Citrus Sinensis ID: 012664

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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-------46
Protein Sequence
MAMTADSTSNHVTPRGSGFSGDGLSSPQLRRKNSPSQWSEVVRGEHDPASTTVNHSQSSPSPPLTTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGNAARPKKLAWNKPSNGVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPHLPQKVSNANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPMPPNSFANLVTAMPDPSPREPLYRGSNWDARPVGGFVSQSHPMNDQRNSSRRGNYGQRGDGNYNNNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMRPFPNPMGFPEFIYIPPMPVEAAALRGVTGMPPFIPPAPVLMPVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccHHHHHHcccccccEEcHHHccccHHHHHcccHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccHEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHccccccEEEEEEEccccEEEcccHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mamtadstsnhvtprgsgfsgdglsspqlrrknspsqwsevvrgehdpasttvnhsqsspsppltttslpeptgsvspskavasapsspppdnpiaagssdadkgnaarpkklawnkpsngvvevgpvmgaaswpalsestkpspksssadsssskpvadgsvsgtqvpliphlpqkvsnananpnsnanrtmparqrlkrsgggvsnagsgpaqtrptqpppppppppfpvfpmppnsfanlvtampdpspreplyrgsnwdarpvggfvsqshpmndqrnssrrgnygqrgdgnynnnfggrhdqdrgnysnardahvqpqrgpprgfvrpappnaaafappqpmrpfpnpmgfpefiyippmpveAAALrgvtgmppfippapvlmpvpepsLAAMLIHQIDyyfsdanlvkdeflksnmddqgwvpitliasfprvsfysQISYFLITCSQFSL
Flexible Loop (DISEMBL)
mamtadstsnhvtprgsgfsgdglsspqlrrknspsqWSEVVRGEHDPASttvnhsqsspspplTTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGNAARpkklawnkpsngvVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPHLPQKVSnananpnsnanrtmpARQRLKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPMPPNSFANLVTAMPDPSPREPLYRGSNWDARPVGGFvsqshpmndqrnssrrgnygqrgDGNYNNNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMRPFPNPMGFPEFIYIPPMPVEAAALRGVTGMPPFIPPAPVLMPVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL
Low Complexity Region (SEG)
MAMTADSTSNHVTPRGSGFSGDGLSSPQLRRKNSPSQWSEVVRGEHDPASTTVNHSQsspsppltttslpeptGsvspskavasapsspppdnpiaaGSSDADKGNAARPKKLAWNKPSNGVVEVGPVMGAASWPALsestkpspksssadsssskpVADGSVSGTQVPLIPHLPQKVsnananpnsnanRTMPARQRLKRSGGGVSNAGSGPAQTRPTQpppppppppfpvfpmppNSFANLVTAMPDPSPREPLYRGSNWDARPVGGFVSQSHPMNDQRNSSRRGNYGQRGDGNYNNNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRpappnaaafappqpmrpfpnpmGFPEFIYIPPMPVEAAALRGVTGMppfippapvlmpvpepSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL
Disordered region (IsUnstruct)
******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************GFPEFIYIPPMPVEAAALRGVTGMPPFIPPAPVLMPVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCS****
Disordered Region (DISOPRED)
*********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************IPPAPVLMPVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFS*
Disordered Region (DISEMBL)
**************************************************************************************************************KKLAWNKPSNGVVEVGPVMGAASW*******************************TQVPLIPHLPQKVSNANANPNSNANRTMP******************************PPPPPFPVFPMPPNSFANLVTAMPDPSPREPLYRGSNWDARPVGGFVSQS*************NYGQRGDGNYNNNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMRPFPNPMGFPEFIYIPPMPVEAAALRGVTGMPPFIPPAPVLMPVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL
Disordered Region (DISPRO)
***********************************************************************************************************************************************************************************************************************************************************************************************************************************RGPPRGFVRPAPPNAAAFAPPQPMRPFPNPMGFPEFIYIPPMPVEAAALRGVTGMPPFIPPAPVLMPVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQF**
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAMTADSTSNHVTPRGSGFSGDGLSSPQLRRKNSPSQWSEVVRGEHDPASTTVNHSQSSPSPPLTTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGNAARPKKLAWNKPSNGVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPHLPQKVSNANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPMPPNSFANLVTAMPDPSPREPLYRGSNWDARPVGGFVSQSHPMNDQRNSSRRGNYGQRGDGNYNNNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMRPFPNPMGFPEFIYIPPMPVEAAALRGVTGMPPFIPPAPVLMPVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL
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	458	2.2.26 [Sep-21-2011]
Q9P6K0	475	Uncharacterized HTH La-ty	yes	no	0.126	0.122	0.440	3e-09
Q659C4	914	La-related protein 1B OS=	yes	no	0.115	0.057	0.509	6e-09
Q6PKG0	1096	La-related protein 1 OS=H	no	no	0.115	0.048	0.509	2e-07
Q9VAW5	1673	La-related protein OS=Dro	yes	no	0.100	0.027	0.5	5e-07
P10881	404	Lupus La protein homolog	no	no	0.102	0.116	0.458	5e-07
Q26457	383	La protein homolog OS=Aed	N/A	no	0.111	0.133	0.423	5e-07
Q6ZQ58	1072	La-related protein 1 OS=M	no	no	0.098	0.041	0.555	5e-07
P05455	408	Lupus La protein OS=Homo	no	no	0.102	0.115	0.458	5e-07
P32067	415	Lupus La protein homolog	no	no	0.102	0.113	0.458	1e-06
P38656	415	Lupus La protein homolog	no	no	0.102	0.113	0.458	1e-06

>sp|Q9P6K0|YLA3_SCHPO Uncharacterized HTH La-type RNA-binding protein C1527.03 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC1527.03 PE=1 SV=1

 Score = 63.5 bits (153), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 39/59 (66%), Gaps = 1/59 (1%)

Query: 396 LAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV-SFYSQISYFLITC 453
           + A L  Q++YYFS  NL KD FL+ +MDD+G+VP+  +ASF R+ SF + ++     C
Sbjct: 325 VQAFLTSQLEYYFSIENLCKDMFLRKHMDDEGYVPLAFLASFNRIKSFSTDLNLLHAAC 383

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

>sp|Q659C4|LAR1B_HUMAN La-related protein 1B OS=Homo sapiens GN=LARP1B PE=1 SV=2

 Score = 62.8 bits (151), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 36/53 (67%)

Query: 388 LMPVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
           + PV E  L   +  QI+YYFS  NL +D FL+  MD+QG++PI+LIA F RV
Sbjct: 207 VYPVEEALLKEYIKRQIEYYFSVENLERDFFLRGKMDEQGFLPISLIAGFQRV 259

Homo sapiens (taxid: 9606)

>sp|Q6PKG0|LARP1_HUMAN La-related protein 1 OS=Homo sapiens GN=LARP1 PE=1 SV=2

 Score = 58.2 bits (139), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 34/53 (64%)

Query: 388 LMPVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
           L  V +  L   +  QI+YYFS  NL +D FL+  MD  G++PITLIASF RV
Sbjct: 395 LYSVDQELLKDYIKRQIEYYFSVDNLERDFFLRRKMDADGFLPITLIASFHRV 447

Homo sapiens (taxid: 9606)

>sp|Q9VAW5|LARP_DROME La-related protein OS=Drosophila melanogaster GN=larp PE=1 SV=5

 Score = 56.2 bits (134), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 32/46 (69%)

Query: 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
           S+   +  Q++YYFS  NL  D FL+  MD +G++P+TLIASF RV
Sbjct: 728 SIKEAIKKQVEYYFSVDNLTGDFFLRRKMDPEGYIPVTLIASFHRV 773

Drosophila melanogaster (taxid: 7227)

>sp|P10881|LA_BOVIN Lupus La protein homolog OS=Bos taurus GN=SSB PE=2 SV=2

 Score = 56.2 bits (134), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%), Gaps = 1/48 (2%)

Query: 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
           +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R++
Sbjct: 12  ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLN 59

Binds to the 3' poly(U) terminii of nascent RNA polymerase III transcripts, protecting them from exonuclease digestion and facilitating their folding and maturation.

Bos taurus (taxid: 9913)

>sp|Q26457|LA_AEDAL La protein homolog OS=Aedes albopictus PE=1 SV=1

 Score = 56.2 bits (134), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 35/52 (67%), Gaps = 1/52 (1%)

Query: 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNM-DDQGWVPITLIASFPRVSFYSQ 445
            L A  I Q++YYF DANL +D+FL+  +  D+GWVP+ ++ +F R+   S+
Sbjct: 42  KLEASTIRQLEYYFGDANLARDKFLQEQISKDEGWVPVDVLLTFKRLKSLSE 93

May be involved in transcription termination by RNA polymerase III. Binds RNA and DNA. Binds to the 3' end of the minus strand of Sindbis virus RNA. This may be significant for Sindbis virus RNA replication.

Aedes albopictus (taxid: 7160)

>sp|Q6ZQ58|LARP1_MOUSE La-related protein 1 OS=Mus musculus GN=Larp1 PE=1 SV=2

 Score = 56.2 bits (134), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 25/45 (55%), Positives = 31/45 (68%)

Query: 396 LAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
           L   +  QI+YYFS  NL +D FL+  MD  G++PITLIASF RV
Sbjct: 378 LKDYIKRQIEYYFSVDNLERDFFLRRKMDADGFLPITLIASFHRV 422

Mus musculus (taxid: 10090)

>sp|P05455|LA_HUMAN Lupus La protein OS=Homo sapiens GN=SSB PE=1 SV=2

 Score = 56.2 bits (134), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%), Gaps = 1/48 (2%)

Query: 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
           +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R++
Sbjct: 12  ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLN 59

Binds to the 3' poly(U) terminii of nascent RNA polymerase III transcripts, protecting them from exonuclease digestion and facilitating their folding and maturation.

Homo sapiens (taxid: 9606)

>sp|P32067|LA_MOUSE Lupus La protein homolog OS=Mus musculus GN=Ssb PE=2 SV=1

 Score = 55.1 bits (131), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%), Gaps = 1/48 (2%)

Query: 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
           +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+  +  F R++
Sbjct: 12  ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLETMIKFNRLN 59

Binds to the 3' poly(U) terminii of nascent RNA polymerase III transcripts, protecting them from exonuclease digestion and facilitating their folding and maturation.

Mus musculus (taxid: 10090)

>sp|P38656|LA_RAT Lupus La protein homolog OS=Rattus norvegicus GN=Ssb PE=2 SV=1

 Score = 54.7 bits (130), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%), Gaps = 1/48 (2%)

Query: 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
           +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+  +  F R++
Sbjct: 12  ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLETMIKFNRLN 59

Binds to the 3' poly(U) terminii of nascent RNA polymerase III transcripts, protecting them from exonuclease digestion and facilitating their folding and maturation.

Rattus norvegicus (taxid: 10116)

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	458
359492285	565	PREDICTED: uncharacterized protein LOC10	0.906	0.734	0.502	2e-90
317106588	536	JHL20J20.1 [Jatropha curcas]	0.910	0.777	0.524	2e-88
302142718	559	unnamed protein product [Vitis vinifera]	0.711	0.583	0.530	1e-81
449437412	540	PREDICTED: uncharacterized protein LOC10	0.941	0.798	0.464	6e-80
356552054	527	PREDICTED: uncharacterized protein LOC10	0.917	0.796	0.493	8e-79
224085930	502	predicted protein [Populus trichocarpa]	0.864	0.788	0.468	8e-74
356517961	511	PREDICTED: uncharacterized protein LOC10	0.879	0.788	0.464	4e-69
357438541	681	La-related protein [Medicago truncatula]	0.851	0.572	0.467	9e-68
302143562	568	unnamed protein product [Vitis vinifera]	0.893	0.720	0.379	9e-56
255539032	449	lupus la ribonucleoprotein, putative [Ri	0.344	0.351	0.628	2e-51

>gi|359492285|ref|XP_002279250.2| PREDICTED: uncharacterized protein LOC100243746 [Vitis vinifera]

 Score =  339 bits (870), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 234/466 (50%), Positives = 289/466 (62%), Gaps = 51/466 (10%)

Query: 1   MAMTADSTSNHVTPRGSGFSGDGLSSPQLRRKNSPSQWSEVVRGEHDPASTTVNHSQSSP 60
           MA T DS+     PRGSGFS DG+ SP LRR+N  S W+++VRGE +  S+ V HS +S 
Sbjct: 1   MATTTDSS-----PRGSGFSADGVHSP-LRRRNLSSPWAQIVRGETESMSS-VPHSPTSS 53

Query: 61  SPPLTTTSLPEPTG--SVSPSKAVASAPSSPPPDNPIAAG-----SSDADKGNAARPKKL 113
           S     TS PE       SP+K ++ +PS  P  +    G     +SD    NA R KK 
Sbjct: 54  S---PVTSCPEQISFSECSPTKPLSPSPSRSPAPDNSGVGEALLENSDGCGSNAGRQKKP 110

Query: 114 AWNKPSNGVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPH 173
           AWNKPSN VVEVGPVMGA SWPALSEST+ SP+SSS    S KP  DGS +  Q P+IPH
Sbjct: 111 AWNKPSNDVVEVGPVMGAVSWPALSESTRASPRSSS---DSPKPAVDGSAASIQGPVIPH 167

Query: 174 LPQKVSNANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVF 233
            PQK   AN NPNS+ N   P RQR  +SGGG S    G   ++P  PPPP P     +F
Sbjct: 168 SPQKQVPANTNPNSSQNHASPFRQRSIKSGGGSSQTVHGHLPSQPPPPPPPYP-----LF 222

