Psyllid ID: psy7757

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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---
Protein Sequence
MSARINAMVLVARHAATTIVKENMSTPVADIVMGAGDSMGVANATVNNIQHSSDEGGSSETSPSVSPSLQGQMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMDFLRSQRDV
Secondary Structure (PSIPRED)
cccccccHHHHHHccccEEEEccccccccEEEEccccEEEEccccEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHccccEEEEccccccccccccccccccccccHHHHHHHHHHcccEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHEHccccEEEcccccccccEEEEcccEEEEEEcccEEEEEEEccccccccccccccccccHHHHHHHHHHHHHHHcccccEEEHHHHHHHHHHHHHHHcHHHccHHHHHHHHHHHcccEEEEEcccccccccc
Coil and Loop (DISEMBL)
MSARINAMVLVARHAATTIVkenmstpvadIVMGAGDSMGVANATVnniqhssdeggssetspsvspslqgQMSLLCRELVDLLKtfphcqmvfnkfipayhhhfgrqcrvadyGFTKLIDLLEAIPHVVQVIMDFLRSQRDV
Flexible Loop (DISEMBL)
MSARINAMVLVARHAAttivkenmstPVADIVMGAGDSMGVANATVNNIQHSSDEGGSSETSPSVSPSLQGQMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMDFLRSQRDV
Low Complexity Region (SEG)
MSARINAMVLVARHAATTIVKENMSTPVADIVMGAGDSMGVANATVNNIQHSSDeggssetspsvspsLQGQMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMDFLRSQRDV
Disordered region (IsUnstruct)
*****NAMVLVARHAATTIVKENMSTPVADIVMGAG*************************************SLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMDFL******
Disordered Region (DISOPRED)
******A**LVARHAATTIVKENMSTPVADIVMGAGDSMGVANATVNN*************************SLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMDFL******
Disordered Region (DISEMBL)
MSARINAMVLVARHAATTIVKENMSTPVADIVMGAGDSMGVANATVNNIQ********************GQMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMDFLRSQRDV
Disordered Region (DISPRO)
****INAMVLVARHAATTIVKENMSTPVADIVMGAGDSMGVANATVNNIQHSSDE***********PSLQGQMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMD********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSARINAMVLVARHAATTIVKENMSTPVADIVMGAGDSMGVANATVNNIQHSSDEGGSSETSPSVSPSLQGQMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMDFLRSQRDV
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

No hits with e-value below 0.001 by BLAST

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	143
MGI|MGI:2444505	1730	Marf1 "meiosis arrest female 1	0.433	0.035	0.596	5.8e-17
RGD|1595602	1647	LOC678813 "similar to limkain	0.391	0.034	0.660	2.4e-16
RGD|619770	1735	Marf1 "meiosis arrest female 1	0.391	0.032	0.660	2.5e-16
UNIPROTKB|Q8VIG2	1735	Marf1 "Meiosis arrest female p	0.391	0.032	0.660	2.5e-16
UNIPROTKB|I3LNV7	1690	KIAA0430 "Uncharacterized prot	0.433	0.036	0.564	5.1e-16
UNIPROTKB|I3LH01	1697	KIAA0430 "Uncharacterized prot	0.433	0.036	0.564	5.1e-16
UNIPROTKB|E2R571	1744	KIAA0430 "Uncharacterized prot	0.433	0.035	0.564	5.3e-16
UNIPROTKB|C9JKX0	1430	KIAA0430 "Meiosis arrest femal	0.433	0.043	0.564	5.3e-16
UNIPROTKB|G8JLP4	1577	KIAA0430 "Meiosis arrest femal	0.433	0.039	0.564	6e-16
UNIPROTKB|E1BZ85	1741	MARF1 "Meiosis arrest female p	0.433	0.035	0.564	6.7e-16

MGI|MGI:2444505 Marf1 "meiosis arrest female 1" [Mus musculus (taxid:10090)]

 Score = 224 (83.9 bits), Expect = 5.8e-17, P = 5.8e-17
 Identities = 37/62 (59%), Positives = 52/62 (83%)

