.4e-10, P = 2.4e-10
 Identities = 53/156 (33%), Positives = 81/156 (51%)

Query:    25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSD 84
             ISL SK+EIRYEG+L+ I+TE S++ L   R     +      +PP D+++EYI+FRGSD
Sbjct:    12 ISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSD 71

Query:    85 IKHCLLTITGDAISGPRLSQTRDWTL-RSVIRKDIQDLQ-VKSSPPV--QTTTSIHNDPA 140
             IK   LT+       P+ S  +D  + +S +       Q V S  P     T S  +  +
Sbjct:    72 IKD--LTVCEPP--KPQCSLPQDPAIVQSSLGSSTSSFQSVGSYGPFGRMPTYSQFSPSS 127

Query:   141 IIQSHYSQAAIASTTLPS-GT-GSLPDPTSQTSQLG 174
             ++   +    +A ++L S GT  S     SQ+S +G
Sbjct:   128 LVGQQFGAVGVAGSSLTSFGTEASSSSALSQSSVVG 163

GO:0000932 "cytoplasmic mRNA processing body" evidence=ISS

GO:0010494 "cytoplasmic stress granule" evidence=ISS

GO:0033962 "cytoplasmic mRNA processing body assembly" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	493
cd01736	74	cd01736, LSm14_N, Like-Sm protein 14, N-terminal d	4e-28
pfam12701	81	pfam12701, LSM14, Scd6-like Sm domain	2e-26
pfam14438	113	pfam14438, SM-ATX, SM domain found in Ataxin-2	4e-06

>gnl|CDD|212483 cd01736, LSm14_N, Like-Sm protein 14, N-terminal domain

 Score =  106 bits (266), Expect = 4e-28
 Identities = 39/70 (55%), Positives = 51/70 (72%)

Query: 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYE 76
             YIGS ISL SKS+IRYEG+L+ I+TE+S+I L+N R         G  +PPSD++Y+
Sbjct: 1  GTPYIGSKISLISKSDIRYEGILYTIDTEDSTIALKNVRSFGTEGRPTGRPIPPSDEVYD 60

Query: 77 YILFRGSDIK 86
          YI+FRGSDIK
Sbjct: 61 YIVFRGSDIK 70

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. 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. Length = 74

>gnl|CDD|221724 pfam12701, LSM14, Scd6-like Sm domain

 Score =  101 bits (254), Expect = 2e-26
 Identities = 44/72 (61%), Positives = 55/72 (76%), Gaps = 4/72 (5%)

Query: 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEE--KIGPQVPPSDKI 74
          A  YIGS ISL SKS+IRYEG+L++I+TEES+I L N R    G E  K   ++PPSD++
Sbjct: 1  ATDYIGSKISLISKSDIRYEGILYSIDTEESTITLANVR--SFGTEGRKTDGEIPPSDEV 58

Query: 75 YEYILFRGSDIK 86
          YEYI+FRGSDIK
Sbjct: 59 YEYIVFRGSDIK 70

The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from the newt Pleurodeles walt, and its orthologs from fungi, animals, plants and apicomplexans. The domain is also found in Dcp3p and the human EDC3/FLJ21128 protein where it is fused to the the Rossmanoid YjeF-N domain. In addition both EDC3 and Scd6p are found fused to the FDF domain. Length = 81

>gnl|CDD|222754 pfam14438, SM-ATX, SM domain found in Ataxin-2

 Score = 45.3 bits (108), Expect = 4e-06
 Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 5/70 (7%)

Query: 19 SYIGSLISLTSKSEIRYEGVLFNINTE-ESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEY 77
          + IG  + +T K+   YEG+    + E +  + L+  R+  K +       P   KI + 
Sbjct: 9  NLIGQRVEVTLKNGSVYEGIFHTASPEDDFGVVLKMARVLPKSDASG----PLRGKIVDT 64

Query: 78 ILFRGSDIKH 87
          ++    DI  
Sbjct: 65 LIIPSKDIVQ 74

SM domain found in Ataxin-2. Length = 113

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	493
KOG1073	361	consensus Uncharacterized mRNA-associated protein	100.0
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	100.0
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	100.0
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	97.79
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	97.76
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	96.36
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	95.93
cd01737	62	LSm16_N LSm16 belongs to a family of Sm-like prote	95.9
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	95.84
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	95.62
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	95.58
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	95.57
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	95.49
PRK00737	72	small nuclear ribonucleoprotein; Provisional	95.39
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	94.28
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	94.24
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	94.19
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	94.0
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	93.25
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	93.19
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	93.1
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	92.84
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	90.71
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	88.28
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	87.46
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	83.81
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	80.81

>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]

Probab=100.00  E-value=1.1e-38  Score=322.04  Aligned_cols=145  Identities=43%  Similarity=0.644  Sum_probs=117.6

Q ss_pred             CCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcccccccccc
Q 011128           16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITG   94 (493)
Q Consensus        16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK~~~~~~~g   94 (493)
                      .+++|||||||||||.|||||||||+||++||||+|+||| ||||||+++++++|+.++|||||||||||||        
T Consensus         3 ~~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIK--------   74 (361)
T KOG1073|consen    3 LVTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIK--------   74 (361)
T ss_pred             cccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccc--------
Confidence            5799999999999999999999999999999999999999 9999999999999999999999999999999        


Q ss_pred             cCCCCCCcccccccchhhccccCCCCceEecCCCCCCCCCCCCChhhhcccCCcccccccCCCC-CCCCCCCCCCCCCCC
Q 011128           95 DAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHNDPAIIQSHYSQAAIASTTLPS-GTGSLPDPTSQTSQL  173 (493)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~Dl~v~~~p~~~~~~~~~~dpai~~s~~~~~~~assslPs-~sGsl~~~ss~~~q~  173 (493)
                                               ||+||+.|..+.....+.+|+|...         .++++ .+++.+..+.+..+.
T Consensus        75 -------------------------DL~V~~~p~~~~~~~~p~~pp~p~~---------~~~~s~~s~~~~~~s~~~~~~  120 (361)
T KOG1073|consen   75 -------------------------DLIVQETPAGQIPCSLPVPPPMPPQ---------SSIPSQQSGSDPKISFQFAQA  120 (361)
T ss_pred             -------------------------eeeeccCcccCccccccCCCCCCcc---------cccccccCCcccccccccccC
Confidence                                     9999998765555667777777221         11222 344555555565555


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 011128          174 GLSRPPFQGNPPLYQPGGSLGAWGSSPMP  202 (493)
Q Consensus       174 g~p~P~fqg~~PlYQPg~~lg~wG~sPpp  202 (493)
                      +-+.-.++++++.+++....|.|.....+
T Consensus       121 ~~~~~~~P~~~~~~~~~~~~g~~~~~~~~  149 (361)
T KOG1073|consen  121 GNPVIGNPQGLITTNPVPAEGSIYGSFQP  149 (361)
T ss_pred             CCcccCCcCccccCCCCccccccccccCC
Confidence            55555566777788888888998887744

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

Probab=100.00  E-value=2.9e-36  Score=257.07  Aligned_cols=93  Identities=54%  Similarity=0.916  Sum_probs=71.8

Q ss_pred             CCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcccccccccc
Q 011128           16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITG   94 (493)
Q Consensus        16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK~~~~~~~g   94 (493)
                      ++++|||++||||||++|||||+||+||.+++||+|+||| ||||||+++. +|||++++||||+|||+|||        
T Consensus         2 m~~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~-~ipp~~~v~~~I~Fr~sDIk--------   72 (96)
T PF12701_consen    2 MADPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDR-EIPPSDEVYDYIVFRGSDIK--------   72 (96)
T ss_dssp             -CCCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS----C-CSSSSEEEEETTTEE--------
T ss_pred             ccccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCc-ccCCCCceeeEEEEEccccc--------
Confidence            5789999999999999999999999999999999999999 9999999886 89999999999999999999        


Q ss_pred             cCCCCCCcccccccchhhccccCCCCceEecCCCCCCCCCCCCChhhhccc
Q 011128           95 DAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHNDPAIIQSH  145 (493)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~Dl~v~~~p~~~~~~~~~~dpai~~s~  145 (493)
                                               ||+|++.++.   ...++||||++.+
T Consensus        73 -------------------------dL~v~e~~~~---~~~~~dpAiv~~~   95 (96)
T PF12701_consen   73 -------------------------DLKVIEPPPP---PPAPQDPAIVSVS   95 (96)
T ss_dssp             -------------------------EEEECE-S-S---SSS----------
T ss_pred             -------------------------eEEEEcCCCC---CCCCCCCceeecC
Confidence                                     9999998754   5579999999864

>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=100.00  E-value=8.6e-35  Score=238.84  Aligned_cols=70  Identities=60%  Similarity=1.058  Sum_probs=68.1

Q ss_pred             CCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        17 ~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      +.+|||++||||||+||||||+||+||.+++||+|+||| ||||||++++++|||+++|||||+|||+|||
T Consensus         1 ~~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIk   71 (74)
T cd01736           1 VTPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIK   71 (74)
T ss_pred             CccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccc
Confidence            468999999999999999999999999999999999999 9999999988789999999999999999999

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.

>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=97.79  E-value=4.2e-05  Score=58.74  Aligned_cols=58  Identities=19%  Similarity=0.414  Sum_probs=49.9

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+..+.+..|+|+|..+| +...|.|+|+. +.++++          ...++.++.||+.|+
T Consensus         2 ~~~~g~~V~V~l~~g~~~~G~L~~~D-~~~Ni~L~~~~~~~~~~~----------~~~~~~~~irG~~I~   60 (63)
T cd00600           2 KDLVGKTVRVELKDGRVLEGVLVAFD-KYMNLVLDDVEETIKEGK----------KRVLGLVLIRGDNVR   60 (63)
T ss_pred             hHHCCCEEEEEECCCcEEEEEEEEEC-CCCCEEECCEEEEecCCc----------EEECCeEEEECCEEE
Confidence            46899999999999999999999999 45599999999 888733          233778999999998

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

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

Probab=97.76  E-value=1.3e-05  Score=65.05  Aligned_cols=66  Identities=23%  Similarity=0.430  Sum_probs=43.3

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCC--CCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTE--ESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e--~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..+||+++.+..|.+-+|||||+..|.+  +..|.|+.+| -..+....   .-.-+.++-+.++|+++||-
T Consensus         8 ~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~---~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    8 TNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN---SDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS---------EEEEEEE-GGGEEE-----
T ss_pred             HhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc---CCccCCCCCceEEEeccccC
Confidence            3579999999999999999999999998  8999999999 76665432   23566778888999999985

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

Probab=96.36  E-value=0.006  Score=47.73  Aligned_cols=59  Identities=20%  Similarity=0.382  Sum_probs=48.7

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+..+.+..|+|+|..+|. .--+.|+|+. .-.+++         ...-++.++.||+.|.
T Consensus         4 ~~~~g~~V~V~l~~g~~~~G~L~~~D~-~~Nl~L~~~~~~~~~~~---------~~~~~~~~~irG~~I~   63 (67)
T PF01423_consen    4 QKLIGKRVRVELKNGRTYRGTLVSFDQ-FMNLVLSDVTETIKNGP---------EKRSLGLVFIRGSNIR   63 (67)
T ss_dssp             HHTTTSEEEEEETTSEEEEEEEEEEET-TEEEEEEEEEEEETTES---------EEEEEEEEEEEGGGEE
T ss_pred             HHhCCcEEEEEEeCCEEEEEEEEEeec-hheEEeeeEEEEECCCC---------cEeECcEEEEECCEEE
Confidence            358999999999999999999999995 6779999999 655554         2233577889999987

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 ....