Query: 234 PMPPNSFANLVTAMPDPSPREPLYRGSNWDARPVGGFVSQSHPMNDQ---RNSSRRGNYG 290
            MP N +A +   + D S REP YR + W+ RP+GGFV Q   ++D    RNS RRGN+G
Sbjct: 223 EMPQNKYAKMAPQVLDSSTREPPYRNNTWETRPIGGFVPQPRGLSDHPLPRNS-RRGNFG 281

Query: 291 Q--RGDGNYNNNFGGRHDQDRGNY------SNARDAHVQPQRGPPRGFVRPAPPNAA-AF 341
              RGDG ++NN+GGR DQDRGNY      SN RD H+QPQR PPRGF+R AP +++  F
Sbjct: 282 PHPRGDGPHHNNYGGRRDQDRGNYEWNSRSSNVRDIHMQPQRAPPRGFIRAAPQSSSPRF 341

Query: 342 APPQPMRPFPNPMGFP----EFIYIPPMPVEAAALRGVTGMPPFIPPAPVLMPVP---EP 394
             PQP+RPF NP G+P    +  Y P +P E    R V    PF+  AP         +P
Sbjct: 342 MTPQPIRPFMNPAGYPDMPSQMYYFPALPSEP--FRSV----PFVAHAPPPPMFIPVPDP 395

Query: 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
            L  +L++QI+YYFSD NL+KD++L+S MDDQGWVPITLIA FPRV
Sbjct: 396 PLPTLLVNQIEYYFSDVNLIKDDYLRSYMDDQGWVPITLIAGFPRV 441

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|317106588|dbj|BAJ53096.1| JHL20J20.1 [Jatropha curcas]

 Score =  332 bits (851), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 244/465 (52%), Positives = 307/465 (66%), Gaps = 48/465 (10%)

Query: 1   MAMTADSTSNHVTPRGSGFSGDGLSSPQLRRKNSPSQWSEVVRGEHDPASTTVNHSQSSP 60
           MAMTADS+ +  +  GS  S DG++SPQ + K+  S W+++VRGE +      +     P
Sbjct: 1   MAMTADSSQSPRSGSGSVLSVDGVNSPQ-KHKSLHSPWAQIVRGEPESVPPLNHSPPPPP 59

Query: 61  SPPLTTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGNAARPKKLAWNKPSN 120
               +  S+      ++ ++    +  SP           +  + NA +PKKLAW KPSN
Sbjct: 60  LQSSSPPSI------LTSNEQSTFSDCSP-----------ENFESNAEKPKKLAWKKPSN 102

Query: 121 GVVE-VGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPHLPQKVS 179
           GV E V PVMGA SWPALSESTK SPKSSSADSS        S++  QVP+IP  P++ S
Sbjct: 103 GVAEAVSPVMGAVSWPALSESTKSSPKSSSADSSDG------SIANNQVPVIP--PKQTS 154

Query: 180 NANANPNSNANRTMPARQR-LKRSGGGVSNAGSGPAQ--------TRPTQPPPPPPPPPF 230
            +NA  N+ +N++MPARQR +KR G G S    G           T P  PPPPPPPPPF
Sbjct: 155 -SNAKSNATSNQSMPARQRSIKRGGSGSSTTSGGGHSHSHSQSNFTHPPPPPPPPPPPPF 213

Query: 231 PVFPMPPNSFANLVTAMPDPSPREPLYRGSN-WDARPVGGFVSQSHPMNDQRNSSRRGNY 289
           P+F MPPN + N+V AMPD SPR+P YRG+N W+ RPVGGFV+Q   +ND R+SSRRGN+
Sbjct: 214 PLFAMPPNGYGNMVPAMPDRSPRDPPYRGNNNWEPRPVGGFVTQPPAVNDHRHSSRRGNF 273

Query: 290 GQRGDGNYNNNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMRP 349
           G RGDG Y++NFGGR DQDRG+Y N RDA VQ QR  PRGFVRP PPN   F PPQP+RP
Sbjct: 274 GSRGDGTYHHNFGGRRDQDRGHYGNVRDAPVQQQRS-PRGFVRPPPPNTTTFVPPQPVRP 332

Query: 350 FPNPMGFPEFIYIPPMPVEAAALRGVTGMPPFIPPAP---VLMPVPEPSLAAMLIHQIDY 406
           F NP+GFP+ +YIP +P+E    RGV    PFI  AP   +++PVPEP L AML+HQI+Y
Sbjct: 333 FANPIGFPDVVYIPTLPLE--PFRGV----PFITHAPAPGIIVPVPEPPLPAMLVHQIEY 386

Query: 407 YFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLI 451
           YFSDANL+KD+FLKSNMDDQGWV ITLIA F RV   ++    ++
Sbjct: 387 YFSDANLIKDDFLKSNMDDQGWVSITLIAGFNRVKSMTKDVQLIL 431

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302142718|emb|CBI19921.3| unnamed protein product [Vitis vinifera]

 Score =  310 bits (794), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 191/360 (53%), Positives = 231/360 (64%), Gaps = 34/360 (9%)

Query: 100 SDADKGNAARPKKLAWNKPSNGVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVA 159
           SD    NA R KK AWNKPSN VVEVGPVMGA SWPALSEST+ SP+SSS    S KP  
Sbjct: 91  SDGCGSNAGRQKKPAWNKPSNDVVEVGPVMGAVSWPALSESTRASPRSSS---DSPKPAV 147

Query: 160 DGSVSGTQVPLIPHLPQKVSNANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPT 219
           DGS +  Q P+IPH PQK   AN NPNS+ N   P RQR  +SGGG S    G   ++P 
Sbjct: 148 DGSAASIQGPVIPHSPQKQVPANTNPNSSQNHASPFRQRSIKSGGGSSQTVHGHLPSQPP 207

Query: 220 QPPPPPPPPPFPVFPMPPNSFANLVTAMPDPSPREPLYRGSNWDARPVGGFVSQSHPMND 279
            PPPP P     +F MP N +A +   + D S REP YR + W+ RP+GGFV Q   ++D
Sbjct: 208 PPPPPYP-----LFEMPQNKYAKMAPQVLDSSTREPPYRNNTWETRPIGGFVPQPRGLSD 262

Query: 280 Q---RNSSRRGNYGQ--RGDGNYNNNFGGRHDQDRGNY------SNARDAHVQPQRGPPR 328
               RNS RRGN+G   RGDG ++NN+GGR DQDRGNY      SN RD H+QPQR PPR
Sbjct: 263 HPLPRNS-RRGNFGPHPRGDGPHHNNYGGRRDQDRGNYEWNSRSSNVRDIHMQPQRAPPR 321

Query: 329 GFVRPAPPNAA-AFAPPQPMRPFPNPMGFP----EFIYIPPMPVEAAALRGVTGMPPFIP 383
           GF+R AP +++  F  PQP+RPF NP G+P    +  Y P +P E    R V    PF+ 
Sbjct: 322 GFIRAAPQSSSPRFMTPQPIRPFMNPAGYPDMPSQMYYFPALPSEP--FRSV----PFVA 375

Query: 384 PAPVLMPVP---EPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
            AP         +P L  +L++QI+YYFSD NL+KD++L+S MDDQGWVPITLIA FPRV
Sbjct: 376 HAPPPPMFIPVPDPPLPTLLVNQIEYYFSDVNLIKDDYLRSYMDDQGWVPITLIAGFPRV 435

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437412|ref|XP_004136486.1| PREDICTED: uncharacterized protein LOC101220887 [Cucumis sativus] gi|449505790|ref|XP_004162569.1| PREDICTED: uncharacterized LOC101220887 [Cucumis sativus]

 Score =  304 bits (779), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 211/454 (46%), Positives = 271/454 (59%), Gaps = 23/454 (5%)

Query: 1   MAMTADSTSNHVTPRGSGFSGDGLSSPQLRRKNSPSQWSEVVRGEHDPASTTVNHSQSSP 60
           M    D +SNH +P G+  +GD  +S + RRKN  S W++VVRGE  P S        SP
Sbjct: 1   MGKATDFSSNHRSPSGTSLAGDNTNSSEFRRKNLQSPWAQVVRGE--PESI-------SP 51

Query: 61  SPPLTTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGNAARPKKLAWNKPSN 120
                 +S      S++ S     AP+SPP DN  ++ + DA+ GNAA  KK AWNKP+N
Sbjct: 52  VDQSQLSSSSSSLSSLAVSATETPAPASPPSDNFTSSENCDANDGNAAS-KKQAWNKPTN 110

Query: 121 GVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPL-IPHLPQKVS 179
           GVVE G VMGA SWPAL+ES + SPK +    S  K   + +V  +Q P+ +P   Q  +
Sbjct: 111 GVVEGGSVMGADSWPALAESARASPKLTV--DSPPKVTVEVAVPPSQGPINVPPQRQATN 168

Query: 180 NANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPMPPNS 239
           NA +NP            R    GGG S  G      RP  PPPPPPPPPFPVF + PNS
Sbjct: 169 NAKSNPTLKNPVVARRSSRRGGGGGGSSVGGPRGGYYRPPPPPPPPPPPPFPVFQVSPNS 228

Query: 240 FANLVTAMPDPSPREPLYRGSNWDARPVGGFVSQSHPMNDQRNSSRRGNY--GQRGDGNY 297
           + N++ A+PDPS  EPL+R  NWD R V GFV Q +   D RN   RGN+    RGD +Y
Sbjct: 229 YCNMIPAIPDPSSGEPLFRSPNWDPRAVAGFVPQLNFGTDHRNFFPRGNFPLHPRGDSHY 288

Query: 298 NNNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMRPFPNPMGFP 357
           +NN GG+  QDRG Y NARDAH Q  R   RGF+RP PP    F  PQ +RP  NPM  P
Sbjct: 289 HNNRGGKRGQDRGIYFNARDAHFQQHRPHTRGFMRPLPPFTGQF--PQGVRPHLNPMAHP 346

Query: 358 EFIYIPPMPVEAAALRGVTGMPPFIPPAPVLMPVPEPSLAAMLIHQIDYYFSDANLVKDE 417
           EF+Y+P +P+EA       G  PF+P   +  P  +P+L+A ++ QI+YYFSD NLVKD+
Sbjct: 347 EFVYVPTLPLEA-----YRGGLPFMPRPAMNYPTVDPTLSASIVKQIEYYFSDGNLVKDD 401

Query: 418 FLKSNMDDQGWVPITLIASFPRV-SFYSQISYFL 450
           +L+S MDDQGWVPI+LIA+FP V S  + I + +
Sbjct: 402 YLRSQMDDQGWVPISLIATFPMVLSLTNNIQWIV 435

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552054|ref|XP_003544386.1| PREDICTED: uncharacterized protein LOC100785504 [Glycine max]

 Score =  300 bits (769), Expect = 8e-79,   Method: Compositional matrix adjust.
 Identities = 224/454 (49%), Positives = 273/454 (60%), Gaps = 34/454 (7%)

Query: 3   MTADSTSNH---VTPRGSGFSGDGLSSPQLRRKNSPSQWSEVVRGEHDPASTTVNHSQSS 59
           +TA  +SNH    +       GDG +SP+  RKN PS W++VVRG  +P S    H    
Sbjct: 2   VTAAKSSNHHSPPSAPSPAQPGDG-NSPKFPRKNLPSPWAQVVRGG-EPESAGGIHQSPP 59

Query: 60  PSPPLTTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAG---SSDADKGNAARPKKLAWN 116
            S   +++SL       +PS  V   P S P DN    G   SSD  +GNA   KK  WN
Sbjct: 60  SSSSSSSSSL---VADQAPSSEVI--PVSSPVDNSNTVGDVDSSDGAEGNADCSKKPVWN 114

Query: 117 KPSNGVV--EVGPVMGAA-SWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPH 173
           KPSNGVV  E GPVMGAA SWP L  STK S K   A+SSS     DGS+S +Q P+   
Sbjct: 115 KPSNGVVVVETGPVMGAAESWPTLLASTKGSAKLP-AESSSKTVTDDGSLSTSQWPMTSQ 173

Query: 174 LPQKVSNANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVF 233
            PQK +   A P+S  N  +P+RQR  +  GG S             PP PPPPPPFPV+
Sbjct: 174 SPQKQATTIAKPSSAPNYNVPSRQRSMKRVGGSSTGSGPSQSNFSNPPPTPPPPPPFPVY 233

Query: 234 PMPPNSFANLVTAMPDPSPREPLYRGSNWDARP-VGGFVSQSHPMNDQRNSSRRGNYG-- 290
            +PP S+ N+V  +PD +PR+  YR +NWDARP VGGFV     MN+ R SSRRG +G  
Sbjct: 234 QLPPVSYGNMVPGVPDHAPRD-HYRNNNWDARPLVGGFVPA---MNEYRGSSRRGYFGPH 289

Query: 291 QRGDGNYNNNFGGRHD-QDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMRP 349
            RGDG+Y+N++G R D QDRGNY NARDA +   R PPRG +R  PPN AAF  PQP+ P
Sbjct: 290 PRGDGSYHNSYGSRRDHQDRGNYVNARDAFLPQPRMPPRGLLRHPPPNTAAFVGPQPIGP 349

Query: 350 FPNPMGFPEFIYIPPMPVEAAALRGVTGMPPFI---PPAPVLMPVPEPSLAAMLIHQIDY 406
           F NP+ FPEF Y  P+ VE       TGMP F    PP P       P L+ M+++QI+Y
Sbjct: 350 FANPISFPEFYYYQPVTVEQ-----FTGMPFFTHSPPPTPFFSAAESP-LSNMIVYQIEY 403