Query:    72 QMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQ 131
             Q+    RE++DLLKT P C +  + FIP+YHHHFG+QCRV+DYG++KLI+LLEA+PHV+Q
Sbjct:  1089 QLIQFSREVIDLLKTQPSCILPVSNFIPSYHHHFGKQCRVSDYGYSKLIELLEAVPHVLQ 1148

Query:   132 VI 133
             ++
Sbjct:  1149 IL 1150

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005777 "peroxisome" evidence=ISO

GO:0007126 "meiosis" evidence=IEA

GO:0007143 "female meiosis" evidence=IMP

GO:0010468 "regulation of gene expression" evidence=IMP

GO:0010923 "negative regulation of phosphatase activity" evidence=ISO

GO:0030154 "cell differentiation" evidence=IEA

GO:0048477 "oogenesis" evidence=IMP

RGD|1595602 LOC678813 "similar to limkain b1" [Rattus norvegicus (taxid:10116)]

 Score = 218 (81.8 bits), Expect = 2.4e-16, P = 2.4e-16
 Identities = 37/56 (66%), Positives = 50/56 (89%)

Query:    78 RELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVI 133
             +++VDLL+  PH +M FNKFIP+YHHHFGRQC++A YGFTKL++LLEAIP ++QV+
Sbjct:  1172 KDVVDLLRHQPHFRMPFNKFIPSYHHHFGRQCKLAYYGFTKLLELLEAIPEILQVL 1227

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

RGD|619770 Marf1 "meiosis arrest female 1" [Rattus norvegicus (taxid:10116)]

 Score = 218 (81.8 bits), Expect = 2.5e-16, P = 2.5e-16
 Identities = 37/56 (66%), Positives = 50/56 (89%)

Query:    78 RELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVI 133
             +++VDLL+  PH +M FNKFIP+YHHHFGRQC++A YGFTKL++LLEAIP ++QV+
Sbjct:  1262 KDVVDLLRHQPHFRMPFNKFIPSYHHHFGRQCKLAYYGFTKLLELLEAIPEILQVL 1317

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA;ISO

GO:0007143 "female meiosis" evidence=ISO;ISS

GO:0010468 "regulation of gene expression" evidence=ISO;ISS

GO:0010923 "negative regulation of phosphatase activity" evidence=ISO;ISS

GO:0030154 "cell differentiation" evidence=IEA

GO:0048477 "oogenesis" evidence=ISO;ISS

UNIPROTKB|Q8VIG2 Marf1 "Meiosis arrest female protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 218 (81.8 bits), Expect = 2.5e-16, P = 2.5e-16
 Identities = 37/56 (66%), Positives = 50/56 (89%)

Query:    78 RELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVI 133
             +++VDLL+  PH +M FNKFIP+YHHHFGRQC++A YGFTKL++LLEAIP ++QV+
Sbjct:  1262 KDVVDLLRHQPHFRMPFNKFIPSYHHHFGRQCKLAYYGFTKLLELLEAIPEILQVL 1317

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|I3LNV7 KIAA0430 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 215 (80.7 bits), Expect = 5.1e-16, P = 5.1e-16
 Identities = 35/62 (56%), Positives = 51/62 (82%)

Query:    72 QMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQ 131
             Q+    RE++DLLK+ P C +  + FIP+YHHHF +QCRV+DYG++KLI+LLEA+PHV+Q
Sbjct:  1041 QLIQFSREVIDLLKSQPSCVIPISNFIPSYHHHFAKQCRVSDYGYSKLIELLEAVPHVLQ 1100

Query:   132 VI 133
             ++
Sbjct:  1101 IL 1102

GO:0005777 "peroxisome" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|I3LH01 KIAA0430 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 215 (80.7 bits), Expect = 5.1e-16, P = 5.1e-16
 Identities = 35/62 (56%), Positives = 51/62 (82%)

Query:    72 QMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQ 131
             Q+    RE++DLLK+ P C +  + FIP+YHHHF +QCRV+DYG++KLI+LLEA+PHV+Q
Sbjct:  1048 QLIQFSREVIDLLKSQPSCVIPISNFIPSYHHHFAKQCRVSDYGYSKLIELLEAVPHVLQ 1107