>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=95.93  E-value=0.016  Score=47.52  Aligned_cols=59  Identities=19%  Similarity=0.331  Sum_probs=47.9

Q ss_pred             CCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        17 ~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ...||+++|.++-|.+..|+|+|..+| +---|.|+|+. +--+++          ...+.-++-||+.|.
T Consensus         5 L~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~E~~~~~~----------~~~lg~v~IRG~~I~   64 (72)
T cd01719           5 LKKYMDKKLSLKLNGNRKVSGILRGFD-PFMNLVLDDAVEVNSGGE----------KNNIGMVVIRGNSIV   64 (72)
T ss_pred             hHHhCCCeEEEEECCCeEEEEEEEEEc-ccccEEeccEEEEccCCc----------eeEeceEEECCCEEE
Confidence            457899999999999999999999999 66778999997 531111          234677999999998

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.

>cd01737 LSm16_N LSm16 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=95.90  E-value=0.021  Score=46.74  Aligned_cols=56  Identities=27%  Similarity=0.529  Sum_probs=45.0

Q ss_pred             CccccceEEEEecCCce-eEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIR-YEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIR-YEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..|||+-+||-...++- |.|.+..||.++.||.|++-- -|-  |+.    +|      | ++||.-|||
T Consensus         2 ~dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~~ngi--k~~----~~------E-Vt~~~~DI~   59 (62)
T cd01737           2 QDWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPFHNGV--KCL----VP------E-VTFRAGDIR   59 (62)
T ss_pred             CcccceEEEEecCCceEEEEEEEEEeCccceEEEEeecccCCc--ccc----Cc------e-EEEEEcchh
Confidence            67999999999998874 999999999999999998722 222  221    12      2 899999999

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. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.

>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=95.84  E-value=0.021  Score=46.00  Aligned_cols=58  Identities=16%  Similarity=0.264  Sum_probs=46.2

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+..|+|+|..+| +.--|.|+|+. +--+++          ...++.++-||+.|.
T Consensus         7 ~~~~g~~V~V~Lk~g~~~~G~L~~~D-~~mNi~L~~~~e~~~~~~----------~~~lg~~~IRG~~I~   65 (68)
T cd01722           7 NDLTGKPVIVKLKWGMEYKGTLVSVD-SYMNLQLANTEEYIDGKS----------TGNLGEVLIRCNNVL   65 (68)
T ss_pred             HHcCCCEEEEEECCCcEEEEEEEEEC-CCEEEEEeeEEEEeCCcc----------ccCcCcEEEECCEEE
Confidence            35799999999999999999999999 57788999986 421111          123677899999987

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.

>smart00651 Sm snRNP Sm proteins

Probab=95.62  E-value=0.021  Score=44.54  Aligned_cols=59  Identities=19%  Similarity=0.326  Sum_probs=47.1

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+..|+|+|..+|. .-.+.|+|+. ...++         ....-++.++.||+.|.
T Consensus         4 ~~~~~~~V~V~l~~g~~~~G~L~~~D~-~~NlvL~~~~e~~~~~---------~~~~~~~~~~IrG~~I~   63 (67)
T smart00651        4 KKLIGKRVLVELKNGREYRGTLKGFDQ-FMNLVLEDVEETVKDG---------EKKRKLGLVFIRGNNIV   63 (67)
T ss_pred             HHhCCcEEEEEECCCcEEEEEEEEECc-cccEEEccEEEEecCC---------cEEeEeCCEEEcCCEEE
Confidence            468999999999999999999999995 6788999988 55542         11223556888999887

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

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

Probab=95.58  E-value=0.022  Score=45.55  Aligned_cols=58  Identities=12%  Similarity=0.248  Sum_probs=46.6

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+..|.+-.|+|+|..+|. .--|.|+|+. +-.+++          ..-+..++.||+.|.
T Consensus         6 ~~~~~~~V~V~l~~g~~~~G~L~~~D~-~mNlvL~~~~e~~~~~~----------~~~lg~~~iRG~~I~   64 (68)
T cd01731           6 KDSLNKPVLVKLKGGKEVRGRLKSYDQ-HMNLVLEDAEEIDDGEP----------VRKYGRVVIRGDNVL   64 (68)
T ss_pred             HHhcCCEEEEEECCCCEEEEEEEEECC-cceEEEeeEEEEecCCe----------EeEcCcEEEeCCEEE
Confidence            358999999999999999999999997 5678899987 543332          122577899999987

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.

>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=95.57  E-value=0.025  Score=45.35  Aligned_cols=58  Identities=19%  Similarity=0.348  Sum_probs=46.4

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+..|+|+|..+| +.=-|.|+|+. +-.++++          ..++.++-||+.|.
T Consensus         6 ~~~~~~~V~V~Lk~g~~~~G~L~~~D-~~mNlvL~~~~~~~~~~~~----------~~~~~v~IRG~~I~   64 (67)
T cd01726           6 KAIIGRPVVVKLNSGVDYRGILACLD-GYMNIALEQTEEYVNGQLK----------NKYGDAFIRGNNVL   64 (67)
T ss_pred             HhhCCCeEEEEECCCCEEEEEEEEEc-cceeeEEeeEEEEeCCcee----------eEeCCEEEECCEEE
Confidence            35799999999999999999999999 56778999987 5432221          13677999999987

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.

>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=95.49  E-value=0.034  Score=46.07  Aligned_cols=61  Identities=11%  Similarity=0.182  Sum_probs=48.6

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..||+++|.++-|.+-.|.|+|..+| +.-.|.|.|+. +-.++.+.       .+.....+++||..|-
T Consensus         8 ~~~l~k~v~V~l~~gr~~~G~L~~fD-~~~NlvL~d~~E~~~~~~~~-------~~~~lG~~viRG~~V~   69 (74)
T cd01728           8 VDDLDKKVVVLLRDGRKLIGILRSFD-QFANLVLQDTVERIYVGDKY-------GDIPRGIFIIRGENVV   69 (74)
T ss_pred             HHhcCCEEEEEEcCCeEEEEEEEEEC-CcccEEecceEEEEecCCcc-------ceeEeeEEEEECCEEE
Confidence            57899999999999999999999999 56789999997 55444111       1223678999999886

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=95.39  E-value=0.026  Score=45.92  Aligned_cols=58  Identities=14%  Similarity=0.248  Sum_probs=46.8

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+..|.+-.|+|+|..+|. .--|.|+|+. +-.+++          ..-++.++.||+.|.
T Consensus        10 ~~~~~k~V~V~lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~----------~~~lg~v~iRG~~V~   68 (72)
T PRK00737         10 NNALNSPVLVRLKGGREFRGELQGYDI-HMNLVLDNAEEIQDGEV----------VRKLGKVVIRGDNVV   68 (72)
T ss_pred             HHhCCCEEEEEECCCCEEEEEEEEEcc-cceeEEeeEEEEcCCCe----------EeEcCcEEEeCCEEE
Confidence            467999999999999999999999997 6778999987 532211          123677999999987

>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=94.28  E-value=0.13  Score=42.51  Aligned_cols=69  Identities=13%  Similarity=0.223  Sum_probs=51.5

Q ss_pred             CCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        17 ~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      -..|||++|.+.-+.+=.|+|+|..+|. ...|.|.|+. +-++.++............+.-++.||..|.
T Consensus         5 l~~~l~~~V~V~l~dgR~~~G~L~~~D~-~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv   74 (79)
T cd01717           5 MLQLINYRLRVTLQDGRQFVGQFLAFDK-HMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIV   74 (79)
T ss_pred             hHHHcCCEEEEEECCCcEEEEEEEEEcC-ccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEE
Confidence            4579999999999999999999999995 5778999998 7765543211111112224678999999987

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=94.24  E-value=0.13  Score=43.09  Aligned_cols=59  Identities=17%  Similarity=0.279  Sum_probs=46.5

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..+|++|.+--|.+..|+|+|..+|.- =-|.|+||. ...++..        ....++.|..||+.|+
T Consensus         8 ~l~g~~V~VeLKng~~~~G~L~~vD~~-MNi~L~n~~~~~~~~~~--------~~~~~~~v~IRG~~I~   67 (81)
T cd01725           8 TLVGKEVTVELKNDLSIRGTLHSVDQY-LNIKLTNISVTDPEKYP--------HMLSVKNCFIRGSVVR   67 (81)
T ss_pred             hCCCCEEEEEECCCcEEEEEEEEECCC-cccEEEEEEEEcCCCcc--------cccccCeEEEECCEEE
Confidence            358999999999999999999999964 468999998 6443321        1223578999999999

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.