Query: 407 YFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
           YFSDANLVKD FL+S MD+QGWVP+TLIA FPRV
Sbjct: 404 YFSDANLVKDAFLRSKMDEQGWVPVTLIADFPRV 437

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224085930|ref|XP_002307743.1| predicted protein [Populus trichocarpa] gi|222857192|gb|EEE94739.1| predicted protein [Populus trichocarpa]

 Score =  284 bits (726), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 219/467 (46%), Positives = 282/467 (60%), Gaps = 71/467 (15%)

Query: 1   MAMTADSTSNHVTPRGSGFSGDGLSSPQLRRKNSPSQWSEVVRGEHDPASTTVNHSQSSP 60
           M  T DS++   +PR   F  DG+ S Q RR+ S S  SE V GE +  ++ +  S    
Sbjct: 1   MVYTVDSSN---SPR---FPRDGVRSSQ-RREKSSSPKSETVSGEAESINSMLEQS---- 49

Query: 61  SPPLTTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGNAARPKKLAWNKPS- 119
                                          ++  A  SSD+ KGNA + KK AWNKP+ 
Sbjct: 50  -------------------------------NDWAAIESSDSKKGNAGKAKKPAWNKPTS 78

Query: 120 NGVVEV-GPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPHLPQKV 178
           NGV E+  PVM A SWPALSESTKPSPK S A+ SSSK V+DGS+  +Q P+I + P+K 
Sbjct: 79  NGVAEITSPVMDATSWPALSESTKPSPKPSPAE-SSSKIVSDGSIPTSQGPVIANSPKKQ 137

Query: 179 SNANANPNSNANRTMPARQR-LKR--SGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPM 235
            N+NA   S  N TMP RQR ++R   G   S++G G +Q   T PPPPPPPPPFP+FPM
Sbjct: 138 GNSNAKSISATNHTMPVRQRPVRRGSGGSSGSSSGGGHSQNSFTHPPPPPPPPPFPIFPM 197

Query: 236 PPNSFANLVTAMPDPSPREPLYRGSNWDARPVGGFVSQSHPMNDQRNSSRRGNYGQ-RGD 294
           PPN F NLV AMPD SPRE LYRG+NW+ RP+GGFV     +++ R  SRRGN+GQ  GD
Sbjct: 198 PPNGFTNLVPAMPDQSPRETLYRGNNWEPRPIGGFVPPPPVVSEHRRPSRRGNFGQPPGD 257

Query: 295 GNYNNNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMRPFPNPM 354
           G++ NN+ GR +QDRG++ N+RD HVQ QR P RGF RP+P N+  F PPQ +RPF NPM
Sbjct: 258 GSHRNNYVGRREQDRGHHGNSRDVHVQQQRAPTRGFPRPSPQNSGTFIPPQSVRPFANPM 317

Query: 355 GFPEFIYIPPMPVEAAALRGVTGMPPFIPPAPVLMPVPEPSL--------AAMLIHQIDY 406
           G+ + ++IPP              P  + P PV+  +  P++          +L++QI+Y
Sbjct: 318 GYHDMLFIPP--------------PITLEPYPVVPHMQSPTMLMPIPQPLPLLLLNQIEY 363

Query: 407 YFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITC 453
           YFSD NL KD FLKS MDD+GWVPITLIA F RV   +    F++ C
Sbjct: 364 YFSDMNLSKDGFLKSKMDDEGWVPITLIAGFNRVRIMTNNIQFILEC 410

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356517961|ref|XP_003527653.1| PREDICTED: uncharacterized protein LOC100792549 [Glycine max]

 Score =  268 bits (685), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 216/465 (46%), Positives = 266/465 (57%), Gaps = 62/465 (13%)

Query: 1   MAMTADSTSNHVTPRGSGFSGDGLSSPQLRRKNSPSQWSEVVRGEHDPASTTVNHSQSSP 60
           +  T DS+SNH +P  +  S +        +K  PS W++VVRG                
Sbjct: 2   VTTTVDSSSNHHSPTAADTSNN------FPQKTMPSPWAQVVRG---------------- 39

Query: 61  SPPLTTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGNAARPKKLAWNKP-S 119
                  +  EP     PS + +S+  S   + P A  +SD     A +P   AW KP +
Sbjct: 40  -------ADAEPNDQSPPSSSSSSSLDSINSNGP-AVQTSDI----AVKP---AWKKPEA 84

Query: 120 NGVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPHLPQKVS 179
           NGV EVGPVMGA SWP LSESTKP+ K +S DSS      + S +  Q P+    PQK +
Sbjct: 85  NGVAEVGPVMGAHSWPDLSESTKPTAKLTS-DSSVKTAADEESTTTPQGPVTSDPPQKQA 143

Query: 180 NANANPNSN--ANRTMPARQRLKRSGGGVS--NAGSGPAQTR----PTQPPPPPPPPPFP 231
            ANA P+     N  M  RQR  +  GG +  N GSGP Q          PPPPPPPPFP
Sbjct: 144 TANAKPSPTPAMNYGMANRQRSMKQRGGANGNNVGSGPVQNNFSGTTPNLPPPPPPPPFP 203

Query: 232 VFPMPPNSFANLVTAMPDPSPREPLYRGSNWDARPV-GGFVSQSHPMNDQRNSSRRGNYG 290
           V  MPP++FA+ +   P P+PR+P YR +NWDARP  GGF+    PMN+ R+ S RGN G
Sbjct: 204 VLLMPPSTFAHGIPGAPVPTPRDP-YRNNNWDARPQHGGFMP---PMNEHRSPSHRGNAG 259

Query: 291 Q--RGDGNYNNNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMR 348
              RG+G Y+N++G R DQDR  Y+N RDAHV  QR PPRG +RP PPN A F  PQPMR
Sbjct: 260 HHPRGEGPYHNSYGNRRDQDRVGYANTRDAHVNQQRMPPRGLMRPPPPNPAPFMGPQPMR 319

Query: 349 PFPNPMGFPEFIYIPPMPVEAAALRGVTGMPPFI--PPAPVLMPVPEPSLAAMLIHQIDY 406
           P  NP GFPE+ Y P +  E        GMP F   PP  +  PV E  L   + +QIDY
Sbjct: 320 PLANPAGFPEYYYFPTLQFEPFG-----GMPFFTHAPPPAMFYPVAETPLTNTIANQIDY 374

Query: 407 YFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV-SFYSQISYFL 450
           YFSDANLVKDE+L+SNMD+QGWVPI+LIASFPRV S  S I   L
Sbjct: 375 YFSDANLVKDEYLRSNMDEQGWVPISLIASFPRVRSLTSNIKLIL 419

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357438541|ref|XP_003589546.1| La-related protein [Medicago truncatula] gi|355478594|gb|AES59797.1| La-related protein [Medicago truncatula]

 Score =  264 bits (674), Expect = 9e-68,   Method: Compositional matrix adjust.
 Identities = 210/449 (46%), Positives = 264/449 (58%), Gaps = 59/449 (13%)

Query: 27  PQLRRKNSPSQWSEVVRG------EHDPASTTVNHSQSSPSPP------LTTTSLPEPTG 74
           P   RKN PS W++VVRG      E    S T  H QS PS        LTT   P P+ 
Sbjct: 26  PNFIRKNLPSPWAQVVRGGSGWDTESQSQSPTGIH-QSLPSSSSSSSSSLTTVDQPPPSD 84

Query: 75  --------SVSPSKAVASAPS-SPPPDNPIAAGSSDADKGNAARPKKLAWNK-PSNGV-V 123
                   S SP   V S+P  +P   N     S   D GNA   KK AWNK P NGV V
Sbjct: 85  DSPKAAVVSSSPKAVVVSSPLPAPMEKNSNTIASDGGDGGNAGGSKKPAWNKQPLNGVAV 144

Query: 124 EVGPVMGAASWPALSESTKPSPKSSSADSSSSK----PVADGSVSGTQVPLIPHLPQKV- 178
           E+GPVMGA SWPALSES K  P     +SSSSK       DGS S +Q P+I H PQ+  
Sbjct: 145 EIGPVMGAESWPALSESAK-IPGKLPPESSSSKIAPPAAVDGSPSTSQGPIISHSPQRQG 203

Query: 179 SNANANPNSNANRTMPARQR-LKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPMPP 237
           S +N   +S AN  +P R R ++R  G  SN G  PAQ+  + PP PPP PP+PV+ +PP
Sbjct: 204 STSNTKSSSMANNNLPNRPRPMRRISG--SNIGPCPAQSSLSNPPTPPPLPPYPVYQLPP 261

Query: 238 N-SFANLVTAMPDPSPREPLYRGSNWDARP-VGGFVSQSHPMNDQRNSSRRGNYGQ--RG 293
             S+ N++ ++PD SPR+  +R +NWDARP VGG             SSRRG++G   RG
Sbjct: 262 AVSYPNMLPSIPDSSPRD-HHRNNNWDARPFVGG-------------SSRRGHFGSHPRG 307

Query: 294 DGNYN-NNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMRPFPN 352
           DG+Y+ N++  R + DRGNY+N RDAH    R PPRG +RP PP+ AAF  PQ + PFP 
Sbjct: 308 DGSYHQNSYSSRREHDRGNYANTRDAHAPQPRMPPRGILRPPPPSTAAFLGPQTIGPFPA 367

Query: 353 PMGFPEFIYIPPMPVEAAALRGVTGMPPF--IPPAPVLMPVPEPSLAAMLIHQIDYYFSD 410
           P+ +P+F Y P +P++        GMP F  +P      P  E SL+ ++++QIDYYFSD
Sbjct: 368 PVAYPDFYYFPTVPLDP-----FRGMPVFPHMPSPATFFPAAESSLSNVIVNQIDYYFSD 422

Query: 411 ANLVKDEFLKSNMDDQGWVPITLIASFPR 439
            NL  DEFLKSNMD++GWVPITLIA+FPR
Sbjct: 423 INLANDEFLKSNMDEEGWVPITLIANFPR 451

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143562|emb|CBI22123.3| unnamed protein product [Vitis vinifera]

 Score =  224 bits (570), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 182/480 (37%), Positives = 253/480 (52%), Gaps = 71/480 (14%)

Query: 11  HVTPRGSGFSGDGLSSPQLRRKNS----PSQWSEVVRGEHDPASTTVNHSQSSPSPPLTT 66
           H++PR   +S DG SSP+ RR  +     S W++VVRGE +  +       ++PS P+++
Sbjct: 13  HLSPR---YSPDGHSSPKSRRSAARGAVTSPWTQVVRGESESIT-------AAPSSPVSS 62

Query: 67  TSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGNAARPKKLAWNKPSNGVVEVG 126
                 +   SP+KA + +P+SP   + + A    +D GN    K+ AWNKPSNGV EVG
Sbjct: 63  QEQIVVSSDCSPTKATSDSPASPEDSSQVEAQLESSDNGNGNAGKRPAWNKPSNGVAEVG 122

Query: 127 PVMGAASWPALSESTKPSPK------SSSADSSSSKPVADGSVSGTQVPLIPHLPQKVSN 180
           PVMGA+SWPALSES + S K       S  D S S P A   V G+     P    K  N
Sbjct: 123 PVMGASSWPALSESARASAKSASDSLKSPTDGSISTPPAQVHVQGSGNASSP--SHKQVN 180

Query: 181 ANANPNSNANRTMPARQRLKRSG---GGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPMPP 237
            N  P+S  +  +P RQ+  + G   GG S+A +G          P P  P  PV  +PP
Sbjct: 181 NNPIPSSTPSHALPTRQKSMKRGDRSGGSSSANAG---------LPQPAAPQGPVMEVPP 231

Query: 238 NSFANLVTAMPDPSPREPLYRGSNWDARPVGGFVSQSHPMND---QRNSSRRGNYG--QR 292
           N          + SPR+   R  + +    GGFV QSH  ND   QR S R+GN     R
Sbjct: 232 N----------NSSPRDHTNRSIHPEGGQRGGFVPQSHSGNDYPHQRGSYRKGNSAPHSR 281

Query: 293 GDGNYNNNFGGRHDQDRGNY------SNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQP 346
           GDG++++ +GGR DQDR N+      +  R+ H+QP R   RGF+RP   ++A F  P  
Sbjct: 282 GDGSHHHGYGGRRDQDRVNHDWNPHRNFNREPHMQP-RVVARGFIRPPSHSSAQFIAPPH 340

Query: 347 MRPFPNPMGFPEF-------IYIPPMPVEAAALRGVTGMPPFIPPAPVLMPVP--EPSLA 397
           +RPF NP+ + E        +Y+P     A  LR V    PF+ P P  M  P  +  L 
Sbjct: 341 LRPFGNPILYQELASPVSQVVYVPAP--HADPLRTV----PFVAPMPHPMFFPPQDHQLH 394

Query: 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFS 457
           A L+ QIDYYFS+ NL+KD +L+ NMD+QGWVP+ LIA F +V   ++    ++   + S
Sbjct: 395 AKLVAQIDYYFSNENLIKDIYLRQNMDEQGWVPVKLIAGFKKVKLLTENIQLILEAVRTS 454

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255539032|ref|XP_002510581.1| lupus la ribonucleoprotein, putative [Ricinus communis] gi|223551282|gb|EEF52768.1| lupus la ribonucleoprotein, putative [Ricinus communis]

 Score =  209 bits (532), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 105/167 (62%), Positives = 123/167 (73%), Gaps = 9/167 (5%)

Query: 287 GNYGQRGDGNYNNNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQP 346
           GN+G RGDG+YNNNFGGR DQDRG+Y N RD   QPQR P RGFV P P N A F P Q 
Sbjct: 187 GNFGPRGDGSYNNNFGGRRDQDRGHYGNGRDVPAQPQRSP-RGFVSPPPQNTAPFVPSQT 245

Query: 347 MRPFPNPMGFPEFIYIPPMPVEAAALRGVTGMPPFI--PPAPVLMPVPEPSLAAMLIHQI 404
           +RPF NPMGFP+ +YIP +P+E    RGV    PFI  PP+PV+MPV EP L  +L+ QI
Sbjct: 246 VRPFANPMGFPDLVYIPALPLEP--YRGV----PFIAHPPSPVMMPVSEPPLPDILVRQI 299

Query: 405 DYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLI 451
           +YYFSD NLVKD+FLKSNMDDQGWVPITLIASF RV   +   + ++
Sbjct: 300 EYYFSDGNLVKDDFLKSNMDDQGWVPITLIASFNRVRKMTNDIHLVL 346

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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	458
TAIR|locus:2156912	453	LARP1b "AT5G66100" [Arabidopsi	0.091	0.092	0.476	1e-15
TAIR|locus:2125334	523	LARP1c "La related protein 1c"	0.622	0.544	0.236	2.1e-15
POMBASE|SPAC1527.03	475	SPAC1527.03 "RNA-binding prote	0.122	0.117	0.456	9.4e-08
UNIPROTKB|E9PFL9	134	SSB "Lupus La protein" [Homo s	0.102	0.350	0.458	2.6e-07
UNIPROTKB|E7ERC4	184	SSB "Lupus La protein" [Homo s	0.102	0.255	0.458	3.9e-06
UNIPROTKB|Q5ZKS1	137	SSB "Uncharacterized protein"	0.109	0.364	0.411	1.5e-05
UNIPROTKB|E9PFH8	361	SSB "Lupus La protein" [Homo s	0.102	0.130	0.458	5e-05
UNIPROTKB|F1S1V1	402	SSB "Uncharacterized protein"	0.102	0.116	0.458	6.1e-05
UNIPROTKB|P10881	404	SSB "Lupus La protein homolog"	0.102	0.116	0.458	6.1e-05
UNIPROTKB|E2RH09	406	SSB "Uncharacterized protein"	0.102	0.115	0.458	6.2e-05

TAIR|locus:2156912 LARP1b "AT5G66100" [Arabidopsis thaliana (taxid:3702)]

 Score = 123 (48.4 bits), Expect = 1.0e-15, Sum P(3) = 1.0e-15
 Identities = 20/42 (47%), Positives = 33/42 (78%)

Query:   400 LIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVS 441
             ++ Q++YYFS  NL +DE L+  M+D+GWVP+ +IA+F R++
Sbjct:   339 ILTQVEYYFSADNLSRDEHLRDQMNDEGWVPVRVIAAFRRLA 380

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0010150 "leaf senescence" evidence=IMP

TAIR|locus:2125334 LARP1c "La related protein 1c" [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 2.1e-15, Sum P(2) = 2.1e-15
 Identities = 73/309 (23%), Positives = 105/309 (33%)

Query:     2 AMTADSTSNHVTPRG-SGFSGDGLSS----PQLRRKNSPSQWSEVVRGEHDPASTTVNHS 56
             A + +  S+ ++PR  SG  G   +S    P+   +   S W+++VRGE +P +     +
Sbjct:     4 ATSNNPASSSMSPRRISGNHGSPTASVAQSPRRPSRQVSSPWTQIVRGESEPIAAAAAVA 63

Query:    57 QXXXXXXXXXXXXXXXXGXXXXXXXXXXXXXXXXXXXXXXXGSSDADKGNAARPKKLAWN 116
                                                      G  D    NA   KK  W 
Sbjct:    64 GPSSPQSRAPIEPIASVSVAAPTAAVLTVEAAAGDEKSEASGGQD----NAG--KKPVWK 117

Query:   117 KPSNGVVEVGPVMGAASWPALXXXXXX-XXXXXXXXXXXXXXVADGSVSGTQVPLIPHLP 175
             +PSNG  EVGPVMGA+SWPAL                     V   S + + VP+   + 
Sbjct:   118 RPSNGASEVGPVMGASSWPALSETTKAPSNKSSSDSLKSLGDVPSSSSASSSVPVTQGIA 177

Query:   176 QKVXXXXXXXXXXXXRTMP--ARQRLKRSGGGVSNAGSGPAQTRPTQXXXXXXXXXXXX- 232
                               P  +RQR  +   G S + +G       Q             
Sbjct:   178 NASVPAPKQAGRANPNPTPNHSRQRSFKQRNGASGSANGTVSQPSAQGSFTELPSHNPSP 237

Query:   233 -XXXXXNSFANLVTA-MPDPSPREPLYRGSNWDARPV-GGFVSQSHPMND---QRN-SSR 285
                   N FA+       +PS R+  YR  N +     GG  +Q H   +   QR+ + R
Sbjct:   238 RGQNQKNGFASQNHGGTENPSQRDS-YRNQNGNHHQSHGGRRNQEHGNQNWTFQRSFNGR 296

Query:   286 RGN-YGQRG 293
              GN   QRG
Sbjct:   297 EGNAQSQRG 305

GO:0009507 "chloroplast" evidence=ISM

GO:0048523 "negative regulation of cellular process" evidence=RCA

GO:0005737 "cytoplasm" evidence=IDA

GO:0010150 "leaf senescence" evidence=IMP

POMBASE|SPAC1527.03 SPAC1527.03 "RNA-binding protein (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 135 (52.6 bits), Expect = 9.4e-08, Sum P(2) = 9.4e-08
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query:   398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV-SFYSQISYFLITC 453
             A L  Q++YYFS  NL KD FL+ +MDD+G+VP+  +ASF R+ SF + ++     C
Sbjct:   327 AFLTSQLEYYFSIENLCKDMFLRKHMDDEGYVPLAFLASFNRIKSFSTDLNLLHAAC 383

GO:0002181 "cytoplasmic translation" evidence=NAS

GO:0003723 "RNA binding" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0005844 "polysome" evidence=ISO

GO:0006412 "translation" evidence=ISO

UNIPROTKB|E9PFL9 SSB "Lupus La protein" [Homo sapiens (taxid:9606)]

 Score = 124 (48.7 bits), Expect = 2.6e-07, P = 2.6e-07
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query:   395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
             +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R++
Sbjct:    12 ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLN 59

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|E7ERC4 SSB "Lupus La protein" [Homo sapiens (taxid:9606)]

 Score = 124 (48.7 bits), Expect = 3.9e-06, P = 3.9e-06
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query:   395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
             +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R++
Sbjct:    12 ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLN 59

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q5ZKS1 SSB "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 108 (43.1 bits), Expect = 1.5e-05, P = 1.5e-05
 Identities = 21/51 (41%), Positives = 33/51 (64%)

Query:   396 LAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVSFYSQ 445
             L + +  QI+YYF + NL +D+FLK  +  D GWVP+ ++  F R+S  S+
Sbjct:    13 LESKICQQIEYYFGNHNLPRDKFLKEQIKLDDGWVPLEVMIKFNRLSRLSK 63

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E9PFH8 SSB "Lupus La protein" [Homo sapiens (taxid:9606)]

 Score = 124 (48.7 bits), Expect = 5.0e-05, P = 5.0e-05
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query:   395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
             +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R++
Sbjct:    12 ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLN 59

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|F1S1V1 SSB "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 124 (48.7 bits), Expect = 6.1e-05, P = 6.1e-05
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query:   395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
             +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R++
Sbjct:    12 ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLN 59

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|P10881 SSB "Lupus La protein homolog" [Bos taurus (taxid:9913)]

 Score = 124 (48.7 bits), Expect = 6.1e-05, P = 6.1e-05
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query:   395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
             +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R++
Sbjct:    12 ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLN 59

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RH09 SSB "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 124 (48.7 bits), Expect = 6.2e-05, P = 6.2e-05
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query:   395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
             +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R++
Sbjct:    12 ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLN 59

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" 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

Your Input: GSVIVG00014357001 SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (548 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	458
cd07323	75	cd07323, LAM, LA motif RNA-binding domain	6e-22
smart00715	80	smart00715, LA, Domain in the RNA-binding Lupus La	1e-18
pfam05383	59	pfam05383, La, La domain	2e-18
cd08034	73	cd08034, LARP_1_2, La RNA-binding domain proteins	2e-16
cd08038	73	cd08038, LARP_2, La RNA-binding domain of La-relat	8e-13
cd08033	77	cd08033, LARP_6, La RNA-binding domain of La-relat	2e-12
cd08028	82	cd08028, LARP_3, La RNA-binding domain of La-relat	4e-12
cd08037	73	cd08037, LARP_1, La RNA-binding domain of La-relat	6e-12
cd08031	75	cd08031, LARP_4_5_like, La RNA-binding domain of p	5e-11
cd08030	90	cd08030, LA_like_plant, La-motif domain of plant p	6e-08
cd08029	76	cd08029, LA_like_fungal, La-motif domain of fungal	7e-08
cd08032	82	cd08032, LARP_7, La RNA-binding domain of La-relat	1e-06
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	4e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-05
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	2e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	3e-04
COG5193	438	COG5193, LHP1, La protein, small RNA-binding pol I	4e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	7e-04
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	7e-04
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	0.001
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.001
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.002
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.002
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	0.002

>gnl|CDD|153396 cd07323, LAM, LA motif RNA-binding domain

 Score = 89.1 bits (222), Expect = 6e-22
 Identities = 26/43 (60%), Positives = 33/43 (76%)

Query: 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
             +  Q++YYFSD NL KD FL+S MDD GWVP++L+ASF RV
Sbjct: 2   EKIKKQVEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRV 44

This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Length = 75

>gnl|CDD|128955 smart00715, LA, Domain in the RNA-binding Lupus La protein; unknown function

 Score = 79.6 bits (197), Expect = 1e-18
 Identities = 24/46 (52%), Positives = 33/46 (71%), Gaps = 1/46 (2%)

Query: 396 LAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRV 440
           L   +  Q++YYFSD NL +D+FL+  MD + G+VPI+ IASF RV
Sbjct: 3   LKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRV 48

Length = 80

>gnl|CDD|203243 pfam05383, La, La domain

 Score = 78.4 bits (194), Expect = 2e-18
 Identities = 23/42 (54%), Positives = 32/42 (76%), Gaps = 1/42 (2%)

Query: 400 LIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRV 440
           +  Q++YYFSD NL +D+FL+  MD D G+VPI+ IASF R+
Sbjct: 1   IKKQVEYYFSDENLPRDKFLRKQMDKDPGYVPISTIASFKRI 42

This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain. Length = 59

>gnl|CDD|153403 cd08034, LARP_1_2, La RNA-binding domain proteins similar to La-related proteins 1 and 2

 Score = 73.2 bits (180), Expect = 2e-16
 Identities = 24/38 (63%), Positives = 29/38 (76%)

Query: 403 QIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
           QI+YYFS  NL KD FL+  MD +G++PI LIASF RV
Sbjct: 7   QIEYYFSVDNLEKDFFLRRKMDPEGYLPIALIASFHRV 44

This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Length = 73

>gnl|CDD|153407 cd08038, LARP_2, La RNA-binding domain of La-related protein 2

 Score = 63.0 bits (153), Expect = 8e-13
 Identities = 23/38 (60%), Positives = 29/38 (76%)

Query: 403 QIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
           QI+YYFS  NL +D FL+  MD QG++PI+LIA F RV
Sbjct: 7   QIEYYFSTENLERDFFLRRKMDLQGFLPISLIAGFYRV 44

This domain is found in vertebrate La-related protein 2 (LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Length = 73

>gnl|CDD|153402 cd08033, LARP_6, La RNA-binding domain of La-related protein 6

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 22/43 (51%), Positives = 33/43 (76%), Gaps = 2/43 (4%)

Query: 400 LIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRV 440
           ++ Q++YYFSD NL+KD FL  ++  + +G+VPI LIASF +V
Sbjct: 4   IVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKV 46

This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Length = 77

>gnl|CDD|153397 cd08028, LARP_3, La RNA-binding domain of La-related protein 3

 Score = 61.5 bits (150), Expect = 4e-12
 Identities = 21/47 (44%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 396 LAAMLIHQIDYYFSDANLVKDEFLKSNM-DDQGWVPITLIASFPRVS 441
           L   +I QI+YYF D NL +D+FLK  + +D GWVP+ ++  F R+ 
Sbjct: 4   LEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLK 50

This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B). Length = 82

>gnl|CDD|153406 cd08037, LARP_1, La RNA-binding domain of La-related protein 1

 Score = 60.7 bits (147), Expect = 6e-12
 Identities = 23/38 (60%), Positives = 30/38 (78%)

Query: 403 QIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
           QI+YYFS  NL +D FL+  MD+ G++P+TLIASF RV
Sbjct: 7   QIEYYFSVDNLERDFFLRRKMDEDGFLPVTLIASFHRV 44

This domain is found in vertebrate La-related protein 1 (LARP1). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Length = 73

>gnl|CDD|153400 cd08031, LARP_4_5_like, La RNA-binding domain of proteins similar to La-related proteins 4 and 5

 Score = 58.2 bits (141), Expect = 5e-11
 Identities = 19/42 (45%), Positives = 27/42 (64%)

Query: 399 MLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
           +L  Q++YYFS  NL  D +L S MD   +VPI  IA+F ++
Sbjct: 3   LLKRQLEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKI 44