Query:   132 VI 133
             ++
Sbjct:  1108 IL 1109

GO:0048477 "oogenesis" evidence=IEA

GO:0010923 "negative regulation of phosphatase activity" evidence=IEA

GO:0010468 "regulation of gene expression" evidence=IEA

GO:0007143 "female meiosis" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2R571 KIAA0430 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 215 (80.7 bits), Expect = 5.3e-16, P = 5.3e-16
 Identities = 35/62 (56%), Positives = 51/62 (82%)

Query:    72 QMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQ 131
             Q+    RE++DLLK+ P C +  + FIP+YHHHF +QCRV+DYG++KLI+LLEA+PHV+Q
Sbjct:  1101 QLIQFSREVIDLLKSQPSCVIPISNFIPSYHHHFAKQCRVSDYGYSKLIELLEAVPHVLQ 1160

Query:   132 VI 133
             ++
Sbjct:  1161 IL 1162

GO:0048477 "oogenesis" evidence=IEA

GO:0010923 "negative regulation of phosphatase activity" evidence=IEA

GO:0010468 "regulation of gene expression" evidence=IEA

GO:0007143 "female meiosis" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|C9JKX0 KIAA0430 "Meiosis arrest female protein 1" [Homo sapiens (taxid:9606)]

 Score = 214 (80.4 bits), Expect = 5.3e-16, P = 5.3e-16
 Identities = 35/62 (56%), Positives = 51/62 (82%)

Query:    72 QMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQ 131
             Q+    RE++DLLK+ P C +  + FIP+YHHHF +QCRV+DYG++KLI+LLEA+PHV+Q
Sbjct:   701 QLIQFSREVIDLLKSQPSCVIPISHFIPSYHHHFAKQCRVSDYGYSKLIELLEAVPHVLQ 760

Query:   132 VI 133
             ++
Sbjct:   761 IL 762

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

UNIPROTKB|G8JLP4 KIAA0430 "Meiosis arrest female protein 1" [Homo sapiens (taxid:9606)]

 Score = 214 (80.4 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 35/62 (56%), Positives = 51/62 (82%)

Query:    72 QMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQ 131
             Q+    RE++DLLK+ P C +  + FIP+YHHHF +QCRV+DYG++KLI+LLEA+PHV+Q
Sbjct:   934 QLIQFSREVIDLLKSQPSCVIPISHFIPSYHHHFAKQCRVSDYGYSKLIELLEAVPHVLQ 993

Query:   132 VI 133
             ++
Sbjct:   994 IL 995

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

UNIPROTKB|E1BZ85 MARF1 "Meiosis arrest female protein 1 homolog" [Gallus gallus (taxid:9031)]

 Score = 214 (80.4 bits), Expect = 6.7e-16, P = 6.7e-16
 Identities = 35/62 (56%), Positives = 51/62 (82%)

Query:    72 QMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQ 131
             Q+    RE++DLLK+ P C +  +KFIP YHHHF +QCRV+DYG++KL++LLEA+PHV+Q
Sbjct:  1097 QLIQFSREVIDLLKSQPSCIIPVSKFIPTYHHHFAKQCRVSDYGYSKLMELLEAVPHVLQ 1156

Query:   132 VI 133
             ++
Sbjct:  1157 IL 1158

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

GO:0007143 "female meiosis" evidence=IEA

GO:0010468 "regulation of gene expression" evidence=IEA

GO:0010923 "negative regulation of phosphatase activity" evidence=IEA

GO:0048477 "oogenesis" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	143
cd09979	72	cd09979, LOTUS_3_Limkain_b1, The third LOTUS domai	1e-35
cd09981	71	cd09981, LOTUS_5_Limkain_b1, The fifth LOTUS domai	2e-33
cd08824	70	cd08824, LOTUS, LOTUS is an uncharacterized small	1e-16
cd09980	72	cd09980, LOTUS_4_Limkain_b1, The fourth LOTUS doma	5e-07
pfam12872	74	pfam12872, OST-HTH, OST-HTH/LOTUS domain	5e-07
cd09984	76	cd09984, LOTUS_8_Limkain_b1, The eighth LOTUS doma	5e-05
cd09975	70	cd09975, LOTUS_2_TDRD5, The second LOTUS domain on	0.002