>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=94.19  E-value=0.092  Score=43.20  Aligned_cols=58  Identities=22%  Similarity=0.236  Sum_probs=47.1

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..+|++|.+--|.+..|+|+|..+|. .-.+.|+||. ...+|.+..         .++.++-||+.|+
T Consensus         8 ~~~g~~V~VeLkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~g~~~~---------~~~~v~IRG~~I~   66 (76)
T cd01723           8 TAQNHPMLVELKNGETYNGHLVNCDN-WMNIHLREVICTSKDGDKFW---------KMPECYIRGNTIK   66 (76)
T ss_pred             hcCCCEEEEEECCCCEEEEEEEEEcC-CCceEEEeEEEECCCCcEee---------eCCcEEEeCCEEE
Confidence            46899999999999999999999996 5678999998 655554211         1466889999998

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

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

Probab=94.00  E-value=0.15  Score=41.93  Aligned_cols=60  Identities=18%  Similarity=0.320  Sum_probs=47.3

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-ccc-CCCCCCCCCCCCCCCcee-EEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQ-KGEEKIGPQVPPSDKIYE-YILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGT-EgR~~~~~~IPPsd~Vye-yIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+..|.|+|..+|.- --|.|+||. ... +|+..        ...+. .++-||+.|+
T Consensus        13 ~~~~~~~V~V~lk~g~~~~G~L~~~D~~-mNlvL~d~~e~~~~~~~~~--------~~~~~~~~~IRG~~I~   75 (79)
T COG1958          13 KKLLNKRVLVKLKNGREYRGTLVGFDQY-MNLVLDDVEEIISHDGEKN--------VRRLGGEVLIRGDNIV   75 (79)
T ss_pred             HHhhCCEEEEEECCCCEEEEEEEEEccc-eeEEEeceEEEeccCCccc--------cceeccEEEEECCcEE
Confidence            4678999999999999999999999975 456899999 665 33321        22244 7999999998

>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=93.25  E-value=0.18  Score=41.22  Aligned_cols=61  Identities=13%  Similarity=0.259  Sum_probs=47.0

Q ss_pred             CCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-c--ccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-L--EQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        17 ~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-f--GTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      -..||+++|.++-+.+-.|+|+|..+|.. --|.|.++. +  .++..    .    ....+..|+.||+.|-
T Consensus         4 L~~~l~~~V~V~l~dgr~~~G~L~~~D~~-~NlvL~~~~E~~~~~~~~----~----~~~~lG~~~iRG~~I~   67 (74)
T cd01727           4 LEDYLNKTVSVITVDGRVIVGTLKGFDQA-TNLILDDSHERVYSSDEG----V----EQVVLGLYIIRGDNIA   67 (74)
T ss_pred             HHHhcCCEEEEEECCCcEEEEEEEEEccc-cCEEccceEEEEecCCCC----c----eeeEeceEEECCCEEE
Confidence            46799999999999999999999999976 667888875 2  22111    0    1234788999999987

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.

>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=93.19  E-value=0.19  Score=40.91  Aligned_cols=58  Identities=21%  Similarity=0.359  Sum_probs=47.3

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ...+|++|.+--|.+..|+|+|..+|. .-.+.|+||. ...+|+.          .-++.+.-||+.|+
T Consensus         6 ~~~~g~~V~VeLk~g~~~~G~L~~~D~-~MNl~L~~~~~~~~~g~~----------~~~~~v~IRG~nI~   64 (70)
T cd01721           6 HEAEGHIVTVELKTGEVYRGKLIEAED-NMNCQLKDVTVTARDGRV----------SQLEQVYIRGSKIR   64 (70)
T ss_pred             hhCCCCEEEEEECCCcEEEEEEEEEcC-CceeEEEEEEEECCCCcE----------eEcCcEEEeCCEEE
Confidence            356899999999999999999999997 6688999998 4444431          12577899999998

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.

>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=93.10  E-value=0.19  Score=43.01  Aligned_cols=57  Identities=12%  Similarity=0.233  Sum_probs=47.1

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..+|+.|.+--|.+..|+|+|..+|. .=-|.|+||. +-.+++.          .-|+.++-||+.|+
T Consensus         8 ~l~g~~V~VeLKng~~~~G~L~~vD~-~MNl~L~~a~~~~~~~~~----------~~~~~v~IRG~nI~   65 (90)
T cd01724           8 KLTNETVTIELKNGTIVHGTITGVDP-SMNTHLKNVKLTLKGRNP----------VPLDTLSIRGNNIR   65 (90)
T ss_pred             hCCCCEEEEEECCCCEEEEEEEEEcC-ceeEEEEEEEEEcCCCce----------eEcceEEEeCCEEE
Confidence            46899999999999999999999996 4578999998 6544331          23788999999999

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=92.84  E-value=0.33  Score=40.67  Aligned_cols=66  Identities=11%  Similarity=0.214  Sum_probs=48.4

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..||+++|.+.-|.+-.|+|+|..+|. ---|.|.|+. +-.+...  ..++.-....+.-++.||..|-
T Consensus         8 ~~~i~k~V~V~l~~gr~~~G~L~~~D~-~mNlvL~~~~E~~~~~~~--~~~~~~~~~~lG~v~iRG~nV~   74 (81)
T cd01729           8 SKYVDKKIRVKFQGGREVTGILKGYDQ-LLNLVLDDTVEYLRDPDD--PYKLTDKTRQLGLVVCRGTSVV   74 (81)
T ss_pred             HHhcCCeEEEEECCCcEEEEEEEEEcC-cccEEecCEEEEEccCCc--ccccccceeEccEEEEcCCEEE
Confidence            578999999999999999999999996 4567899986 4322111  1112223344788999999997

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.

>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=90.71  E-value=0.51  Score=39.46  Aligned_cols=57  Identities=18%  Similarity=0.373  Sum_probs=45.9

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..+|+.|.+--|.+..|+|+|..+|. .=.|.|+||. ...++..          .-++.|+-||+.|+
T Consensus        16 ~l~g~~V~VeLKng~~~~G~L~~vD~-~MNl~L~~~~~~~~~~~~----------~~~~~v~IRG~nI~   73 (78)
T cd01733          16 GLQGKVVTVELRNETTVTGRIASVDA-FMNIRLAKVTIIDRNGKQ----------VQVEEIMVTGRNIR   73 (78)
T ss_pred             HCCCCEEEEEECCCCEEEEEEEEEcC-CceeEEEEEEEEcCCCce----------eECCcEEEECCEEE
Confidence            45899999999999999999999996 4578999998 5333221          13788999999998

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.

>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=88.28  E-value=1.4  Score=36.81  Aligned_cols=64  Identities=14%  Similarity=0.288  Sum_probs=47.6

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..|||+++.++-+.+--|+|+|..+|. ..-|.|.|+. |-.....    ........+.-++-||..|.
T Consensus         6 ~~~l~~~v~V~l~dgR~~~G~l~~~D~-~~NivL~~~~E~~~~~~~----~~~~~~r~lGlv~IrG~~Iv   70 (75)
T cd06168           6 RSLLGRTMRIHMTDGRTLVGVFLCTDR-DCNIILGSAQEYRPPPDS----FSPTEPRVLGLVMIPGHHIV   70 (75)
T ss_pred             HHhcCCeEEEEEcCCeEEEEEEEEEcC-CCcEEecCcEEEEcccCc----cCCccEEEeeeEEEeCCeEE
Confidence            568999999999999999999999996 4567899986 4322111    01122235788999999998

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

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

Probab=87.46  E-value=1.4  Score=36.73  Aligned_cols=60  Identities=25%  Similarity=0.325  Sum_probs=45.5

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .+++++|.+..|.+-.|+|+|..+|. --.+.|+|+. += +  ..++.    ...-++-++.||..|.
T Consensus        10 ~~~~~~V~V~l~~gr~~~G~L~g~D~-~mNlvL~da~E~~-~--~~~~~----~~~~lg~v~iRG~nV~   70 (76)
T cd01732          10 KCIGSRIWIVMKSDKEFVGTLLGFDD-YVNMVLEDVTEYE-I--TPEGR----KITKLDQILLNGNNIC   70 (76)
T ss_pred             HhCCCEEEEEECCCeEEEEEEEEecc-ceEEEEccEEEEE-E--cCCCc----eeeEcCeEEEeCCeEE
Confidence            46899999999999999999999995 5778999987 42 1  11111    1123677999999998

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.

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

Probab=83.81  E-value=0.56  Score=40.38  Aligned_cols=59  Identities=25%  Similarity=0.393  Sum_probs=46.8

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-c--ccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-L--EQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-f--GTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      +.-||+||-+|=|+|-.++|+|...|-= -.+.|++|. |  -+|||+...         .+.|+.+|..|-
T Consensus        13 DkcIgski~iimksdkE~~GtL~GFDd~-VNmvLeDvtEye~~~egr~~tk---------~~~iLLnGNni~   74 (84)
T KOG1775|consen   13 DKCIGSKIWIIMKSDKEFVGTLVGFDDF-VNMVLEDVTEYEITPEGRRMTK---------LDQILLNGNNIT   74 (84)
T ss_pred             HHhcCceEEEEEccCceeeeEEechHHH-HHHHHHhhhheeeCCCcceeee---------eeeeeecCCcEE
Confidence            4569999999999999999999988742 235788988 5  457776432         678999999987

>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=80.81  E-value=5  Score=34.54  Aligned_cols=65  Identities=9%  Similarity=0.172  Sum_probs=47.5

Q ss_pred             ccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCC---CCCCCCCCceeEEEEecCCcc
Q 011128           21 IGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIG---PQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        21 IGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~---~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .|++|.+.-|.+-.|.|+|..+|. .-.|.|.|+. +-++..+...   .+.......+..|+.||..|.
T Consensus        13 ~~~~V~V~lr~~r~~~G~L~~fD~-hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv   81 (87)
T cd01720          13 NNTQVLINCRNNKKLLGRVKAFDR-HCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI   81 (87)
T ss_pred             CCCEEEEEEcCCCEEEEEEEEecC-ccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence            389999999999999999999996 6789999998 6555322111   111112223588999999987

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	493
2vxe_A	88	Solution Structure Of The Lsm Domain Of Drosophila		4e-09
2fb7_A	95	Nmr Solution Structure Of Protein From Zebra Fish D		2e-08

>pdb|2VXE|A Chain A, Solution Structure Of The Lsm Domain Of Drosophila Melanogaster Tral (Trailer Hitch) Length = 88

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 41/62 (66%)
Query: 25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSD 84
          ISL SK++IRYEG L+ ++ +E +I L + R     +     Q+ P  +IY+YILFRGSD
Sbjct: 16 ISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSD 75
Query: 85 IK 86
          IK
Sbjct: 76 IK 77

>pdb|2FB7|A Chain A, Nmr Solution Structure Of Protein From Zebra Fish Dr.13312 Length = 95

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/62 (48%), Positives = 41/62 (66%)
Query: 25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSD 84
          ISL SK+EIRYEG+L+ I+TE S++ L   R     +      + P D+ +EYI+FRGSD
Sbjct: 22 ISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSD 81
Query: 85 IK 86
          IK
Sbjct: 82 IK 83

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	493
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	6e-23
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	8e-23
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04

>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 Length = 95

 Score = 91.8 bits (228), Expect = 6e-23
 Identities = 34/75 (45%), Positives = 45/75 (60%)

Query: 12 SSSGSADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPS 71
                  YIGS ISL SK+EIRYEG+L+ I+TE S++ L   R     +      + P 
Sbjct: 9  EDPSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPR 68

Query: 72 DKIYEYILFRGSDIK 86
          D+ +EYI+FRGSDIK
Sbjct: 69 DETFEYIIFRGSDIK 83

>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster} Length = 88

 Score = 91.4 bits (227), Expect = 8e-23
 Identities = 31/76 (40%), Positives = 46/76 (60%)