This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Length = 75

>gnl|CDD|153399 cd08030, LA_like_plant, La-motif domain of plant proteins similar to the La autoantigen

 Score = 49.7 bits (119), Expect = 6e-08
 Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 396 LAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRV 440
               ++ Q+++YFSD+NL +D+FL   +  D  G V + LI SF R+
Sbjct: 1   TKEKVLRQVEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRM 47

This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Length = 90

>gnl|CDD|153398 cd08029, LA_like_fungal, La-motif domain of fungal proteins similar to the La autoantigen

 Score = 49.2 bits (118), Expect = 7e-08
 Identities = 20/39 (51%), Positives = 27/39 (69%), Gaps = 2/39 (5%)

Query: 403 QIDYYFSDANLVKDEFL--KSNMDDQGWVPITLIASFPR 439
           Q+++YFSD+NL  D+FL   +   + GWVPI  IASF R
Sbjct: 7   QVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKR 45

This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Length = 76

>gnl|CDD|153401 cd08032, LARP_7, La RNA-binding domain of La-related protein 7

 Score = 46.1 bits (109), Expect = 1e-06
 Identities = 15/40 (37%), Positives = 27/40 (67%), Gaps = 2/40 (5%)

Query: 403 QIDYYFSDANLVKDEFLKSNMDDQ--GWVPITLIASFPRV 440
           Q+D++F D NL KD FL+  ++    G++ I+L+ SF ++
Sbjct: 12  QVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKM 51

LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation. Length = 82

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 49.2 bits (117), Expect = 4e-06
 Identities = 44/223 (19%), Positives = 68/223 (30%), Gaps = 6/223 (2%)

Query: 47   DPASTTVNHSQSSPSPPLTTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGN 106
             PA   V    ++P  P      P   G  +P+   A+  + PP      A +S ++   
Sbjct: 2738 APAPPAVPAGPATPGGPARPARPPTTAGPPAPA-PPAAPAAGPPRRLTRPAVASLSESRE 2796

Query: 107  AARPKKLAWNKPSNGVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGT 166
            +  P       P   V+     +  A+ PA       S + ++       P     + G+
Sbjct: 2797 SL-PSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGS 2855

Query: 167  QVPLIPHLPQKVSNANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPTQPPPPPP 226
              P      ++   + +     A    P  +RL R    VS +    A        PP P
Sbjct: 2856 VAPGGDV--RRRPPSRSPAAKPAAPARPPVRRLARPA--VSRSTESFALPPDQPERPPQP 2911

Query: 227  PPPFPVFPMPPNSFANLVTAMPDPSPREPLYRGSNWDARPVGG 269
              P P  P P           P P PR         D    G 
Sbjct: 2912 QAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGE 2954

Length = 3151

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 46.9 bits (112), Expect = 2e-05
 Identities = 29/203 (14%), Positives = 48/203 (23%), Gaps = 14/203 (6%)

Query: 56  SQSSPSPPLTTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGNAARPKKLAW 115
              +P+          P    +P+   A AP+        A+ +            K   
Sbjct: 599 GPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVA 658

Query: 116 NKPSNGVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPHLP 175
                      P          +++   +P +     + + P A    +  Q    P   
Sbjct: 659 ----------VPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAAT 708

Query: 176 QKVSNANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPM 235
                A+            A      +   V           P   P  PPPPP P    
Sbjct: 709 PPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAA 768

Query: 236 PPNSFANLVTAMPDPSPREPLYR 258
            P +          PS  E +  
Sbjct: 769 APAA----APPPSPPSEEEEMAE 787

Length = 824

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 39/230 (16%), Positives = 68/230 (29%), Gaps = 22/230 (9%)

Query: 48  PASTTVNHSQSSPSPPLTTTSLPEPTGSVSPSKAVASAP-SSPPPDNPIAAGSSDADKGN 106
            A+   +   +  +      +   P  + + +   A AP ++P P      G   AD   
Sbjct: 388 AAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDA 447

Query: 107 AARPKKLAWNKPSNGVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGT 166
               K  A     +   E      A S  A + ++   P ++   +  +   +  + +  
Sbjct: 448 PVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAV 507

Query: 167 QVPLIPHLPQKVSN--ANANPNSNANRTMPARQRLKRSGGGVS-------NAG------- 210
                P    +     A A P   A    PA        GG +       NAG       
Sbjct: 508 PDARAPAAASREDAPAAAAPPAPEARPPTPAAAAPAARAGGAAAALDVLRNAGMRVSSDR 567

Query: 211 ----SGPAQTRPTQPPPPPPPPPFPVFPMP-PNSFANLVTAMPDPSPREP 255
               +  A+        P P  P     +P P + A    A P+ + R  
Sbjct: 568 GARAAAAAKPAAAPAAAPKPAAPRVAVQVPTPRARAATGDAPPNGAARAE 617

Length = 830

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 43.4 bits (102), Expect = 3e-04
 Identities = 35/211 (16%), Positives = 61/211 (28%), Gaps = 15/211 (7%)

Query: 60   PSPPLTTTSLPEPTGSVSPSKAVASAPSSP-PPDNPIAAGSSDADKGNAARPKKLAWNKP 118
            P+P    ++ P P G  +  +A  + P++P PP  P    +       A  P       P
Sbjct: 2710 PAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAP 2769

Query: 119  SNGVVEVGPVMGAASWPALS------ESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIP 172
            +             + PA++      ES       +   ++   P A    + +    +P
Sbjct: 2770 APPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLP 2829

Query: 173  HLPQKVSNANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPTQPPPPP------- 225
                    A   P      ++P    +   G       S     +P  P  PP       
Sbjct: 2830 PPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARP 2889

Query: 226  -PPPPFPVFPMPPNSFANLVTAMPDPSPREP 255
                    F +PP+           P P+  
Sbjct: 2890 AVSRSTESFALPPDQPERPPQPQAPPPPQPQ 2920

Length = 3151

>gnl|CDD|227520 COG5193, LHP1, La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]

 Score = 42.3 bits (99), Expect = 4e-04
 Identities = 37/157 (23%), Positives = 51/157 (32%), Gaps = 23/157 (14%)

Query: 296 NYNNNFGGRHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMR-PFPNP- 353
            Y N FG     +        D  +Q             PP+  A       R  + N  
Sbjct: 177 VYQNGFGKEDVNNASRPEQQEDLEIQ------------FPPHYHAPPSQIRNRRDWLNKN 224

Query: 354 ---MGFPEFIYIPPMPVEAAALRGVTGMPPF--IPPAPVLMPVPEPSLAAMLI-HQIDYY 407
                F EF Y            G      +   P       V    L+ M    QI+YY
Sbjct: 225 FRGSVFVEFKYFR---EAQRFNNGFYRNKKYPNDPETVYYYSVEPILLSIMAKKEQIEYY 281

Query: 408 FSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYS 444
           FS+ NL  DEFL+      G++P++ I  F R   + 
Sbjct: 282 FSEENLKSDEFLRKKFKKAGFIPLSFIGKFYRNLSFG 318

Length = 438

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 41.8 bits (98), Expect = 7e-04
 Identities = 77/376 (20%), Positives = 100/376 (26%), Gaps = 52/376 (13%)

Query: 63   PLTTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGNAARPKKLAWNK----- 117
            P    + P+P G   P      APS   P     A   D   G    P+ L W +     
Sbjct: 2489 PFAAGAAPDPGGGGPPDPDAPPAPSRLAP-----AILPDEPVGEPVHPRMLTWIRGLEEL 2543

Query: 118  PSNGVVEVGPVMGAASWPALSESTKPSPKSS---------------SADSSSSKPVADGS 162
             S+   +  P +  A+ PA  + + P P+ +                A   S++P A   
Sbjct: 2544 ASDDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVD 2603

Query: 163  VSGT-------------QVPLIPHLPQKVSNANANPNSNANRT-MPARQRLKRSGGGVSN 208
              G                   P  P     AN            P R R   + G VS 
Sbjct: 2604 DRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSR 2663

Query: 209  AGSGPAQTRPTQPPPPPPPPPFPVFPMPPNSFANLVTAMPDPSPREPLYRGSNW----DA 264
                    R  Q   PP  P          S  +L  A P P P  P             
Sbjct: 2664 PRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSL--ADPPPPPPTPEPAPHALVSATPL 2721

Query: 265  RPVGGFVSQSHPMNDQRNSSRRGNYGQRGDGNYNNNFGGRHDQDRGNYSNARDAHVQPQR 324
             P      Q+ P      +      G    G        R     G  + A  A   P  
Sbjct: 2722 PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARP--ARPPTTAGPPAPAPPA--APAA 2777

Query: 325  GPPRGFVRPAPPNAAAFAPPQPMRPFPNPMGFPEFIYIPPMPVEAAALRGVTGMPPFIPP 384
            GPPR   RPA  + +      P    P     P    + P      A      +PP    
Sbjct: 2778 GPPRRLTRPAVASLSESRESLPSPWDPAD---PPAAVLAPAAALPPAASPAGPLPPPTSA 2834

Query: 385  APVLMPVPEPSLAAML 400
             P   P P       L
Sbjct: 2835 QPTAPPPPPGPPPPSL 2850

Length = 3151

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.8 bits (98), Expect = 7e-04
 Identities = 30/181 (16%), Positives = 50/181 (27%), Gaps = 9/181 (4%)

Query: 62  PPLTTTSLPEPTGSVSPSKAV----ASAPSSPPPDNPIAAGSSDADKGNAARPKKLAWNK 117
           P +T    P        + AV    A A ++       A  +     G A  PK  A   
Sbjct: 360 PAVTGGGAPGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAA--- 416

Query: 118 PSNGVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSG--TQVPLIPHLP 175
            +       P    A           +   +   + ++   +  S        P      
Sbjct: 417 AAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGS 476

Query: 176 QKVSNANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPM 235
                ++A P++       A      +   V +A +  A +R   P    PP P    P 
Sbjct: 477 ASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPT 536

Query: 236 P 236
           P
Sbjct: 537 P 537

Length = 830

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 26/148 (17%), Positives = 39/148 (26%), Gaps = 13/148 (8%)

Query: 117 KPSNGVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPHLPQ 176
           KP+       P          + +   +P + +A + +       + S    P     P 
Sbjct: 365 KPAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPA 424

Query: 177 KVSNANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPMP 236
            V+   A   + A    PA   L  +      A    A      P P          P P
Sbjct: 425 PVAAPAAAAPAAAPAAAPAAVALAPAPPAQ-AAPETVAIPVRVAPEPAVASAA----PAP 479

Query: 237 PNSFANLVTAMPDPSPREPLYRGSNWDA 264
                    A P  +   P   G  W A
Sbjct: 480 A--------AAPAAARLTPTEEGDVWHA 499

Length = 618

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 40/226 (17%), Positives = 69/226 (30%), Gaps = 18/226 (7%)

Query: 47  DPASTTVNHSQSSPSPPLTTTSLPEPTGSV--SPSKAVASAPSSPPPDNPIAAGSSDADK 104
              +     S  +  PP T  +   P      SP  A AS+P+  P  +      + +  
Sbjct: 179 PEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSD 238

Query: 105 GNAARPKKLAWN------KPSNGVVEVGPVMGAASWPALSESTKPSPKSSSADSSSSKPV 158
            +++      W        P    + +   +  AS      S      SSS+    S   
Sbjct: 239 SSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSP 298

Query: 159 ADGSVSGTQVPLIPHLPQKVSNANANPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRP 218
           +  S         P  P+  S+++++  S+++ T         S      A   P  +  
Sbjct: 299 SPSSPGS---GPAPSSPRASSSSSSSRESSSSST-------SSSSESSRGAAVSPGPSPS 348

Query: 219 TQPPPPPPPPPFPVFPMPPNSFANLVTAMPDPSPREPLYRGSNWDA 264
             P P  PPPP            +   + P  S   P  R +    
Sbjct: 349 RSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAV 394

Length = 1352

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 68/385 (17%), Positives = 94/385 (24%), Gaps = 28/385 (7%)

Query: 30   RRKNSPSQWSEVVRGEHDPASTTVNHSQSSPSPPLTT-----TSLPEPTGSVSPSKAVAS 84
            RR ++P Q S   R   D        +  SP PP T         P P  +        +
Sbjct: 2587 RRPDAPPQ-SARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPT 2645

Query: 85   APSSPPPDNPIAAGSSDADKGNAARPKKLAWNKPSNGVVE------VGPVMGAASWPALS 138
             P    P +  A G     +      +    + P            VG +   A  P   
Sbjct: 2646 VPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPP 2705

Query: 139  ESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPHLPQKVSNANANPNSNANRTMPARQR 198
             + +P+P +  + +      A    +   +P  P  P  V    A P   A    P    
Sbjct: 2706 PTPEPAPHALVSATPLPPGPAAARQASPALPAAP-APPAVPAGPATPGGPARPARPPTT- 2763

Query: 199  LKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPMPPNSFANLVTAMPDPSPREPLYR 258
                          P       PP     P          S  +       P+       
Sbjct: 2764 -------AGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAA 2816

Query: 259  GSNWDARPVGGFVSQSHPMNDQRNSSRRGNYGQRGDGNYNNNFGGRHDQDRGNYSNARDA 318
                 A P G     +                        +   G   + R    +    
Sbjct: 2817 ALPPAASPAGPLPPPTSAQ--PTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAK 2874

Query: 319  HVQPQRGPPRGFVRPAPPNAA---AFAPPQPMRPFPNPMGFP--EFIYIPPMPVEAAALR 373
               P R P R   RPA   +    A  P QP RP       P       PP P       
Sbjct: 2875 PAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPP 2934