>gnl|CDD|193593 cd09979, LOTUS_3_Limkain_b1, The third LOTUS domain on Limkain b1(LKAP)

 Score =  117 bits (295), Expect = 1e-35
 Identities = 38/61 (62%), Positives = 53/61 (86%)

Query: 73  MSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQV 132
           +    RE++DLLK+ P C + F++FIPAYHHHFG+QCRV+DYG+TKLI+LLEA+PHV+Q+
Sbjct: 1   LIQFSREVIDLLKSQPSCLLPFSRFIPAYHHHFGKQCRVSDYGYTKLIELLEAVPHVLQI 60

Query: 133 I 133
           +
Sbjct: 61  L 61

The third LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. Length = 72

>gnl|CDD|193595 cd09981, LOTUS_5_Limkain_b1, The fifth LOTUS domain on Limkain b1(LKAP)

 Score =  111 bits (280), Expect = 2e-33
 Identities = 36/56 (64%), Positives = 48/56 (85%)

Query: 78  RELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVI 133
           +E+V+LL+  PH +M F KFIP+YHHHFGRQC+++ YGFTKL++L EAIP VVQV+
Sbjct: 6   KEVVELLRHQPHFRMPFTKFIPSYHHHFGRQCKLSYYGFTKLLELFEAIPDVVQVL 61

The fifth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. Length = 71

>gnl|CDD|193585 cd08824, LOTUS, LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7

 Score = 68.8 bits (169), Expect = 1e-16
 Identities = 22/55 (40%), Positives = 35/55 (63%), Gaps = 1/55 (1%)

Query: 78  RELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQV 132
           ++L  LL+++P   +  +K    Y   FG+   +++YGF+KL DLLEA+P VV V
Sbjct: 6   KQLRSLLQSYPGG-LPLSKLPQLYKKKFGKPLDLSEYGFSKLSDLLEALPGVVIV 59

LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. Length = 70

>gnl|CDD|193594 cd09980, LOTUS_4_Limkain_b1, The fourth LOTUS domain on Limkain b1(LKAP)

 Score = 44.3 bits (105), Expect = 5e-07
 Identities = 21/55 (38%), Positives = 27/55 (49%)

Query: 79  ELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVI 133
           +L+ +LK+    Q++   F  AY   FGR     DYG   L DLL  IP    VI
Sbjct: 7   DLLRVLKSQASKQVIVKDFGQAYEWCFGRDWDPVDYGLCDLQDLLSEIPDNTIVI 61

The fourth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. Length = 72

>gnl|CDD|221822 pfam12872, OST-HTH, OST-HTH/LOTUS domain

 Score = 44.2 bits (105), Expect = 5e-07
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 78  RELVDLLKTFPH--CQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQV 132
           + L   L++          ++    Y   F       +YG++KL DLLEAIP + +V
Sbjct: 8   KLLRKALESSSDEDGWASLSELGSEYRKLF-PDFDPRNYGYSKLSDLLEAIPDLFEV 63

A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA.In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNAse domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains. Length = 74

>gnl|CDD|193598 cd09984, LOTUS_8_Limkain_b1, The eighth LOTUS domain on Limkain b1(LKAP)

 Score = 39.1 bits (91), Expect = 5e-05
 Identities = 18/56 (32%), Positives = 30/56 (53%)

Query: 75  LLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVV 130
              + +  LL T+ + Q+  ++F  AY  + G   +  +YG+  L +LL AIP VV
Sbjct: 3   QFAKNVRSLLHTYHYQQIFLHEFSSAYSKYVGETLQPKNYGYNSLEELLGAIPQVV 58

The eighth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. Length = 76

>gnl|CDD|193589 cd09975, LOTUS_2_TDRD5, The second LOTUS domain on Tudor-containing protein 5 (TDRD5)

 Score = 34.9 bits (80), Expect = 0.002
 Identities = 19/63 (30%), Positives = 25/63 (39%), Gaps = 3/63 (4%)

Query: 78  RELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMDFL 137
            EL DLL   P       K   AY   FGR  +   YGF  ++++L A    + V     
Sbjct: 6   SELKDLLSHSPVLLSELEK---AYVARFGRSFQYTQYGFFSMLEVLSAASDFIIVKQTRT 62