Query: 11 SSSSGSADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPP 70
          + +       +GS ISL SK++IRYEG L+ ++ +E +I L + R     +     Q+ P
Sbjct: 2  AMAMSGGLPELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAP 61

Query: 71 SDKIYEYILFRGSDIK 86
            +IY+YILFRGSDIK
Sbjct: 62 QSQIYDYILFRGSDIK 77

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 46.7 bits (110), Expect = 1e-05
 Identities = 28/206 (13%), Positives = 49/206 (23%), Gaps = 22/206 (10%)

Query: 147 SQAAIASTTLPSGTGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWGSSPMPTTNG 206
           +Q        P    +   P    +  G+S       P    P      + +      + 
Sbjct: 12  AQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQ 71

Query: 207 AGLAMPMYWQGFYGSPNGLQGQQQPLLQPPPGLSMLPSMQQSMQYPAMNPSLPTGVSNL- 265
                       +     L          P     + +  Q  Q P   P+     + + 
Sbjct: 72  QIDQATTSMNDMHLHNVPLVDPNAY--MQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMG 129

Query: 266 ----------PASQLAEHRPPLM------PPISTGTLNLLSPMLPAQSSAMISDSSTNLI 309
                     P   L E  PP+       PP+      +L P   + +S     S+ N +
Sbjct: 130 QNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPDYIRSTLNAV 189

Query: 310 P---DKASTQTLPTAAPSTSLPLVPP 332
           P          LP          +  
Sbjct: 190 PKNSSLLKKSKLPFGLVIRPYQHLYD 215

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 46.4 bits (109), Expect = 2e-05
 Identities = 17/157 (10%), Positives = 35/157 (22%)

Query: 144 SHYSQAAIASTTLPSGTGSLPDPTSQTSQLGLSRPPFQGNPPLYQPGGSLGAWGSSPMPT 203
           SH+ +       L  G  + P                  +                    
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61

Query: 204 TNGAGLAMPMYWQGFYGSPNGLQGQQQPLLQPPPGLSMLPSMQQSMQYPAMNPSLPTGVS 263
              A   +         S N +     PL+ P   +     +Q           +     
Sbjct: 62  LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAY 121

Query: 264 NLPASQLAEHRPPLMPPISTGTLNLLSPMLPAQSSAM 300
             P++ + ++  P+        L  L P +   +   
Sbjct: 122 GQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPP 158

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 42.9 bits (100), Expect = 2e-04
 Identities = 31/164 (18%), Positives = 41/164 (25%), Gaps = 3/164 (1%)

Query: 168 SQTSQLGLSRPPFQGNPPLYQPGGSLGAWGSSPMPTTNGAGLAMPMYWQGFYGSPNGLQG 227
               Q G +  P Q  P  + P     A G S          A+P   Q  + +P   Q 
Sbjct: 11  QAQLQYGQNATPLQQ-PAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69

Query: 228 QQQPLLQPPPGLSMLPSMQQSMQYPAMNPSLPTGVSNLPASQLAEHRPPLMPPISTGTLN 287
            QQ          M       +   A            P  Q    +P   P     +  
Sbjct: 70  HQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQ--QQPMAAPAYGQPSAA 127

Query: 288 LLSPMLPAQSSAMISDSSTNLIPDKASTQTLPTAAPSTSLPLVP 331
           +   M P      I   +    P    T   P         LVP
Sbjct: 128 MGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVP 171

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.9 bits (100), Expect = 2e-04
 Identities = 46/368 (12%), Positives = 97/368 (26%), Gaps = 118/368 (32%)

Query: 19  SYIGSLISLTSKSEIRYEGVL--FNIN------TEESSIGLRNDRLEQKGEEKIGPQVPP 70
            Y   L+ L     ++       FN++      T    +    D L       I      
Sbjct: 242 PYENCLLVL---LNVQNAKAWNAFNLSCKILLTTRFKQV---TDFLSAATTTHI-SLDHH 294

Query: 71  SDKIYE---------YILFRGSDIKH--C-----LLTITGDAIS-GP----RLSQTRDWT 109
           S  +           Y+  R  D+           L+I  ++I  G              
Sbjct: 295 SMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDK 354

Query: 110 LRSVIRKDIQDLQVKSSPPVQTTTSIHNDPAIIQSHYSQAAI--ASTTLPSGT------- 160
           L ++I   +  L                +PA  +  + + ++   S  +P+         
Sbjct: 355 LTTIIESSLNVL----------------EPAEYRKMFDRLSVFPPSAHIPTILLSLIWFD 398

Query: 161 ---------------GSL--PDPTSQTSQL-GL---SRPPFQGNPPL-------YQPGGS 192
                           SL    P   T  +  +    +   +    L       Y    +
Sbjct: 399 VIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKT 458

Query: 193 LGAWGSSPMPTTNGAGLAMPMYWQGFYG--SPNGLQGQQQPLLQPPPGLSMLPS------ 244
             +    P             Y+    G    N    ++         +++         
Sbjct: 459 FDSDDLIPPYLDQ--------YFYSHIGHHLKNIEHPER---------MTLFRMVFLDFR 501

Query: 245 -MQQSMQYPAMNPSLPTGVSNLPASQLAEHRPPLMP--PISTGTLNLLSPMLPAQSSAMI 301
            ++Q +++ +   +    + N    QL  ++P +    P     +N +   LP     +I
Sbjct: 502 FLEQKIRHDSTAWNASGSILNT-LQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLI 560

Query: 302 SDSSTNLI 309
               T+L+
Sbjct: 561 CSKYTDLL 568

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	493
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	100.0
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	100.0
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	99.27
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	97.34
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	96.81
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	96.2
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	96.18
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	96.06
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	95.94
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	95.94
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	95.92
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	95.66
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	95.64
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	95.54
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	95.34
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	94.89
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	94.87
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	94.79
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	94.69
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	94.66
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	94.65
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	94.4
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	94.39
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	94.17
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	94.05
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	93.91
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	93.7
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	90.33
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	86.98
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	86.35

>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=100.00  E-value=2.3e-37  Score=262.72  Aligned_cols=72  Identities=47%  Similarity=0.812  Sum_probs=65.6

Q ss_pred             CCCCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           14 SGSADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        14 ~~~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ++++++|||++||||||+|||||||||+||++++||+|+||| ||||||++++ +|||+++|||||+|||+|||
T Consensus        11 ~~~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~-~ipp~~~vyeyIvFrGsDIK   83 (95)
T 2fb7_A           11 PSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDR-PIAPRDETFEYIIFRGSDIK   83 (95)
T ss_dssp             -----CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSS-CCCSCCCCSSCEEECSTTEE
T ss_pred             CCccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCC-ccCCCCcceeEEEEcCCCcc
Confidence            457899999999999999999999999999999999999999 9999999875 59999999999999999999

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

Probab=100.00  E-value=3.9e-36  Score=252.30  Aligned_cols=70  Identities=44%  Similarity=0.758  Sum_probs=67.6

Q ss_pred             CCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|||++||||||+|||||||||+||.+++||+|+||| ||||||+++ ++|||+++|||||+|||+|||
T Consensus         7 ~~~~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~-~~ipp~~~vy~yIvFrgsDIK   77 (88)
T 2vxe_A            7 GGLPELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQ-FQIAPQSQIYDYILFRGSDIK   77 (88)
T ss_dssp             SSSCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCS-SCCCCCCSCEEEEEEETTTEE
T ss_pred             CCCcccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCC-cccCCCCceeeEEEEccCCcc
Confidence            4699999999999999999999999999999999999999 999999976 579999999999999999999

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

Probab=99.27  E-value=3.5e-12  Score=106.65  Aligned_cols=60  Identities=22%  Similarity=0.421  Sum_probs=48.9

Q ss_pred             CCCCccccceEEEEecCCc-eeEEEeeeecCCCCeeEecccccccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           15 GSADSYIGSLISLTSKSEI-RYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        15 ~~~~~yIGskISLISKsdI-RYEGiL~~Id~e~sTIaL~nVRfGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      +.++.||||.|||.++.+| +|+|+|++||++++||+|+|| |    |  ++. .+++.+    |+||+.||+
T Consensus         2 ~Ma~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~-f----~--NG~-~~~s~e----Vtls~~DI~   62 (84)
T 2vc8_A            2 AMATDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRP-F----H--NGV-KCLVPE----VTFRAGDIT   62 (84)
T ss_dssp             ---CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEE-E----E--TTE-ECSSSE----EEEEGGGCS
T ss_pred             cccccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehh-h----h--CCC-CCCCcE----EEEEecChh
Confidence            4568999999999999999 999999999999999999999 4    2  222 233333    999999999

>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=97.34  E-value=0.0051  Score=59.57  Aligned_cols=70  Identities=9%  Similarity=0.109  Sum_probs=52.9

Q ss_pred             CCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ...+||+++|.++-|.+-.|+|+|..+|. .--|.|+||. |-++..+.+....-..+..+..|+.||+.|.
T Consensus         8 kL~klIdKrV~V~LkdGRel~GtLkgFDq-~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV   78 (231)
T 3pgw_B            8 KMLQHIDYRMRCILQDGRIFIGTFKAFDK-HMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLV   78 (231)
T ss_pred             HHHHhcCCeEEEEECCCcEEEEEEEEEcc-cccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEE
Confidence            45689999999999999999999999995 6788999999 7653222111111123455778999999999

>2rm4_A CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-BODY component, SM-like protein,, protein binding; NMR {Drosophila melanogaster}

Probab=96.81  E-value=0.0033  Score=54.34  Aligned_cols=58  Identities=16%  Similarity=0.336  Sum_probs=45.7

Q ss_pred             CCCccccceEEEEecCCc-eeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           16 SADSYIGSLISLTSKSEI-RYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        16 ~~~~yIGskISLISKsdI-RYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..+.|||+.+|+-...++ -|.|.+..||.  .+|+|.+.- =|--=|+..          =| ++|+..||+
T Consensus         6 ~~edwiG~~VSI~C~d~LGVyQG~I~~V~~--~~ItL~kaFrNGiplk~~~----------~E-VtLsa~DI~   65 (103)
T 2rm4_A            6 TDQDWIGCAVSIACDEVLGVFQGLIKQISA--EEITIVRAFRNGVPLRKQN----------AE-VVLKCTDIR   65 (103)
T ss_dssp             CSGGGTTCEEEEEECTTTCEEEEEEEEEET--TEEEEEEEEETTEECSCSS----------SC-EEEETTTEE
T ss_pred             cccceeceEEEEeeCCcceEeeEEEEEccc--ceeEEhhhhhcCcCcCCCC----------ce-EEEEecchh
Confidence            346899999999999999 99999999996  459998755 444333322          22 899999999