Query: 374  GVTGMPPFIPPAPVLMPVPEPSLAA 398
                  P + P        EPS A 
Sbjct: 2935 PPPRPQPPLAPTTDPAGAGEPSGAV 2959

Length = 3151

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 40.3 bits (94), Expect = 0.002
 Identities = 70/393 (17%), Positives = 105/393 (26%), Gaps = 30/393 (7%)

Query: 5    ADSTSNHVTPRGSGFSGDGLSSPQLRRKNSPSQWSEVVRGEHDPASTTVNHSQSSPSPPL 64
              S S                  + R   +P + S   R      +   +     P    
Sbjct: 2628 PPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRR- 2686

Query: 65   TTTSLPEPTGSVSPSKAVASAPSSPPPDNPIAAGSSDADKGNAARPKKLAWNKPSNGVVE 124
               +     GS++        P +P P       ++    G AA  +      P+     
Sbjct: 2687 ---AARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQA----SPALPAAP 2739

Query: 125  VGPVMGAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPHLPQKVS-NANA 183
              P + A        +    P +++   + + P A  +    ++          S  +  
Sbjct: 2740 APPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLP 2799

Query: 184  NPNSNANRTMPARQRLKRSGGGVSNAGSGPAQTRPTQPPPPPPPPPFPVFPMPPNSFANL 243
            +P   A+                S AG  P  T      PPPPP P P    P       
Sbjct: 2800 SPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPP----PSLPLGGS 2855

Query: 244  VTAMPDPSPREPLYRGSNWDARPVGGFVSQSHPMNDQRNSSRRGNYGQRGDGNYNNNFGG 303
            V    D   R P          P     + + P              +        +F  
Sbjct: 2856 VAPGGDVRRRPP-------SRSPAAKPAAPARP--------PVRRLARPAVSRSTESFAL 2900

Query: 304  RHDQDRGNYSNARDAHVQPQRGPPRGFVRPAPPNAAAFAPPQPMRPFPNPMGFPEFIYIP 363
              DQ             QPQ  PP    +P PP      P  P+ P  +P G  E     
Sbjct: 2901 PPDQPERPPQPQAPPPPQPQPQPPPP-PQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAV 2959

Query: 364  PMPVEAAALRGVTGMPPFIPPAPV-LMPVPEPS 395
            P P   A + G   +P F  P P      P  S
Sbjct: 2960 PQPWLGALVPGRVAVPRFRVPQPAPSREAPASS 2992

Length = 3151

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 29/132 (21%), Positives = 41/132 (31%), Gaps = 5/132 (3%)

Query: 130 GAASWPALSESTKPSPKSSSADSSSSKPVADGSVSGTQVPLIPHLPQKVSNANANPNSNA 189
           GA    A +        +++A ++++   A    +    P      + V+ A A  +   
Sbjct: 371 GAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAP 430

Query: 190 NRTMPARQRLKRSGGGVSNAGSGPA-----QTRPTQPPPPPPPPPFPVFPMPPNSFANLV 244
                ARQ   R  GG       PA       RP    P P        P      A   
Sbjct: 431 EALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPA 490

Query: 245 TAMPDPSPREPL 256
            A  DP P E L
Sbjct: 491 PADDDPPPWEEL 502

Length = 700

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	458
cd08036	75	LARP_5 La RNA-binding domain of La-related protein	99.94
cd08035	75	LARP_4 La RNA-binding domain of La-related protein	99.93
cd08038	73	LARP_2 La RNA-binding domain of La-related protein	99.93
cd08037	73	LARP_1 La RNA-binding domain of La-related protein	99.93
cd08034	73	LARP_1_2 La RNA-binding domain proteins similar to	99.92
cd08032	82	LARP_7 La RNA-binding domain of La-related protein	99.92
cd08031	75	LARP_4_5_like La RNA-binding domain of proteins si	99.92
cd08028	82	LARP_3 La RNA-binding domain of La-related protein	99.91
cd08033	77	LARP_6 La RNA-binding domain of La-related protein	99.91
smart00715	80	LA Domain in the RNA-binding Lupus La protein; unk	99.91
PF05383	61	La: La domain; InterPro: IPR006630 Human Ro ribonu	99.9
cd07323	75	LAM LA motif RNA-binding domain. This domain is fo	99.9
cd08029	76	LA_like_fungal La-motif domain of fungal proteins	99.89
cd08030	90	LA_like_plant La-motif domain of plant proteins si	99.88
KOG1855	484	consensus Predicted RNA-binding protein [General f	99.73
KOG2590	448	consensus RNA-binding protein LARP/SRO9 and relate	99.72
KOG2591	684	consensus c-Mpl binding protein, contains La domai	99.62
KOG4213	205	consensus RNA-binding protein La [RNA processing a	99.54
COG5193	438	LHP1 La protein, small RNA-binding pol III transcr	99.18
COG5193	438	LHP1 La protein, small RNA-binding pol III transcr	98.44
KOG2590	448	consensus RNA-binding protein LARP/SRO9 and relate	90.28
KOG2278	207	consensus RNA:NAD 2'-phosphotransferase TPT1 [Tran	84.51

>cd08036 LARP_5 La RNA-binding domain of La-related protein 5

Probab=99.94  E-value=1.7e-27  Score=195.02  Aligned_cols=62  Identities=23%  Similarity=0.371  Sum_probs=60.0

Q ss_pred             HHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       397 ~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      ++.|++||||||||+||++|.||+++||+||||||++||+|||||+||+|+++|++|||+|+
T Consensus         1 ~e~i~kQvEyYFS~~NL~~D~fLr~~md~~g~Vpi~~ia~F~rik~Lt~D~~lI~~aL~~S~   62 (75)
T cd08036           1 RELLKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLP   62 (75)
T ss_pred             ChhhhcceeeeechhhccccHHHHHHhccCCCEehHHHhccHHHHHhcCCHHHHHHHHhhCC
Confidence            36899999999999999999999999999999999999999999999999999999999985

This domain is found in vertebrate La-related protein 5 (LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

>cd08035 LARP_4 La RNA-binding domain of La-related protein 4

Probab=99.93  E-value=3.2e-27  Score=193.51  Aligned_cols=62  Identities=27%  Similarity=0.387  Sum_probs=60.1

Q ss_pred             HHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       397 ~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      +++|++||||||||+||++|.||+++|+.||||||++|++|||||+||+|+++|++||+.|+
T Consensus         1 ~e~i~~QvEyYFSd~NL~~D~fL~~~md~~G~Vpi~~iasF~rik~lt~d~~~I~~AL~~S~   62 (75)
T cd08035           1 RECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSP   62 (75)
T ss_pred             ChHHHhhHHhhcCHhhcccCHHHHHhhCcCCCEehHHHhccHHHHHhcCCHHHHHHHHHcCC
Confidence            37899999999999999999999999999999999999999999999999999999999985

This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

>cd08038 LARP_2 La RNA-binding domain of La-related protein 2

Probab=99.93  E-value=1.4e-26  Score=188.95  Aligned_cols=61  Identities=39%  Similarity=0.608  Sum_probs=59.8

Q ss_pred             HHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       398 ~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      ++|++||||||||+||++|.||+++|+.||||||++|++|||||+||.|+++|++||+.|+
T Consensus         2 e~I~~QvEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~ia~F~rmk~lt~d~~~I~~Al~~S~   62 (73)
T cd08038           2 EYIKRQIEYYFSTENLERDFFLRRKMDLQGFLPISLIAGFYRVQALTTNVDLILEALKDST   62 (73)
T ss_pred             hHHHhhHHhhcchhhhccCHHHHHHhCCCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCC
Confidence            6899999999999999999999999999999999999999999999999999999999985

This domain is found in vertebrate La-related protein 2 (LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

>cd08037 LARP_1 La RNA-binding domain of La-related protein 1

Probab=99.93  E-value=1.5e-26  Score=188.68  Aligned_cols=61  Identities=41%  Similarity=0.635  Sum_probs=59.7

Q ss_pred             HHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       398 ~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      ++|++||||||||+||++|.||+++|+.||||||++|++|||||+||.|+++|++||+.|+
T Consensus         2 ~~I~~QvEyYFSd~NL~~D~fLr~~md~dG~Vpi~~ia~F~rmk~Lt~d~~~I~~Al~~S~   62 (73)
T cd08037           2 DYIKRQIEYYFSVDNLERDFFLRRKMDEDGFLPVTLIASFHRVQALTTDISLIIKALKDSK   62 (73)
T ss_pred             hHHHHHHHHhccHhhhccCHHHHHHhccCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCC
Confidence            6899999999999999999999999999999999999999999999999999999999985

This domain is found in vertebrate La-related protein 1 (LARP1). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

>cd08034 LARP_1_2 La RNA-binding domain proteins similar to La-related proteins 1 and 2

Probab=99.92  E-value=4.7e-26  Score=185.62  Aligned_cols=62  Identities=40%  Similarity=0.614  Sum_probs=60.1

Q ss_pred             HHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       397 ~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      +++|++||||||||+||++|.||+++|+.||||||++|++|||||+||.|+++|++||+.|+
T Consensus         1 ~~~i~~QvEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~   62 (73)
T cd08034           1 KEYIKKQIEYYFSVDNLEKDFFLRRKMDPEGYLPIALIASFHRVQALTTDVNLILEALKDST   62 (73)
T ss_pred             ChHHHhhHHhhcCHhhhccCHHHHHHcCCCCCEeHHHHhccHHHHHHcCCHHHHHHHHHcCC
Confidence            36899999999999999999999999999999999999999999999999999999999985

This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

>cd08032 LARP_7 La RNA-binding domain of La-related protein 7

Probab=99.92  E-value=9.5e-26  Score=187.46  Aligned_cols=65  Identities=28%  Similarity=0.526  Sum_probs=62.6

Q ss_pred             HHHHHHHHhhhhhhcCcCCcCcchHhHhhcC--CCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMD--DQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       394 ~~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md--~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      .+|+++|++||||||||+||++|.||+++|+  .||||||++|++|||||+||.|+++|++||+.|+
T Consensus         3 ~~l~~~I~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~   69 (82)
T cd08032           3 KQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSS   69 (82)
T ss_pred             HHHHHHHHHHHHhhcchhhcccCHHHHHHhcCCCCCCEeHHHHhcchHHHHHcCCHHHHHHHHhcCC
Confidence            5889999999999999999999999999996  7999999999999999999999999999999984

LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.

>cd08031 LARP_4_5_like La RNA-binding domain of proteins similar to La-related proteins 4 and 5

Probab=99.92  E-value=6.9e-26  Score=185.42  Aligned_cols=61  Identities=33%  Similarity=0.535  Sum_probs=59.6

Q ss_pred             HHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       398 ~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      ++|++||||||||+||++|.||+++|+.||||+|++|++|||||+||.|+++|++||+.|+
T Consensus         2 ~~i~~QvEfYFSd~NL~~D~fL~~~m~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~   62 (75)
T cd08031           2 ELLKRQLEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESP   62 (75)
T ss_pred             hHHHHHHHHHcCHhhhccCHHHHHHhCCCCCEEHHHHhCchhHHHHcCCHHHHHHHHHhCC
Confidence            6899999999999999999999999999999999999999999999999999999999985

This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

>cd08028 LARP_3 La RNA-binding domain of La-related protein 3

Probab=99.91  E-value=2.7e-25  Score=184.66  Aligned_cols=65  Identities=35%  Similarity=0.641  Sum_probs=62.2

Q ss_pred             HHHHHHHHhhhhhhcCcCCcCcchHhHhhcC-CCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       394 ~~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md-~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      ++|.++|++||||||||+||++|.||+++|+ .||||+|++|++|||||+||.|+++|++||+.|+
T Consensus         2 ~~l~~~I~~QvEfYFSd~NL~~D~fLr~~m~~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~   67 (82)
T cd08028           2 DDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSK   67 (82)
T ss_pred             hHHHHHHHHHHHhhcCHhhhccCHHHHHHHhccCCCEEhHHHhCChhHHHhcCCHHHHHHHHHhCC
Confidence            3689999999999999999999999999997 5999999999999999999999999999999985

This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).