Query: 138 RSQ 140
            S 
Sbjct: 63  GSL 65

The second LOTUS domain on Tudor-containing protein 5 (TDRD5): TDRD5 contains three N-terminal LOTUS domains and a C-terminal Tudor domain. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice TDRD5 is a component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. The exact molecular function of LOTUS domain on TDRD5 remains to be discovered. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. Length = 70

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	143
PF12872	74	OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B	98.88

>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A

Probab=98.88  E-value=1.4e-09  Score=71.04  Aligned_cols=66  Identities=24%  Similarity=0.398  Sum_probs=54.2

Q ss_pred             hHhHHHHHHHHhhhCCC--cccccCcccchhhhhccccccccccchhhHHHHHhhccceeeeecccccc
Q psy7757          73 MSLLCRELVDLLKTFPH--CQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMDFLRS  139 (143)
Q Consensus        73 l~qFarEvVdLLk~~p~--c~m~F~kFipaYHhHFGrQCRvsdYGftKL~dLleaIp~vVqIlg~~~~~  139 (143)
                      +..+.+++.++|...+.  ..++.+.|-..|..+| ..+...+|||++|.|||+++|++++|...+..+
T Consensus         3 ~~~~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~-~~f~~~~yG~~~l~~ll~~~~~~~~i~~~~~g~   70 (74)
T PF12872_consen    3 LEELKKLLRELLESQKGEDGWVSLSQLGQEYKKKY-PDFDPRDYGFSSLSELLESLPDVVEIEERQHGG   70 (74)
T ss_dssp             -HHHHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHH-TT--TCCTTSSSHHHHHHT-TTTEEEEEEECCC
T ss_pred             HHHHHHHHHHHHHhCcCCCceEEHHHHHHHHHHHC-CCCCccccCCCcHHHHHHhCCCeEEEeeeCCCC
Confidence            45788899999966665  3899999999999999 999999999999999999999999996554433

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	143
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

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

 Score = 38.7 bits (89), Expect = 3e-04
 Identities = 27/184 (14%), Positives = 54/184 (29%), Gaps = 56/184 (30%)

Query: 9   VLVARHAATTIVKENMSTPVADIVMGAGDSMGVANATVNNIQHSSDEGGSSETSPSVSPS 68
            +      +  V+  M   +  + +   +S       +  + +  D   +S +  S +  
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK 224

Query: 69  LQGQMSLLCRELVDLL--KTFPHCQMVF-----NKFIPAYHHHFGRQCR---------VA 112
           L  ++  +  EL  LL  K + +C +V       K   A    F   C+         V 
Sbjct: 225 L--RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA----FNLSCKILLTTRFKQVT 278

Query: 113 DY----------------GFTK--LIDLL-------------EAI---PHVVQVIMDFLR 138
           D+                  T   +  LL             E +   P  + +I + +R
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIR 338

Query: 139 SQRD 142
               
Sbjct: 339 DGLA 342

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	143
3s93_A	102	Tudor domain-containing protein 5; structural geno	96.1
3rco_A	89	Tudor domain-containing protein 7; structural geno	93.75
2kzv_A	92	Uncharacterized protein; structural genomics, PSI-	88.97
2kpm_A	105	Uncharacterized protein; methods development, stru	83.62

>3s93_A Tudor domain-containing protein 5; structural genomics consortium, SGC, transcription; 2.28A {Homo sapiens}

Probab=96.10  E-value=0.0048  Score=44.32  Aligned_cols=64  Identities=19%  Similarity=0.260  Sum_probs=56.6