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

Probab=96.20  E-value=0.0047  Score=48.96  Aligned_cols=58  Identities=12%  Similarity=0.186  Sum_probs=48.3

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+-.|+|+|..+| +.--+.|+|+. +-.+++          ..-++.++.||+.|.
T Consensus        10 ~~~~~~~V~V~L~~g~~~~G~L~~~D-~~mNlvL~d~~e~~~~~~----------~~~lg~v~iRG~~I~   68 (77)
T 1i4k_A           10 NRSLKSPVIVRLKGGREFRGTLDGYD-IHMNLVLLDAEEIQNGEV----------VRKVGSVVIRGDTVV   68 (77)
T ss_dssp             HTTTTSEEEEEETTSCEEEEEEEEEC-TTCCEEEEEEEEEETTEE----------EEEEEEEEECGGGEE
T ss_pred             HHhCCCEEEEEEcCCCEEEEEEEEEc-CCCCeEEeeEEEEecCCc----------EeECCEEEECCCEEE
Confidence            46899999999999999999999999 56788999998 654322          223678999999998

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

Probab=96.18  E-value=0.0095  Score=50.05  Aligned_cols=54  Identities=19%  Similarity=0.252  Sum_probs=45.5

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccccccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVRfGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..|||+++.++...+=.|+|+||++|+..-.|.|.|.   -|            ++-|--++-.|.-||
T Consensus        13 ~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~---~~------------~~~~~~~iI~G~aI~   66 (86)
T 1y96_A           13 QDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF---LE------------DGSMSVTGIMGHAVQ   66 (86)
T ss_dssp             HHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE---CT------------TSCEEEEEECGGGEE
T ss_pred             HhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec---cc------------CCeEEEEEEecceEE
Confidence            4699999999999999999999999999999999985   12            122566777888888

>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=96.06  E-value=0.0051  Score=49.56  Aligned_cols=57  Identities=12%  Similarity=0.240  Sum_probs=48.0

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..|+|++|.+.-|.+-.|+|+|..+| +.--+.|+|+. +  ++.         ...-+..++.||+.|.
T Consensus        17 ~~~~~~~V~V~l~~g~~~~G~L~~~D-~~mNlvL~d~~e~--~~~---------~~~~lg~v~iRG~~I~   74 (81)
T 1i8f_A           17 QDSIGKQVLVKLRDSHEIRGILRSFD-QHVNLLLEDAEEI--IDG---------NVYKRGTMVVRGENVL   74 (81)
T ss_dssp             HTTTTSEEEEEEGGGEEEEEEEEEEC-TTCCEEEEEEEEE--ETT---------EEEEEEEEEECGGGEE
T ss_pred             HHHCCCeEEEEEcCCcEEEEEEEEEc-CCCeeEEccEEEE--cCC---------cccCCCEEEECCCEEE
Confidence            57899999999999999999999999 56789999999 8  221         1233778999999998

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

Probab=95.94  E-value=0.01  Score=47.34  Aligned_cols=60  Identities=13%  Similarity=0.264  Sum_probs=43.8

Q ss_pred             CCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .-..|+|++|.+.-|.+-.|+|+|..+| +.--+.|+|+. +-.++.          ...++.++.||+.|.
T Consensus         8 ~L~~~~~k~V~V~Lk~gr~~~G~L~~~D-~~mNlvL~~~~e~~~~~~----------~~~lg~v~iRG~~I~   68 (76)
T 3s6n_G            8 ELKKFMDKKLSLKLNGGRHVQGILRGFD-PFMNLVIDECVEMATSGQ----------QNNIGMVVIRGNSII   68 (76)
T ss_dssp             ------CCEEEEEETTTEEEEEEEEEEC-TTCCEEEEEEEECCCC--------------CBSSEEECSSSEE
T ss_pred             HHHHhCCCeEEEEECCCcEEEEEEEEEC-CcceEEEeceEEEccCCc----------EeEcCEEEECCCeEE
Confidence            4578999999999999999999999999 56788999998 643321          123667999999998

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

Probab=95.94  E-value=0.0074  Score=48.53  Aligned_cols=58  Identities=17%  Similarity=0.350  Sum_probs=48.3

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+-.|+|+|..+| +.--+.|+|+. +-.+++          ..-++.++.||+.|.
T Consensus        15 ~~~~~~~V~V~l~~g~~~~G~L~~~D-~~mNlvL~d~~e~~~~~~----------~~~lg~v~iRG~~I~   73 (81)
T 1th7_A           15 AESLNNLVLVKLKGNKEVRGMLRSYD-QHMNLVLSDSEEIQSDGS----------GKKLGTIVIRGDNVI   73 (81)
T ss_dssp             HHHTTSEEEEEETTTEEEEEEEEEEC-TTCCEEEEEEEEECSSSC----------EEEEEEEEECGGGEE
T ss_pred             HHhCCCeEEEEEcCCcEEEEEEEEEc-CCCCEEEccEEEEecCCc----------eeECCEEEECCCEEE
Confidence            46899999999999999999999999 56788999998 654321          233778999999998

>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=95.92  E-value=0.012  Score=48.12  Aligned_cols=70  Identities=9%  Similarity=0.114  Sum_probs=50.9

Q ss_pred             CCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .-..|||++|.+.-|.+-.|+|+|..+| +.--|.|+|+. |-++-......+--....-+..++.||+.|.
T Consensus         8 ~L~~~~~k~V~V~l~~gr~~~G~L~~~D-~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~   78 (91)
T 1d3b_B            8 KMLQHIDYRMRCILQDGRIFIGTFKAFD-KHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLV   78 (91)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECC-TTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEE
T ss_pred             HHHHHcCCcEEEEECCCeEEEEEEEEEC-CCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEE
Confidence            5678999999999999999999999999 56788999998 7543111100000011233677999999999

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

Probab=95.66  E-value=0.0092  Score=53.31  Aligned_cols=52  Identities=23%  Similarity=0.296  Sum_probs=44.3

Q ss_pred             CCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccccccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVRfGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      +..+|||++|.|.-|.+-+|.|+|..||...-|+.|+||+.                   ..+.++++||+
T Consensus         6 ~~sqFlGy~V~v~LkDgs~~qG~I~~vd~k~LtL~~~~a~~-------------------s~~~I~asdI~   57 (125)
T 4a53_A            6 SVADFYGSNVEVLLNNDSKARGVITNFDSSNSILQLRLAND-------------------STKSIVTKDIK   57 (125)
T ss_dssp             CHHHHTTCEEEEEETTSCEEEEEEEEEETTTTEEEEEETTT-------------------EEEEEEGGGEE
T ss_pred             cHHHhcCceEEEEECCCCEeeEEEEeecCCeeEEecccccc-------------------ccceeeccccc
Confidence            56799999999999999999999999998877777799841                   11278999999

>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=95.64  E-value=0.014  Score=46.58  Aligned_cols=57  Identities=18%  Similarity=0.310  Sum_probs=47.8

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .++|++|.+.-|.+.+|+|+|..+| +.=-+.|+||. +-.+|+          ..-++.++-||+.|.
T Consensus        12 ~~~g~~V~VeLk~g~~~~G~L~~~D-~~MNl~L~~~~e~~~~~~----------~~~lg~v~IRG~nI~   69 (75)
T 1d3b_A           12 EAEGHIVTCETNTGEVYRGKLIEAE-DNMNCQMSNITVTYRDGR----------VAQLEQVYIRGCKIR   69 (75)
T ss_dssp             HTTTSEEEEEETTSCEEEEEEEEEC-TTCCEEEEEEEEECTTSC----------EEEEEEEEECGGGEE
T ss_pred             HhCCCEEEEEECCCcEEEEEEEEEc-cceeEEEEeEEEECCCCc----------EEEcCeEEEeCCEEE
Confidence            5799999999999999999999999 56678999999 653332          234788999999998

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

Probab=95.54  E-value=0.012  Score=46.42  Aligned_cols=58  Identities=16%  Similarity=0.269  Sum_probs=48.0

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+-.|+|+|..+| +.--+.|+|+. +-.+++          ..-++.++.||+.|.
T Consensus        10 ~~~~~~~V~V~l~~g~~~~G~L~~~D-~~mNlvL~d~~e~~~~~~----------~~~lg~v~iRG~~I~   68 (75)
T 1h64_1           10 HRSLDKDVLVILKKGFEFRGRLIGYD-IHLNVVLADAEMIQDGEV----------VKRYGKIVIRGDNVL   68 (75)
T ss_dssp             HTTTTSEEEEEETTSEEEEEEEEEEC-TTCCEEEEEEEEEETTEE----------EEEEEEEEECGGGEE
T ss_pred             HHHCCCEEEEEECCCCEEEEEEEEEe-CCCCeEEeeEEEEeeCCc----------eeECCEEEECCCEEE
Confidence            46899999999999999999999999 56788999998 654321          223678999999998

>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=95.34  E-value=0.026  Score=48.74  Aligned_cols=77  Identities=13%  Similarity=0.173  Sum_probs=49.7

Q ss_pred             CCCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCccccccccc
Q 011128           15 GSADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTIT   93 (493)
Q Consensus        15 ~~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK~~~~~~~   93 (493)
                      ..-..|||++|.++-+.+-.|+|+|..+|. .--|.|.|+. |-++..   +...--....+..|+.||..|. ++.-++
T Consensus        26 ~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~-~mNLVL~d~~E~~~~~~---~~~~~~~~r~lG~v~IRG~nIv-~I~~~d  100 (113)
T 4emk_C           26 LDLSRYQDQRIQATFTGGRQITGILKGFDQ-LMNLVLDDVEEQLRNPE---DGKLTGAIRKLGLVVVRGTTLV-LIAPMD  100 (113)
T ss_dssp             ------CCSEEEEEETTSCEEEEEEEEECT-TCCEEEEEEEEEC------------CCEEEEEEEEECTTTEE-EEEECC
T ss_pred             HHHHHHcCCcEEEEEeCCeEEEEEEEEEcC-cccEEEeeEEEEEcCCC---CcccccceeEccEEEECCCeEE-EEEecC
Confidence            455689999999999999999999999995 6789999998 654321   0011123445778999999999 555555


Q ss_pred             ccC
Q 011128           94 GDA   96 (493)
Q Consensus        94 g~~   96 (493)
                      |+.
T Consensus       101 ~~e  103 (113)
T 4emk_C          101 GSE  103 (113)
T ss_dssp             ---
T ss_pred             ccc
Confidence            543

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

Probab=94.89  E-value=0.047  Score=45.92  Aligned_cols=59  Identities=22%  Similarity=0.296  Sum_probs=49.1