>cd08033 LARP_6 La RNA-binding domain of La-related protein 6

Probab=99.91  E-value=2.6e-25  Score=182.88  Aligned_cols=61  Identities=38%  Similarity=0.644  Sum_probs=59.1

Q ss_pred             HHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          398 AMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       398 ~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      ++|++||||||||+||++|.||+++|  +.||||||++|++|||||+||.|+++|++||+.|+
T Consensus         2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~l~~d~~~I~~Al~~S~   64 (77)
T cd08033           2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSS   64 (77)
T ss_pred             hHHHhHHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhcchHHHHHcCCHHHHHHHHHhCC
Confidence            68999999999999999999999999  68999999999999999999999999999999985

This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

>smart00715 LA Domain in the RNA-binding Lupus La protein; unknown function

Probab=99.91  E-value=4e-25  Score=182.51  Aligned_cols=64  Identities=39%  Similarity=0.664  Sum_probs=61.9

Q ss_pred             HHHHHHHhhhhhhcCcCCcCcchHhHhhcCC-CCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMDD-QGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       395 ~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md~-dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      +++++|++||||||||+||++|.||+++|+. ||||||++|++|||||+|+.|+++|++||+.|.
T Consensus         2 ~~~~~i~~QvEfYFSd~NL~~D~fLr~~~~~~~g~Vpl~~i~~F~r~k~l~~d~~~i~~Al~~S~   66 (80)
T smart00715        2 ELKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSP   66 (80)
T ss_pred             hHHHHHHHHHHHHcCHhhhhhCHHHHHHhccCCCCEEhHHHhCchhHHHHcCCHHHHHHHHHhCC
Confidence            6889999999999999999999999999987 999999999999999999999999999999984

>PF05383 La: La domain; InterPro: IPR006630 Human Ro ribonucleoproteins (RNPs) are composed of one of the four small Y RNAs and at least two proteins, Ro60 and La

Probab=99.90  E-value=5.3e-25  Score=173.35  Aligned_cols=58  Identities=40%  Similarity=0.736  Sum_probs=53.6

Q ss_pred             HHhhhhhhcCcCCcCcchHhHhhcCC--CCcEehhhhccchhhhhcc-CCHHHHHHHhhhC
Q 012664          400 LIHQIDYYFSDANLVKDEFLKSNMDD--QGWVPITLIASFPRVSFYS-QISYFLITCSQFS  457 (458)
Q Consensus       400 I~kQIEYYFSDeNL~kD~FLrk~Md~--dGwVPIslIasFnRVK~LT-~Di~~Il~ALr~S  457 (458)
                      |++||||||||+||++|+||+++|+.  ||||||++|++|||||+|+ .|+++|++||++|
T Consensus         1 I~~QvEfYFSd~NL~~D~fL~~~~~~~~~g~Vpi~~i~~F~r~k~l~~~~~~~I~~al~~S   61 (61)
T PF05383_consen    1 IKKQVEFYFSDENLPRDKFLRSQMDSNPDGWVPISTILSFNRMKALTNTDIELIVDALRDS   61 (61)
T ss_dssp             HHHHHHHHTSHHHHCC-HHHHHHHCTTTTTBEEHHHHTTSHHHHHH--S-HHHHHHHHHTS
T ss_pred             ChhHHHHhcCHHHhCcCHHHHHHHHhcCCCcEeHHHHHchHHHHHHhcCCHHHHHHHHHcC
Confidence            79999999999999999999999986  9999999999999999999 9999999999987

The La protein is a 47 kDa polypeptide that frequently acts as an autoantigen in systemic lupus erythematosus and Sjogren's syndrome []. In the nucleus, La acts as a RNA polymerase III (RNAP III) transcription factor, while in the cytoplasm, La acts as a translation factor []. In the nucleus, La binds to the 3'UTR of nascent RNAP III transcripts to assist in folding and maturation []. In the cytoplasm, La recognises specific classes of mRNAs that contain a 5'-terminal oligopyrimidine (5'TOP) motif known to control protein synthesis []. The specific recognition is mediated by the N-terminal domain of La, which comprises a La motif and a RNA recognition motif (RRM). The La motif adopts an alpha/beta fold that comprises a winged-helix motif []. Homologous La domain-containing proteins have been identified in a wide range of organisms except Archaea, bacteria and viruses [].; PDB: 1S29_A 1YTY_B 2VOO_B 1S7A_A 2VOP_A 2VON_B 1ZH5_B 2VOD_A 2CQK_A.

>cd07323 LAM LA motif RNA-binding domain

Probab=99.90  E-value=2.3e-24  Score=175.83  Aligned_cols=61  Identities=44%  Similarity=0.749  Sum_probs=59.4

Q ss_pred             HHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       398 ~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      ++|++||||||||+||++|.||+++|+++|||||++|++|||||+|+.|.++|++||+.|.
T Consensus         2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~g~Vpl~~i~~F~r~k~l~~~~~~i~~Al~~s~   62 (75)
T cd07323           2 EKIKKQVEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSS   62 (75)
T ss_pred             hHHHhhhHhccCHhhhCcCHHHHHhcCCCCCEEHHHHhCchHHHHHcCCHHHHHHHHHhCC
Confidence            6899999999999999999999999999999999999999999999999999999999884

This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

>cd08029 LA_like_fungal La-motif domain of fungal proteins similar to the La autoantigen

Probab=99.89  E-value=3.6e-24  Score=175.60  Aligned_cols=60  Identities=35%  Similarity=0.622  Sum_probs=57.1

Q ss_pred             HHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          398 AMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       398 ~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      ++|++||||||||+||++|.|||++|  +.||||||++|++|||||+||.+ ++|++||+.|.
T Consensus         2 ~~I~~QvEfYFSd~NL~~D~fLr~~~~~~~~G~Vpl~~i~~F~rmk~l~~~-~~i~~Al~~S~   63 (76)
T cd08029           2 EEIRKQVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRFQPL-EAVVEALRESE   63 (76)
T ss_pred             hHHHhhHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhCchHHHHcCCH-HHHHHHHHhCC
Confidence            58999999999999999999999999  69999999999999999999965 99999999984

This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

>cd08030 LA_like_plant La-motif domain of plant proteins similar to the La autoantigen

Probab=99.88  E-value=1.2e-23  Score=177.75  Aligned_cols=62  Identities=31%  Similarity=0.516  Sum_probs=58.3

Q ss_pred             HHHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccC------------CHHHHHHHhhhCC
Q 012664          397 AAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQ------------ISYFLITCSQFSL  458 (458)
Q Consensus       397 ~~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~------------Di~~Il~ALr~St  458 (458)
                      +++|++||||||||+||++|+||+++|  +.||||+|++|++|||||+||.            |+++|++||+.|+
T Consensus         2 ~~~i~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~V~i~~i~~F~rmk~l~~~~~~~~~~~~~~~~~~I~~ALk~S~   77 (90)
T cd08030           2 KEKVLRQVEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGGGKPEDVPEDTLKAVAEALRTST   77 (90)
T ss_pred             hHHHHHHHHcccchhhcccCHHHHHHhccCCCCCEehHHHhcChHHHHHhhcccccccccchhHHHHHHHHHccCC
Confidence            589999999999999999999999999  6899999999999999999985            3789999999985

This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=99.73  E-value=1.6e-18  Score=178.43  Aligned_cols=65  Identities=37%  Similarity=0.645  Sum_probs=62.4

Q ss_pred             HHHHHHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       394 ~~L~~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      ++|..+|.+||||||||+||.+|.||.++|  +.+|||+|++|++|||||+||.|+.+|.+|||+|.
T Consensus       138 edl~~kIv~QVEyyFSDenL~~d~fLlkhvrrnkeGyVpv~~vaSFKKvK~LTrd~~~va~ALr~S~  204 (484)
T KOG1855|consen  138 EDLAAKIVDQVEYYFSDENLLKDAFLLKHVRRNKEGYVPVKLVASFKKVKALTRDWKLVADALRKSS  204 (484)
T ss_pred             HHHHHHHHHHhheeeccccccchHHHHHHHhcCCCCceeeehhhhHHHHHHHhhhhHHHHHHHhhcc
Confidence            588999999999999999999999999999  69999999999999999999999999999999883

>KOG2590 consensus RNA-binding protein LARP/SRO9 and related La domain proteins [Posttranslational modification, protein turnover, chaperones; Translation, ribosomal structure and biogenesis]

Probab=99.72  E-value=8e-16  Score=160.41  Aligned_cols=57  Identities=33%  Similarity=0.578  Sum_probs=52.8

Q ss_pred             HHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       397 ~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      .+.|.+|||||||.|||++|.||+++|     |+|.||++|+||+.|+.|+++|++|||+|.
T Consensus       301 ~~~~~~~ie~~FSeE~~~~d~~n~~k~-----~~l~~ia~F~r~ad~s~d~nli~~alr~s~  357 (448)
T KOG2590|consen  301 IAFIQEPIEFYFSEENLQRDRFNREKF-----VPLRVIAKFKRVADLSSDINLILAALRNSL  357 (448)
T ss_pred             ccccccccccccchHHHhhhhhhhccc-----chhhhhhhhhhhhhcccCHHHHHHHHhhhh
Confidence            367899999999999999999999876     669999999999999999999999999873

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=99.62  E-value=2.6e-16  Score=166.06  Aligned_cols=65  Identities=32%  Similarity=0.552  Sum_probs=63.4

Q ss_pred             HHHHHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       394 ~~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      .+|++.|++|||||||.+||..|+||+.+||+|-||||.+||.|++|++||+|+++|+|+||+|+
T Consensus        94 ~~~kq~lk~qlEy~fSreNlssD~YL~sQMDSDqyVPI~tva~~~~i~klttDvdLI~Evlresp  158 (684)
T KOG2591|consen   94 RDLKQLLKKQLEYYFSRENLSSDRYLISQMDSDQYVPINTVANFPEIMKLTTDVDLIVEVLRESP  158 (684)
T ss_pred             hhHHHHHHHHHHHhhccccccchhhhhhhcccccccchhhhccchhhhhhccchHHHHHHHhcCC
Confidence            39999999999999999999999999999999999999999999999999999999999999985

>KOG4213 consensus RNA-binding protein La [RNA processing and modification]

Probab=99.54  E-value=3.2e-15  Score=140.61  Aligned_cols=64  Identities=36%  Similarity=0.705  Sum_probs=61.2

Q ss_pred             HHHHHHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccCCHHHHHHHhhhC
Q 012664          394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFS  457 (458)
Q Consensus       394 ~~L~~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~S  457 (458)
                      +.|.++|++||||||+|.||.||.||+++|  .++|||||.+++.|||+..|++|++.|++||++|
T Consensus        11 a~lE~kii~qleyy~Gd~nl~rdkfl~eqi~k~~~gwvpi~i~i~FnRla~lttD~~~Iv~al~ks   76 (205)
T KOG4213|consen   11 AALEAKIIHQLEYYFGDLNLPRDKFLREQIHKLDDGWVPIEIMIKFNRLASLTTDFNVIVEALSKS   76 (205)
T ss_pred             hHHHHhhhhhhhhhhcccCchHHHHHHHHhhhhccCCccchhhhhhhhhhhccccHHHHHHHHhhC
Confidence            477889999999999999999999999999  3899999999999999999999999999999987

>COG5193 LHP1 La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]

Probab=99.18  E-value=6.5e-12  Score=129.40  Aligned_cols=60  Identities=28%  Similarity=0.555  Sum_probs=57.0

Q ss_pred             HHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhC
Q 012664          398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFS  457 (458)
Q Consensus       398 ~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~S  457 (458)
                      ..|++|||||||.+||+.|.|||++|+++||||+++|..|.|++.|..|.++|+.|||.+
T Consensus       272 ~a~k~QiEyYFseenl~~d~~lrkk~~kaGf~plsfi~kf~Rn~Sf~gd~nLilaa~ke~  331 (438)
T COG5193         272 MAKKEQIEYYFSEENLKSDEFLRKKFKKAGFIPLSFIGKFYRNLSFGGDKNLILAAMKEV  331 (438)
T ss_pred             hhHHhhhHhhhhHHhhhhhhHHHhhhhhcccccHhhhhhhhhccccCCchhhhHHHHHHH
Confidence            567779999999999999999999999999999999999999999999999999999875

>COG5193 LHP1 La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]

Probab=98.44  E-value=4.7e-08  Score=101.41  Aligned_cols=58  Identities=34%  Similarity=0.574  Sum_probs=55.2

Q ss_pred             HHhhhhhhcC-----cCCcCcchHhHhhcC----CCCcEehhhhccchhhhhccCCHHHHHHHhhhC
Q 012664          400 LIHQIDYYFS-----DANLVKDEFLKSNMD----DQGWVPITLIASFPRVSFYSQISYFLITCSQFS  457 (458)
Q Consensus       400 I~kQIEYYFS-----DeNL~kD~FLrk~Md----~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~S  457 (458)
                      +..|+|||||     |.|+.+|+||+.+-.    .+|||+|..|++|+|||.++..++.|..|||+|
T Consensus        75 ~l~qvE~~fS~s~~~d~n~~~dk~~ktta~Kn~~~~kwVpIkt~~tfn~~k~~gs~~~~v~~a~rks  141 (438)
T COG5193          75 TLKQVEFYFSGSKDTDSNFPKDKFLKTTAPKNKKRDKWVPIKTIATFNRMKNSGSPVSAVSGALRKS  141 (438)
T ss_pred             cccceeEEeeccccccccccchhhhccccccccCCCCceeeeeeeeeccccccCCchhhhhhhhhcC
Confidence            8999999999     999999999999863    599999999999999999999999999999988

>KOG2590 consensus RNA-binding protein LARP/SRO9 and related La domain proteins [Posttranslational modification, protein turnover, chaperones; Translation, ribosomal structure and biogenesis]

Probab=90.28  E-value=0.054  Score=58.09  Aligned_cols=71  Identities=24%  Similarity=0.190  Sum_probs=61.4

Q ss_pred             CCCCCCcHHHHHHHHh--hhhhhcCcCCcCcchHhHhhcCCCC---cEehhhhccchhhhhccCCHHHHHHHhhhC
Q 012664          387 VLMPVPEPSLAAMLIH--QIDYYFSDANLVKDEFLKSNMDDQG---WVPITLIASFPRVSFYSQISYFLITCSQFS  457 (458)
Q Consensus       387 ~~~P~~e~~L~~~I~k--QIEYYFSDeNL~kD~FLrk~Md~dG---wVPIslIasFnRVK~LT~Di~~Il~ALr~S  457 (458)
                      ..++.+...|.+.+..  +++|||+-.++.+|.|+...++..|   +.+|+.+..|.++..++++...+..+++.|
T Consensus        88 ~~~~~ps~~l~e~~~~~k~~s~~~~~~~~~~~~~~~~k~~~t~~~~~~~~S~~~~s~~~~~~s~n~~~~~~~~~~s  163 (448)
T KOG2590|consen   88 QVISVPSPPLKEYSKSDKKKSWPASKPFTPRDSFKGSKPTNTGNGTFLPISKISSSGPVSGGSANNSNIRGPLKGS  163 (448)
T ss_pred             cccccccccccccccccccccCcccCCCCccccccCCCccccCCCccCCCccccccccccCcccccccccCcCCCC
Confidence            4455556667776666  9999999999999999999999888   999999999999999999998888887764