Q ss_pred             hhhHhHHHHHHHHhhhCCCcccccCcccchhhhhccccccccccchhhHHHHHhhccceeeeecc
Q psy7757          71 GQMSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMD  135 (143)
Q Consensus        71 ~~l~qFarEvVdLLk~~p~c~m~F~kFipaYHhHFGrQCRvsdYGftKL~dLleaIp~vVqIlg~  135 (143)
                      +-+..-..++-.||-..+. .++-.++..-|.-.-|..--+-.|||..|.|+|.+||+||++.+.
T Consensus         7 ~~l~~vkk~irslLiS~K~-gvtl~~L~~dYr~~~G~~iP~r~lGy~sl~~fL~sipdvv~~~~~   70 (102)
T 3s93_A            7 RIQECLRKEIRSLLISTKD-GLSPQELEKEYLLMVGNHLPLRILGYRSTMELVLDMPDVVRVCPG   70 (102)
T ss_dssp             HHHHHHHHHHHHHHHSSSS-CBCHHHHHHHHHHHHSSCCCTGGGTCSSHHHHHHTCTTTEEEECC
T ss_pred             HHHHHHHHHHHHhheeCCC-CcCHHHHHHHHHHHcCCcCCchhcCcCCHHHHHHcCCCeEEEEec
Confidence            4556777888888888776 689999999999999999999999999999999999999998654

>3rco_A Tudor domain-containing protein 7; structural genomics, structural genomics consortium, SGC, HL DNA binding protein; 1.80A {Homo sapiens} PDB: 2lh9_A

Probab=93.75  E-value=0.037  Score=39.43  Aligned_cols=55  Identities=20%  Similarity=0.381  Sum_probs=47.1

Q ss_pred             HHHHHHHhhhCCCcccccCcccchhhhhccccccccccchhhHHHHHhhccceeee
Q psy7757          77 CRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQV  132 (143)
Q Consensus        77 arEvVdLLk~~p~c~m~F~kFipaYHhHFGrQCRvsdYGftKL~dLleaIp~vVqI  132 (143)
                      .+++-.||...+. -++-.++..-|.-.-|..--+-.+||..+.|+|.+||+||++
T Consensus        15 ~k~iRslL~S~k~-gvtl~~L~~DYr~l~G~~iP~r~lGy~sl~~fL~siPdvv~~   69 (89)
T 3rco_A           15 SKMLRAVLQSHKN-GVALPRLQGEYRSLTGDWIPFKQLGFPTLEAYLRSVPAVVRI   69 (89)
T ss_dssp             HHHHHHHHHTCTT-CEEHHHHHHHHHHHHSSCCCTTTTTCSSHHHHHHTCTTTEEE
T ss_pred             HHHHHHHhhcCCC-CCCHHHHHHHHHHHhCCcCChhhhCcccHHHHHhcccCeEEE
Confidence            4455566666544 488889999999999999999999999999999999999996

>2kzv_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG; NMR {Chromobacterium violaceum}

Probab=88.97  E-value=0.13  Score=36.16  Aligned_cols=22  Identities=14%  Similarity=0.392  Sum_probs=17.6

Q ss_pred             cccchhhHHHHHhhccceeeeec
Q psy7757         112 ADYGFTKLIDLLEAIPHVVQVIM  134 (143)
Q Consensus       112 sdYGftKL~dLleaIp~vVqIlg  134 (143)
                      -+|||.||.+|+++++ ..++-.
T Consensus        46 RnYGy~kLs~Li~~~~-~fe~~~   67 (92)
T 2kzv_A           46 RNWGHGRLSQMVKKLD-FLTVQE   67 (92)
T ss_dssp             TTTCSSHHHHHHHTCT-TEEEEE
T ss_pred             cccCcccHHHHHHhcC-cEEEEE
Confidence            4799999999999965 566643

>2kpm_A Uncharacterized protein; methods development, structural genomics, PSI-2, protein structure initiative; NMR {Nitrosomonas europaea}

Probab=83.62  E-value=0.45  Score=34.52  Aligned_cols=22  Identities=32%  Similarity=0.460  Sum_probs=17.2

Q ss_pred             cccchhhHHHHHhhccceeeee
Q psy7757         112 ADYGFTKLIDLLEAIPHVVQVI  133 (143)
Q Consensus       112 sdYGftKL~dLleaIp~vVqIl  133 (143)
                      =.|||.||.+|+++..+..+|.
T Consensus        59 RnYGy~kLs~Li~a~~~~FEi~   80 (105)
T 2kpm_A           59 RLYGYKKLSDLVKARTDLFVTE   80 (105)
T ss_dssp             GGTTCSSHHHHHHHCTTTEEEE
T ss_pred             cccCcccHHHHHHhhCCcEEEE
Confidence            4799999999999944456654

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00