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..|+|++|.+.-|.+-+|+|+|..+|. ---+.|+|+. +-+++.         ....+..|+.||+.|.
T Consensus        26 ~~~l~k~V~V~Lk~gr~~~G~L~gfD~-~mNlvL~d~~E~~~~~~---------~~~~lg~v~IRG~nI~   85 (94)
T 4emk_A           26 DKCIGSNLWVIMKSEREFAGTLVGFDD-YVNIVLKDVTEYDTVTG---------VTEKHSEMLLNGNGMC   85 (94)
T ss_dssp             HHTTTSEEEEEESSSEEEEEEEEEECT-TCCEEEEEEEEEETTTC---------CEEEEEEEEECSTTEE
T ss_pred             HHHcCCeEEEEECCCcEEEEEEEEEcc-cCCeEeeeEEEEecCCC---------cEeEcCEEEEcCCEEE
Confidence            468999999999999999999999995 6778999998 764321         1345788999999998

>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=94.87  E-value=0.021  Score=46.19  Aligned_cols=59  Identities=20%  Similarity=0.327  Sum_probs=48.5

Q ss_pred             CCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        17 ~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      -..++|++|.+.-|.+-.|+|+|..+| +.--+.|+|+. +-.+++          ..-++.++.||+.|.
T Consensus        20 L~~~~~~~V~V~Lk~g~~~~G~L~~~D-~~mNlvL~d~~e~~~~~~----------~~~lg~v~IRG~~I~   79 (83)
T 1mgq_A           20 LGNSLNSPVIIKLKGDREFRGVLKSFD-LHMNLVLNDAEELEDGEV----------TRRLGTVLIRGDNIV   79 (83)
T ss_dssp             HHHTTTSEEEEEETTTEEEEEEEEEEC-TTCCEEEEEEEEEETTEE----------EEEEEEEEECGGGEE
T ss_pred             HHHhCCCEEEEEEcCCcEEEEEEEEEC-CCceeEEccEEEEecCCc----------ccCCCEEEECCCEEE
Confidence            357899999999999999999999999 56788999998 654321          223778999999987

>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=94.79  E-value=0.041  Score=47.66  Aligned_cols=58  Identities=12%  Similarity=0.193  Sum_probs=47.9

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+..|+|+|..+| +.--|.|+||. +-.++     .     ..-++.|+.||+.|.
T Consensus         8 ~~~~gk~V~V~Lk~g~~~~G~L~~~D-~~MNlvL~d~~e~~~~~-----~-----~~~lg~v~IRG~nI~   66 (119)
T 1b34_A            8 MKLSHETVTIELKNGTQVHGTITGVD-VSMNTHLKAVKMTLKNR-----E-----PVQLETLSIRGNNIR   66 (119)
T ss_dssp             HTCTTCEEEEEETTCCEEEEEEEEEC-TTCCEEEEEEEEECTTS-----C-----CEEEEEEEECGGGEE
T ss_pred             HHhCCCEEEEEEcCCCEEEEEEEEEc-ccceEEeccEEEecCCC-----c-----eeEcceEEEcCCeEE
Confidence            35899999999999999999999999 56788999999 63211     1     245788999999999

>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=94.69  E-value=0.028  Score=48.12  Aligned_cols=59  Identities=22%  Similarity=0.228  Sum_probs=45.8

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+-.|+|+|..+|. .--|.|+||. +-.+|.+         ..-++.|+.||+.|.
T Consensus        22 ~~~igk~V~V~Lk~G~~~~G~L~~~D~-~MNlvL~d~~e~~~dg~~---------~~~lg~v~IRG~nI~   81 (105)
T 4emh_A           22 NATQGRPILVELKNGETFNGHLENCDN-YMNLTLREVIRTMPDGDK---------FFRLPECYIRGNNIK   81 (105)
T ss_dssp             ----CCEEEEEETTSCEEEEEEEEECT-TCCEEEEEEEEECTTSCE---------EEEEEEEEECGGGEE
T ss_pred             HHhCCCEEEEEECCCCEEEEEEEEEcC-CceEEEEEEEEEccCCce---------eeEcCeEEEeCCeEE
Confidence            578999999999999999999999995 6678999998 6444321         123788999999999

>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=94.66  E-value=0.034  Score=44.13  Aligned_cols=58  Identities=19%  Similarity=0.433  Sum_probs=47.3

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+-.|+|+|..+|. .--+.|+|+. +-. |.         ....++.++.||+.|.
T Consensus        10 ~~~~~k~V~V~Lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~~-~~---------~~~~lg~v~iRG~~I~   68 (75)
T 4emk_B           10 NKVIGKKVLIRLSSGVDYKGILSCLDG-YMNLALERTEEYVN-GK---------KTNVYGDAFIRGNNVL   68 (75)
T ss_dssp             HHTTTSEEEEECTTSCEEEEEEEEECT-TCEEEEEEEEEEET-TE---------EEEEEEEEEEEGGGSS
T ss_pred             HHhCCCeEEEEEcCCcEEEEEEEEEcC-cceEEEccEEEEec-CC---------cccEecEEEEcCCeEE
Confidence            358999999999999999999999995 6788999988 632 21         1224778999999998

>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=94.65  E-value=0.03  Score=44.45  Aligned_cols=58  Identities=21%  Similarity=0.324  Sum_probs=47.7

Q ss_pred             CccccceEEEEecCC-ceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSE-IRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsd-IRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..|+|++|.+.-|.+ -+|+|+|..+| +.--+.|+|+. +-..++          ..-++.++.||+.|.
T Consensus        11 ~~~~~~~v~V~lk~g~~~~~G~L~~~D-~~mNlvL~d~~e~~~~~~----------~~~lg~v~iRG~nI~   70 (77)
T 1ljo_A           11 KSMVGKIIRVEMKGEENQLVGKLEGVD-DYMNLYLTNAMECKGEEK----------VRSLGEIVLRGNNVV   70 (77)
T ss_dssp             HHTTTSEEEEEETTCSSEEEEEEEEEC-TTCCEEEEEEEEEETTEE----------EEEEEEEEECGGGEE
T ss_pred             HHHCCCEEEEEEeCCCEEEEEEEEEEC-CcceEEEeeEEEEecCCc----------EeECCeEEEeCCeEE
Confidence            358999999999999 99999999999 56788999998 653211          223778999999998

>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=94.40  E-value=0.049  Score=45.41  Aligned_cols=65  Identities=12%  Similarity=0.197  Sum_probs=49.3

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..+||++|.+.-|.+-.|+|+|..+| +---|.|.|+. +-++..+..   .-....-+..++.||+.|.
T Consensus        16 ~~~i~k~V~V~Lk~gr~~~G~L~~fD-~~mNlVL~d~~E~~~~~~~~~---~~~~~r~lG~v~IRG~nVv   81 (96)
T 3bw1_A           16 KLNLDERVYIKLRGARTLVGTLQAFD-SHCNIVLSDAVETIYQLNNEE---LSESERRCEMVFIRGDTVT   81 (96)
T ss_dssp             GGGTTSEEEEEEGGGCEEEEEEEEEC-TTCCEEEEEEEEEEECCSTTC---CCEEEEEEEEEEECGGGEE
T ss_pred             HHHCCCeEEEEECCCcEEEEEEEEEC-CCCcEEEcCEEEEeccccccc---cCcceeEcCEEEECCCEEE
Confidence            57899999999999999999999999 56788999998 654332110   1111233677999999998

>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=94.39  E-value=0.036  Score=48.09  Aligned_cols=68  Identities=24%  Similarity=0.314  Sum_probs=48.8

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCC----CCC-CCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKI----GPQ-VPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~----~~~-IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..|||++|.+.-|.+-.|+|+|..+| +.--|.|+||. +-++.++.+    +.+ .-....-+..|+.||+.|.
T Consensus        34 ~~~l~k~V~V~Lk~Gr~~~G~L~~fD-~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~nVv  107 (121)
T 2fwk_A           34 DKCIGNRIYVVMKGDKEFSGVLRGFD-EYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVA  107 (121)
T ss_dssp             HHTBTSBCEEEETTTEEECCEEEEEC-TTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEE
T ss_pred             HHHcCCeEEEEECCCcEEEEEEEEEc-ccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCEEE
Confidence            47899999999999999999999999 57889999999 765422211    100 0001334678999999998

>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=94.17  E-value=0.093  Score=46.52  Aligned_cols=83  Identities=12%  Similarity=0.113  Sum_probs=59.3

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcccccccccccCC
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITGDAI   97 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK~~~~~~~g~~~   97 (493)
                      .++|++|.+.-|.+-.|+|+|..+| +.--+.|+|+. +  ++            .-|+.|+.||+.|.   .|.-.|..
T Consensus         7 ~~igk~V~V~Lk~G~~~~G~L~~~D-~~MNlvL~d~~E~--~~------------~~lg~v~IRG~nI~---~I~~~d~~   68 (130)
T 1m5q_A            7 NLLGREVQVVLSNGEVYKGVLHAVD-NQLNIVLANASNK--AG------------EKFNRVFIMYRYIV---HIDSTERR   68 (130)
T ss_dssp             HTTTSEEEEEETTSCEEEEEEEEEC-TTCCEEEEEEECT--TC------------CEEEEEEECGGGEE---EEEECCCC
T ss_pred             HhCCCeEEEEECCCcEEEEEEEEEc-ccceeEEeeEEEE--cC------------CEeceEEEeCCeEE---EEEcCCcc
Confidence            5899999999999999999999999 56788999998 6  21            34788999999998   33333322


Q ss_pred             CCCCcccccccchhhccccCCCCceEec
Q 011128           98 SGPRLSQTRDWTLRSVIRKDIQDLQVKS  125 (493)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~Dl~v~~  125 (493)
                        .|....+|.+.|.    ..-+.++.+
T Consensus        69 --~d~~~f~~~~~r~----~pg~vk~~~   90 (130)
T 1m5q_A           69 --IDMREFAKQAEKI----FPGMVKYIE   90 (130)
T ss_dssp             --CCHHHHHHHHHHH----STTCEEEET
T ss_pred             --cCHHHHHHHHhhc----CCCceeeee
Confidence              4444555555443    344555543

>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=94.05  E-value=0.073  Score=46.95  Aligned_cols=58  Identities=19%  Similarity=0.303  Sum_probs=48.9