>KOG2278 consensus RNA:NAD 2'-phosphotransferase TPT1 [Translation, ribosomal structure and biogenesis]

Probab=84.51  E-value=0.8  Score=44.42  Aligned_cols=38  Identities=16%  Similarity=0.171  Sum_probs=32.8

Q ss_pred             HhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhh
Q 012664          418 FLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQ  455 (458)
Q Consensus       418 FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr  455 (458)
                      -++=+|+.||||+|+.|++.|+.|...-.+++|.++++
T Consensus        24 ~~~L~m~~dGfvpv~~lL~lnq~r~~~~t~ddi~riVk   61 (207)
T KOG2278|consen   24 ELRLNMRGDGFVPVEDLLNLNQFRGANHTIDDIRRIVK   61 (207)
T ss_pred             HhcccccCCCceEHHHHhccchhcccCCcHHHHHHHHh
Confidence            35667899999999999999999998877888888775

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	458
2vod_A	193	Crystal Structure Of N-Terminal Domains Of Human La		3e-07
1s7a_A	103	Nmr Structure Of The La Motif Of Human La Protein L		4e-07
1zh5_A	195	Structural Basis For Recognition Of Uuuoh 3'-Termin		6e-07
1yty_A	194	Structural Basis For Recognition Of Uuuoh 3'-Termin		6e-07

>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La Protein Complexed With Rna Oligomer Auauuuu Length = 193

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%), Gaps = 1/48 (2%)
Query: 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
           +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R++
Sbjct: 11  ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLN 58

>pdb|1S7A|A Chain A, Nmr Structure Of The La Motif Of Human La Protein Length = 103

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 22/48 (45%), Positives = 34/48 (70%), Gaps = 1/48 (2%)
Query: 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
           +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R++
Sbjct: 12  ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLN 59

>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of Nascent Rna Pol Iii Transcripts By La Autoantigen Length = 195

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%), Gaps = 1/48 (2%)
Query: 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
           +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ +   F R++
Sbjct: 13  ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIXIKFNRLN 60

>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of Nascent Rna Pol Iii Transcripts By La Autoantigen Length = 194

Iteration: 1
 Score = 52.0 bits (123), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%), Gaps = 1/48 (2%)
Query: 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVS 441
           +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ +   F R++
Sbjct: 12  ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIXIKFNRLN 59

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	458
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-17
2cqk_A	101	C-MPL binding protein; LA domain, structural genom	7e-17
1s29_A	92	LA protein; winged helix-turn-helix, autoantigen,	1e-16

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 79.1 bits (194), Expect = 3e-17
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 390 PVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVSFYSQISY 448
                +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R++  +    
Sbjct: 6   NEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFN 65

Query: 449 FLITCSQFS 457
            ++     S
Sbjct: 66  VIVEALSKS 74

>2cqk_A C-MPL binding protein; LA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.5.46 Length = 101

 Score = 74.9 bits (184), Expect = 7e-17
 Identities = 18/68 (26%), Positives = 31/68 (45%)

Query: 390 PVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYF 449
            V    L   L  Q+++ FS  NL KD +L S MD   ++PI  +A+   +   +     
Sbjct: 8   AVSTEDLKECLKKQLEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDL 67

Query: 450 LITCSQFS 457
           ++   + S
Sbjct: 68  ILEVLRSS 75

>1s29_A LA protein; winged helix-turn-helix, autoantigen, RNA-binding, RNA binding protein; 1.60A {Trypanosoma brucei} SCOP: a.4.5.46 Length = 92

 Score = 74.0 bits (182), Expect = 1e-16
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 391 VPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQ 445
                    L  Q+++YFSD N+ +D FLK  M  + +G+V +  + +F RV+  + 
Sbjct: 5   PLSSENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTT 61

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	458
2cqk_A	101	C-MPL binding protein; LA domain, structural genom	99.93
1s29_A	92	LA protein; winged helix-turn-helix, autoantigen,	99.92
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.83

>2cqk_A C-MPL binding protein; LA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.5.46

Probab=99.93  E-value=6.7e-27  Score=199.58  Aligned_cols=69  Identities=26%  Similarity=0.401  Sum_probs=66.1

Q ss_pred             CCCcHHHHHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          390 PVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       390 P~~e~~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      ++.+++|+++|++||||||||+||++|.||+++|+.||||+|++|++|||||+||+|+++|++||+.|+
T Consensus         8 ~~~~~~l~~~I~~QvEyYFSd~NL~~D~fL~~~md~~G~Vpl~~iasF~r~k~lt~d~~~i~~al~~S~   76 (101)
T 2cqk_A            8 AVSTEDLKECLKKQLEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSP   76 (101)
T ss_dssp             SCCHHHHHHHHHHHHHHHTSHHHHHHCHHHHHHSCTTSCEEHHHHHHCHHHHHHCCCHHHHHHHHHHSS
T ss_pred             CCCHHHHHHHHHHHHHhhcchhhhccCHHHHHhhhcCCCEEhHHHhCChHHHHHcCCHHHHHHHHHhCC
Confidence            346789999999999999999999999999999999999999999999999999999999999999985

>1s29_A LA protein; winged helix-turn-helix, autoantigen, RNA-binding, RNA binding protein; 1.60A {Trypanosoma brucei} SCOP: a.4.5.46

Probab=99.92  E-value=3.9e-26  Score=191.64  Aligned_cols=66  Identities=27%  Similarity=0.442  Sum_probs=63.6

Q ss_pred             cHHHHHHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          393 EPSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       393 e~~L~~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      +++++++|++||||||||+||++|.||+++|  +.||||+|++|++|||||+||.|+++|++||+.|+
T Consensus         7 ~~~~~~~I~~QvEyYFSd~NL~~D~fL~~~m~~~~~G~Vpl~~i~sF~r~k~lt~d~~~i~~al~~S~   74 (92)
T 1s29_A            7 SSENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSE   74 (92)
T ss_dssp             CHHHHHHHHHHHHHHTSHHHHTTCHHHHHHHTTSTTCCEEHHHHTTSHHHHTTCSCHHHHHHHHTTCS
T ss_pred             CHHHHHHHHHHHHhhcchhhhccCHHHHHHhccCCCCCEEhHHHhCChhHHHHcCCHHHHHHHHhhCC
Confidence            5689999999999999999999999999999  78999999999999999999999999999999985

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.83  E-value=3.1e-21  Score=176.12  Aligned_cols=65  Identities=35%  Similarity=0.679  Sum_probs=62.6

Q ss_pred             cHHHHHHHHhhhhhhcCcCCcCcchHhHhhcC-CCCcEehhhhccchhhhhccCCHHHHHHHhhhC
Q 012664          393 EPSLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVSFYSQISYFLITCSQFS  457 (458)
Q Consensus       393 e~~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md-~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~S  457 (458)
                      .++|+++|++||||||||+||++|.||+++|+ ++|||+|.+|++|+|||.|+.|+++|++||+.|
T Consensus         9 ~~~~~~~i~~q~e~yfs~~nl~~D~fl~~~~~~~~g~V~l~~i~sF~r~k~l~~d~~~I~~Al~~S   74 (193)
T 2voo_A            9 MAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKS   74 (193)
T ss_dssp             CHHHHHHHHHHHHHHTSTTTGGGCHHHHHHHHHTTTCEEHHHHTTSHHHHHHCCCHHHHHHHHHTC
T ss_pred             cHHHHHHHHHHhheecchhhcccCHHHHHHhcccCCcEEeHHHhhhhHHHHhcCCHHHHHHHHhhc
Confidence            35899999999999999999999999999997 799999999999999999999999999999988

---

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	458
d2cqka1	88	a.4.5.46 (A:43-130) La-related protein 4 LARP4 {Hu	5e-21
d1zh5a1	99	a.4.5.46 (A:5-103) Lupus La autoantigen N-terminal	3e-17
d1s29a_	92	a.4.5.46 (A:) Lupus La autoantigen N-terminal doma	9e-15

>d2cqka1 a.4.5.46 (A:43-130) La-related protein 4 LARP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: La-related protein 4 LARP4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 85.1 bits (211), Expect = 5e-21
 Identities = 17/50 (34%), Positives = 26/50 (52%)

Query: 391 VPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRV 440
           V    L   L  Q+++ FS  NL KD +L S MD   ++PI  +A+   +
Sbjct: 2   VSTEDLKECLKKQLEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEI 51

>d1zh5a1 a.4.5.46 (A:5-103) Lupus La autoantigen N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.8 bits (184), Expect = 3e-17
 Identities = 22/50 (44%), Positives = 33/50 (66%), Gaps = 1/50 (2%)

Query: 392 PEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRV 440
              +L A + HQI+YYF D NL +D+FLK  +  D+GWVP+ ++  F R+
Sbjct: 5   KMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRL 54

>d1s29a_ a.4.5.46 (A:) Lupus La autoantigen N-terminal domain {Trypanosoma brucei [TaxId: 5691]} Length = 92

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Trypanosoma brucei [TaxId: 5691]

 Score = 67.5 bits (165), Expect = 9e-15
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 3/54 (5%)

Query: 389 MPVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRV 440
           MP+        L  Q+++YFSD N+ +D FLK  M  + +G+V +  + +F RV
Sbjct: 4   MPLSS-ENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRV 56

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	458
d2cqka1	88	La-related protein 4 LARP4 {Human (Homo sapiens) [	99.92
d1s29a_	92	Lupus La autoantigen N-terminal domain {Trypanosom	99.91
d1zh5a1	99	Lupus La autoantigen N-terminal domain {Human (Hom	99.91

>d2cqka1 a.4.5.46 (A:43-130) La-related protein 4 LARP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: La-related protein 4 LARP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=1.9e-26  Score=190.38  Aligned_cols=68  Identities=26%  Similarity=0.405  Sum_probs=65.3

Q ss_pred             CCcHHHHHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          391 VPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       391 ~~e~~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      +..++|+++|++||||||||+||++|.||+++|++||||+|++|++|||||+||.|+++|++||+.|+
T Consensus         2 v~~~~l~~~i~~QvEfYFSd~NL~~D~fL~~~m~~~G~V~l~~i~~F~r~k~lt~d~~~i~~Al~~S~   69 (88)
T d2cqka1           2 VSTEDLKECLKKQLEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSP   69 (88)
T ss_dssp             CCHHHHHHHHHHHHHHHTSHHHHHHCHHHHHHSCTTSCEEHHHHHHCHHHHHHCCCHHHHHHHHHHSS
T ss_pred             CChHHHHHHHHHHHHhhCCHhhhCcCHHHHHhhcCCCCEEhHHHhcChHHHHHcCCHHHHHHHHhcCC
Confidence            35679999999999999999999999999999999999999999999999999999999999999985

>d1s29a_ a.4.5.46 (A:) Lupus La autoantigen N-terminal domain {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Trypanosoma brucei [TaxId: 5691]

Probab=99.91  E-value=5.9e-26  Score=188.84  Aligned_cols=68  Identities=28%  Similarity=0.476  Sum_probs=63.4

Q ss_pred             CCCcHHHHHHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          390 PVPEPSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       390 P~~e~~L~~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      |.. ++++++|++||||||||+||++|+||+++|  +.||||+|++|++|||||+||.|+++|++||+.|.
T Consensus         5 p~~-~e~~~~I~~QvEfYFSd~NL~~D~fL~~~m~~~~~G~V~i~~i~~F~rmk~lt~d~~~i~~Al~~S~   74 (92)
T d1s29a_           5 PLS-SENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSE   74 (92)
T ss_dssp             CCC-HHHHHHHHHHHHHHTSHHHHTTCHHHHHHHTTSTTCCEEHHHHTTSHHHHTTCSCHHHHHHHHTTCS
T ss_pred             CCC-HHHHHHHHHHHHHHccHhhhccCHHHHHHHhccCCCcEEhHHHhcCcCHHHhcCCHHHHHHHHhhCC
Confidence            344 467899999999999999999999999999  68999999999999999999999999999999984

>d1zh5a1 a.4.5.46 (A:5-103) Lupus La autoantigen N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=1.8e-25  Score=187.89  Aligned_cols=65  Identities=35%  Similarity=0.678  Sum_probs=62.3

Q ss_pred             HHHHHHHHhhhhhhcCcCCcCcchHhHhhcC-CCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012664          394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVSFYSQISYFLITCSQFSL  458 (458)
Q Consensus       394 ~~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md-~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St  458 (458)
                      +.|+++|++||||||||+||++|.||+++|+ +||||+|++|++|||||+||.|+++|++||+.|+
T Consensus         7 ~~l~~~I~~QvEfYFSd~NL~~D~fL~~~m~~~eG~Vpl~~i~~F~r~k~l~~~~~~i~~Al~~S~   72 (99)
T d1zh5a1           7 AALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSK   72 (99)
T ss_dssp             HHHHHHHHHHHHHHTSTTTGGGCHHHHHHHTTTTTCEEHHHHTTSHHHHHHCCCHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHHHHhcCHhhhccCHHHHHHHhcCCCcccHHHHhcchHHHHHcCCHHHHHHHHHhCC
Confidence            5789999999999999999999999999998 6899999999999999999999999999999884