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+..|.|+|..+|. .=-|.|+||. +-.+|.          ..-|+.++-||+.|.
T Consensus        11 ~~~~gk~V~VeLknG~~~~G~L~~~D~-~MNi~L~dv~e~~~~g~----------~~~l~~v~IRGnnI~   69 (126)
T 2y9a_D           11 HEAEGHIVTCETNTGEVYRGKLIEAED-NMNCQMSNITVTYRDGR----------VAQLEQVYIRGSKIR   69 (126)
T ss_dssp             HSCSSCEEEEEESSCCEEEEEEEEECT-TSCEEEEEEEEECTTSC----------CEEEEEEEECGGGEE
T ss_pred             HHhCCCEEEEEECCCcEEEEEEEEEcC-ceEEEEeeEEEEcCCCc----------EeecccEEEeCCEEE
Confidence            368999999999999999999999994 6788999999 654332          234788999999999

>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=93.91  E-value=0.035  Score=45.52  Aligned_cols=66  Identities=15%  Similarity=0.276  Sum_probs=49.3

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCccccccccccc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITGD   95 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK~~~~~~~g~   95 (493)
                      ..++|++|.+.-|.+-.|+|+|..+|. .--+.|+||. +- +|.         ...-++.++.||+.|. ++...+++
T Consensus        12 ~~~~~k~V~V~Lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~-~g~---------~~~~lg~v~IRG~nI~-~i~~~d~~   78 (86)
T 3s6n_F           12 NGLTGKPVMVKLKWGMEYKGYLVSVDG-YMNMQLANTEEYI-DGA---------LSGHLGEVLIRCNNVL-YIRGVEEE   78 (86)
T ss_dssp             HHHTTSEEEEEETTSCEEEEEEEEECT-TCCEEEEEEEEEE-TTE---------EEEEESSEEECGGGEE-EEEECC--
T ss_pred             HHhCCCeEEEEEcCCeEEEEEEEEEcC-ceEEEEeeEEEEc-CCc---------eeeEccEEEEeCCeEE-EEEeCCcc
Confidence            358999999999999999999999996 6678999998 63 111         0123567999999999 44444443

>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=93.70  E-value=0.037  Score=46.18  Aligned_cols=60  Identities=13%  Similarity=0.228  Sum_probs=47.6

Q ss_pred             CCCccccceEEEEecCC-ceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           16 SADSYIGSLISLTSKSE-IRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        16 ~~~~yIGskISLISKsd-IRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .-..++|++|.+.-|.+ ..|+|+|..+| +.--+.|+|+. +- +|.+         ..-++.++.||+.|.
T Consensus        25 ~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D-~~MNlvL~d~~E~~-~~~~---------~~~lg~v~IRG~nI~   86 (93)
T 1n9r_A           25 FLKGLVNHRVGVKLKFNSTEYRGTLVSTD-NYFNLQLNEAEEFV-AGVS---------HGTLGEIFIRCNNVL   86 (93)
T ss_dssp             -CGGGTTSEEEEEESSTTEEEEEEEEECC-TTTCEEEEEEEEEE-TTEE---------EEECCSEEECGGGEE
T ss_pred             HHHHhCCCEEEEEEcCCCEEEEEEEEEEc-cccEEEEeeEEEEc-CCCe---------EeEcCEEEEcCCeEE
Confidence            45678999999999999 99999999999 56788999998 63 2211         113567999999998

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

Probab=90.33  E-value=0.36  Score=40.07  Aligned_cols=68  Identities=12%  Similarity=0.232  Sum_probs=48.1

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCC-CC--CCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKI-GP--QVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~-~~--~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+-.|+|+|..+|. .--+.|+|+. +-++-.+.+ ..  ..-.....+..++.||..|.
T Consensus        15 ~~~~~~~V~V~l~~gr~~~G~L~~~D~-~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nVv   86 (93)
T 4emg_A           15 RLSLDEIVYVKLRGDRELNGRLHAYDE-HLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVI   86 (93)
T ss_dssp             HTTTTSEEEEEETTTEEEEEEEEEECT-TCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGEE
T ss_pred             HHhCCCEEEEEECCCcEEEEEEEEECC-cccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeEE
Confidence            345999999999999999999999995 6789999999 765411100 00  01122345788999999987

>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=86.98  E-value=1.2  Score=38.39  Aligned_cols=67  Identities=10%  Similarity=0.228  Sum_probs=45.3

Q ss_pred             ccc--cceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCC-CCCC---CCCCCCceeEEEEecCCcc
Q 011128           19 SYI--GSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEK-IGPQ---VPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yI--GskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~-~~~~---IPPsd~VyeyIvFRGSDIK   86 (493)
                      .++  |++|.+.-+.+-.|+|+|..+| +.--+.|.||. +-++..+. .+.+   .--.+..+..|+.||+.|.
T Consensus        34 ~~~~~~k~V~V~Lk~gr~~~G~L~~fD-~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~nVv  107 (118)
T 1b34_B           34 QSVKNNTQVLINCRNNKKLLGRVKAFD-RHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVI  107 (118)
T ss_dssp             HHHHHTCEEEEEETTSCEEEEEEEEEC-TTCCEEEEEEEEC-------------------CEEEEEEEECGGGEE
T ss_pred             HHhcCCcEEEEEECCCcEEEEEEEEeC-CceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCCEEE
Confidence            456  5999999999999999999999 67889999998 65432111 0100   0011234788999999998

>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=86.35  E-value=0.5  Score=39.44  Aligned_cols=58  Identities=19%  Similarity=0.387  Sum_probs=44.5

Q ss_pred             ccccceEEE----EecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISL----TSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISL----ISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .|+++++.+    +.|.+.+|+|+|..+|. ---|.|+|+. +-+++.         ....+.-++.||+.|.
T Consensus        23 ~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~-~mNlvL~d~~E~~~~~~---------~~~~lg~v~iRG~nV~   85 (92)
T 3s6n_E           23 RYLQNRSRIQVWLYEQVNMRIEGCIIGFDE-YMNLVLDDAEEIHSKTK---------SRKQLGRIMLKGDNIT   85 (92)
T ss_dssp             HHHHHTCEEEEEESSSCSSEEEEEEEEECT-TCCEEEEEEEEECSSSC---------CEEEEEEEEECGGGEE
T ss_pred             HHhCCCEEEEEEEEecCCEEEEEEEEEEcC-cCcEEEeeeEEEecCCC---------ceeEcCeEEEeCCEEE
Confidence            577888554    45999999999999995 7788999988 654321         1234678999999998

---

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	493
d2vxfa1	80	b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebraf	9e-24

>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]} Length = 80

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]

 Score = 92.8 bits (231), Expect = 9e-24
 Identities = 34/67 (50%), Positives = 45/67 (67%)

Query: 20 YIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYIL 79
          YIGS ISL SK+EIRYEG+L+ I+TE S++ L   R     +      + P D+ +EYI+
Sbjct: 2  YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYII 61

Query: 80 FRGSDIK 86
          FRGSDIK
Sbjct: 62 FRGSDIK 68

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	493
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	100.0
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	97.3
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	96.45
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	96.07
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	95.73
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	95.61
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	95.56
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	95.55
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	95.07
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	95.02
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	94.98
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	93.81
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	88.69
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	87.02

>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=100.00  E-value=6.8e-37  Score=251.11  Aligned_cols=67  Identities=51%  Similarity=0.864  Sum_probs=65.2

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      +|||++||||||+||||||+||+||.+++||+|+||| ||||||++++ +|||+++|||||+|||+|||
T Consensus         1 pyIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~-~ipp~~~vy~~IvFrgsDIK   68 (80)
T d2vxfa1           1 PYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDR-PIAPRDETFEYIIFRGSDIK   68 (80)
T ss_dssp             CSTTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSS-CCCCCCCCEEEEEEETTTEE
T ss_pred             CccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCC-ccCCCCcceeEEEEcCcCcc
Confidence            6999999999999999999999999999999999999 9999998875 69999999999999999999

>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=97.30  E-value=0.00014  Score=57.15  Aligned_cols=69  Identities=9%  Similarity=0.110  Sum_probs=53.4

Q ss_pred             CCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        17 ~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ...||+++|.++.+.+-.|+|+|..+|. ..-|.|+|+. |-++..+......-........++.||..|-
T Consensus         3 L~~~l~~rv~V~l~dgR~~~G~L~~~D~-~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv   72 (81)
T d1d3bb_           3 MLQHIDYRMRCILQDGRIFIGTFKAFDK-HMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLV   72 (81)
T ss_dssp             CGGGTTSEEEEEETTCCEEEEEEEECCT-TCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEE
T ss_pred             hHHHCCCEEEEEEcCCCEEEEEEEEECC-ccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEE
Confidence            4689999999999999999999999995 5778999999 8876665432211111223567999999998

>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=96.45  E-value=0.0013  Score=50.83  Aligned_cols=58  Identities=17%  Similarity=0.335  Sum_probs=48.4

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .+++|++|.+.-|.+..|+|+|..+|. .--|.|+||. +-.++..          .-++.++.||+.|.
T Consensus        13 ~~~~~~~V~V~lk~g~~~~G~L~~~D~-~mNlvL~~~~e~~~~~~~----------~~~~~v~iRG~~I~   71 (76)
T d1th7a1          13 AESLNNLVLVKLKGNKEVRGMLRSYDQ-HMNLVLSDSEEIQSDGSG----------KKLGTIVIRGDNVI   71 (76)
T ss_dssp             HHHTTSEEEEEETTTEEEEEEEEEECT-TCCEEEEEEEEECSSSCE----------EEEEEEEECGGGEE
T ss_pred             HHhCCCEEEEEECCCCEEEEEEEEECC-CCCEEEeEEEEEecCCcc----------cCcceEEEECCEEE
Confidence            468999999999999999999999997 5678999998 6444331          24788999999997

>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=96.07  E-value=0.0026  Score=48.23  Aligned_cols=57  Identities=16%  Similarity=0.283  Sum_probs=47.1

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .++|++|.+..|.+-.|+|+|..+|. .--|.|+|+. +-.+++          ..-++.++.||+.|.
T Consensus         9 ~~~~~~V~V~lk~g~~~~G~L~~~D~-~mNlvL~~~~e~~~~~~----------~~~l~~~~IRG~~I~   66 (71)
T d1h641_           9 RSLDKDVLVILKKGFEFRGRLIGYDI-HLNVVLADAEMIQDGEV----------VKRYGKIVIRGDNVL   66 (71)
T ss_dssp             TTTTSEEEEEETTSEEEEEEEEEECT-TCCEEEEEEEEEETTEE----------EEEEEEEEECGGGEE
T ss_pred             HhCCCEEEEEEcCCCEEEEEEEEECC-CCCeEEeeEEEEecCCc----------EeEcCcEEEECCeEE
Confidence            68999999999999999999999994 6688999998 533222          123788999999997

>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=95.73  E-value=0.004  Score=47.66  Aligned_cols=57  Identities=12%  Similarity=0.233  Sum_probs=47.6

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .+++|++|.+.-|.+..|+|+|..+|. .--|.|+|+. +..|.+           .-++.++.||+.|.
T Consensus         8 ~~~~~k~V~V~Lk~g~~~~G~L~~~D~-~mNivL~~~~e~~~~~~-----------~~~g~v~iRG~~I~   65 (71)
T d1i8fa_           8 QDSIGKQVLVKLRDSHEIRGILRSFDQ-HVNLLLEDAEEIIDGNV-----------YKRGTMVVRGENVL   65 (71)
T ss_dssp             HTTTTSEEEEEEGGGEEEEEEEEEECT-TCCEEEEEEEEEETTEE-----------EEEEEEEECGGGEE
T ss_pred             HHhCCCEEEEEECCCCEEEEEEEEECC-CcceEEccEEEEECCCE-----------EEcceEEEeCCeEE
Confidence            578999999999999999999999997 6778999997 654322           12677999999997

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

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

Probab=95.61  E-value=0.0044  Score=47.43  Aligned_cols=57  Identities=21%  Similarity=0.353  Sum_probs=46.7

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .++|++|.+..|.+-.|+|+|..+|. .--|.|+|+. +-.++.          ..-++.++.||+.|.
T Consensus        13 ~~~~k~V~V~lk~g~~~~G~L~~~D~-~mNl~L~~~~e~~~~~~----------~~~~~~~~IRG~~I~   70 (74)
T d1mgqa_          13 NSLNSPVIIKLKGDREFRGVLKSFDL-HMNLVLNDAEELEDGEV----------TRRLGTVLIRGDNIV   70 (74)
T ss_dssp             HTTTSEEEEEETTTEEEEEEEEEECT-TCCEEEEEEEEEETTEE----------EEEEEEEEECGGGEE
T ss_pred             HhCCCeEEEEECCCCEEEEEEEEECC-CCCeEEeeEEEEeCCCe----------EeEcceEEEeCCEEE
Confidence            58999999999999999999999995 5678999998 632221          234788999999987

>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=95.56  E-value=0.0067  Score=46.34  Aligned_cols=57  Identities=18%  Similarity=0.300  Sum_probs=48.2

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..+|++|.+--|.+..|+|+|..+|. .-.|.|+|+. +-.+++.          ..++-++-||+.|+
T Consensus         9 ~~~g~~V~VeLkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~~~~----------~~~~~v~IRG~~I~   66 (72)
T d1d3ba_           9 EAEGHIVTCETNTGEVYRGKLIEAED-NMNCQMSNITVTYRDGRV----------AQLEQVYIRGCKIR   66 (72)
T ss_dssp             HTTTSEEEEEETTSCEEEEEEEEECT-TCCEEEEEEEEECTTSCE----------EEEEEEEECGGGEE
T ss_pred             hcCCCEEEEEECCCeEEEEEEEEEcC-CeeEEEEEEEEEcCCCcE----------eEcCeEEEECCEEE
Confidence            46899999999999999999999997 5889999998 7555442          23677899999998

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

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

Probab=95.55  E-value=0.0055  Score=46.66  Aligned_cols=57  Identities=12%  Similarity=0.194  Sum_probs=46.8

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .++|++|.+.-|.+-.|+|+|..+|. .--|.|+|+. +-.++++          .-++.++.||+.|.
T Consensus        10 ~~~~~~V~V~lk~g~~~~G~L~~~D~-~mNlvL~~~~e~~~~~~~----------~~~g~~~IRG~~I~   67 (72)
T d1i4k1_          10 RSLKSPVIVRLKGGREFRGTLDGYDI-HMNLVLLDAEEIQNGEVV----------RKVGSVVIRGDTVV   67 (72)
T ss_dssp             TTTTSEEEEEEGGGCEEEEEEEEECT-TCCEEEEEEEEESSSSEE----------EEEEEEEECGGGEE
T ss_pred             HhCCCEEEEEECCCCEEEEEEEEEcC-CCCeEEeeEEEEecCCeE----------eEcceEEEeCCeEE
Confidence            58999999999999999999999997 5667999998 6433221          23788999999997

>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=95.07  E-value=0.0077  Score=46.56  Aligned_cols=57  Identities=21%  Similarity=0.318  Sum_probs=45.3

Q ss_pred             ccccceEEEEecCCc-eeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEI-RYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdI-RYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .++|++|.+.-|.|- .|+|+|..+|. .--+.|+|+. +-.++..          .-++.++-||+.|.
T Consensus        12 ~~~~~~V~V~lk~~~~~~~G~L~~~D~-~mNlvL~~~~e~~~~~~~----------~~~g~~~IRG~~I~   70 (75)
T d1ljoa_          12 SMVGKIIRVEMKGEENQLVGKLEGVDD-YMNLYLTNAMECKGEEKV----------RSLGEIVLRGNNVV   70 (75)
T ss_dssp             HTTTSEEEEEETTCSSEEEEEEEEECT-TCCEEEEEEEEEETTEEE----------EEEEEEEECGGGEE
T ss_pred             HhcCCEEEEEEECCCEEEEEEEEEEcC-CCcEEEeEEEEEcCCCcE----------eEcceEEEeCCEEE
Confidence            589999999999874 59999999995 5678999998 6433321          23778999999997

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.02  E-value=0.017  Score=45.04  Aligned_cols=57  Identities=14%  Similarity=0.250  Sum_probs=49.1

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..+|++|.+--|.+..|+|+|..+|. .-.+.|+||. ...+|+.          .-|+.+.-||+.|+
T Consensus         8 ~~~g~~V~VeLkng~~~~G~L~~~D~-~MNl~L~~~~~~~~~~~~----------~~~~~v~IRG~~Ir   65 (80)
T d1b34a_           8 KLSHETVTIELKNGTQVHGTITGVDV-SMNTHLKAVKMTLKNREP----------VQLETLSIRGNNIR   65 (80)
T ss_dssp             TCTTCEEEEEETTCCEEEEEEEEECT-TCCEEEEEEEEECTTSCC----------EEEEEEEECGGGEE
T ss_pred             HcCCCEEEEEECCCCEEEEEEEEEcC-CcEEEEEEEEEEcCCCCE----------EEcccEEEcCCEEE
Confidence            46899999999999999999999997 5889999999 7655442          13888999999999

>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=94.98  E-value=0.011  Score=46.74  Aligned_cols=67  Identities=21%  Similarity=0.243  Sum_probs=46.8

Q ss_pred             ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCC-C----CCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQ-V----PPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~-I----PPsd~VyeyIvFRGSDIK   86 (493)
                      .++|++|.+..+.+-.|.|+|..+|.. .-|.|+|+. +.++..+..... -    -....-+.-++.||++|-
T Consensus        12 ~~l~k~V~V~l~~gr~~~G~L~~~D~~-~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~Vv   84 (92)
T d2fwka1          12 KCIGNRIYVVMKGDKEFSGVLRGFDEY-VNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVA   84 (92)
T ss_dssp             HTBTSBCEEEETTTEEECCEEEEECTT-CCEEEESCCEEEC---------------CEECCCCSEEEECGGGEE
T ss_pred             HHcCCEEEEEEcCCCEEEEEEEEEcCC-CCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEEE
Confidence            578999999999999999999999975 578999999 776555432110 0    011123567999999997

>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=93.81  E-value=0.049  Score=46.33  Aligned_cols=55  Identities=16%  Similarity=0.260  Sum_probs=45.7

Q ss_pred             CccccceEEEEecCCceeEEEeeeecCCCCeeEecccccccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVRfGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      ..++|++|.+.-|.+..|.|+|..+| +.-.|.|+||..-..+             -|..++-||+.|+
T Consensus         6 ~~~~gk~V~VeLkng~~~~G~L~~~D-~~mNivL~da~~~~~~-------------k~~~v~IRG~~I~   60 (127)
T d1m5q1_           6 NNLLGREVQVVLSNGEVYKGVLHAVD-NQLNIVLANASNKAGE-------------KFNRVFIMYRYIV   60 (127)
T ss_dssp             HTTTTSEEEEEETTSCEEEEEEEEEC-TTCCEEEEEEEETTCC-------------EEEEEEECGGGEE
T ss_pred             HHhCCCEEEEEECCCCEEEEEEEEEC-CCceEEEeEEEECCCC-------------cccEEEEeCCeEE
Confidence            36899999999999999999999999 6788999998621111             1667899999999

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.69  E-value=0.14  Score=38.60  Aligned_cols=57  Identities=12%  Similarity=0.224  Sum_probs=44.1

Q ss_pred             ccccceEEEEec-CCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128           19 SYIGSLISLTSK-SEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        19 ~yIGskISLISK-sdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK   86 (493)
                      .++|++|.+-=| .+..|+|+|..+|. .--|.|+|+. .-.+++.          .-++.++-||+.|.
T Consensus         3 ~~~~~~V~V~Lk~~~~~~~G~L~~~D~-~mNlvL~~~~e~~~~~~~----------~~lg~~~IRG~nI~   61 (68)
T d1n9ra_           3 GLVNHRVGVKLKFNSTEYRGTLVSTDN-YFNLQLNEAEEFVAGVSH----------GTLGEIFIRCNNVL   61 (68)
T ss_dssp             GGTTSEEEEEESSTTEEEEEEEEECCT-TTCEEEEEEEEEETTEEE----------EECCSEEECGGGEE
T ss_pred             hHCCCEEEEEEEcCCEEEEEEEEEECC-cCceEEeeEEEEecCCcc----------cCcCeEEEECCEEE
Confidence            589999999999 45779999999996 4567899988 4333221          23667899999998

>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=87.02  E-value=0.46  Score=37.61  Aligned_cols=64  Identities=9%  Similarity=0.171  Sum_probs=42.8

Q ss_pred             cceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCC-C---CCCCCCceeEEEEecCCcc
Q 011128           22 GSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGP-Q---VPPSDKIYEYILFRGSDIK   86 (493)
Q Consensus        22 GskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~-~---IPPsd~VyeyIvFRGSDIK   86 (493)
                      +++|.++.+.+-.|+|+|...|. .--+.|.||. +-++..+.... +   ..-...-+..++.||..|-
T Consensus        14 ~~rV~V~lr~~r~~~G~L~afD~-~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnVv   82 (93)
T d1b34b_          14 NTQVLINCRNNKKLLGRVKAFDR-HCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVI   82 (93)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECT-TCCEEEEEEEEC-------------------CEEEEEEEECGGGEE
T ss_pred             CcEEEEEECCCCEEEEEEEEecc-ceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEEE
Confidence            78999999999999999999995 5678999999 77665443211 0   1111234788999999986