Citrus Sinensis ID: 012298

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460------
Protein Sequence
MAKRPDPDDDDDFSELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTDFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERVAARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGDQRGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHPVSHNASHFHQRICRQDKVVEDRVREDVQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDIERRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRESYMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTNSEYAGTSYPMDSRGRYPNPMETYPSRAHDTHGGFQRQRREEFGKAYNRY
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHcccccccccccHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccccccEEEEccccccHHHccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHHHHHHcccccccccccccccccHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccEEEEccEEEEEccccEEEEEHHHHHEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
makrpdpdddddfselykeytgppgsmvatSQEKAKANkrslagsdeeeeprdpnavptdftsREAKVWEAKSKATERNWKKRKEEEMICKIcgesghftqgcpstlganrkSQDFFERVAARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKeegdqrgtssshksksrspeqspvgtqlrrsesqrshpvshnashfhQRICRQDKVVEDRVREDvqkfsrgspqaraygsdgargrsshskspgrppyasnlhnsydghnqsmggyrndgwdierrgsdmqsghqfeypafpktlDELELDYTREAMELgrirdkeedeeNYKHRETIREMRESYMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQmsasgfggykqhnyssydgsstnseyagtsypmdsrgrypnpmetypsrahdthggfqRQRREEFGKAYNRY
Flexible Loop (DISEMBL)
makrpdpdddddfsELYKEytgppgsmvatsqeKAKANKRslagsdeeeeprdpnavptdftsreakvweakskaternwkkrkeEEMICKICGESGHFTQGCPSTLGANRKSQDFFERVAARDKHVRALFTEKVIQRiekdisckikmdekfiivsgkdrlilsKGVDAVHKIIkeegdqrgtssshksksrspeqspvgtqLRRSESQrshpvshnashfhqricrQDKVVEDRVREdvqkfsrgspqaraygsdgargrsshskspgrppyaSNLHNSYDGHNQSMGGYRNDGWDIERRGSDMQSGHQFEYPAFPKTLDELELDYTREAMelgrirdkeedeenykhretirEMRESYMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTNSEYAGTSYPMDSRGRYPNPMETYPsrahdthggfqrqrREEFGKAYNRY
Low Complexity Region (SEG)
MAKRpdpdddddFSELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTDFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERVAARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGDQRGTssshksksrsPEQSPVGTQLRRSESQRSHPVSHNASHFHQRICrqdkvvedrvredvqkFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDIERRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRESYMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTNSEYAGTSYPMDSRGRYPNPMETYPSRAHDTHGGFQRQRREEFGKAYNRY
Disordered region (IsUnstruct)
***************************************************************************************MICKICGESGHFTQGCPSTLGANRKSQDFFERVAARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKII******************************************************************************************************************************************************************************************************KQWEEFL**************************************************************************************
Disordered Region (DISOPRED)
******P***DDFSELYKEYT*************************************TDFTSREAKV****************EEEMICKICGESGHFTQGCP****************AARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSK*****************************************************************************************************************************************************AFPKTLDELELDYTREAMELG***************ETIREMRESYMKKLTQVRAMHAKQWEEFL***********************************************************************************N**
Disordered Region (DISEMBL)
************FSELYKEYTGPPG******************************AVPTDFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERVAARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEE**********************************************RICRQDKVVEDRVREDVQ******************************PYASNLHNSYDGHNQSMGGYRNDGWDIERRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRESYMKKLTQVRAMHAKQWEEFLQL**************ASGFGGYKQHNYSSYDGSSTNSEYAGTSYPMDSRGRYPNPMETYPSRA***********REEFGKAYNRY
Disordered Region (DISPRO)
******PDDDDDFSELYKEYTGP*******************************NAVPTDFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLG**RKSQDFFERVAARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEE***********************************************************************************************YASNLHNSYDGHNQSMGGYRNDGWDIERRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRESYMKKLTQVRAMHAKQWEEFLQLDGQRHQHQ*******S*******H***SYDGSSTNSEY*GTSYPMDSRGRYPNPMETYPSRAHDTHGGFQRQRREEFGKAYNRY
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAKRPDPDDDDDFSELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTDFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERVAARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGDQRGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHPVSHNASHFHQRICRQDKVVEDRVREDVQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDIERRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRESYMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTNSEYAGTSYPMDSRGRYPNPMETYPSRAHDTHGGFQRQRREEFGKAYNRY
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

No hits with e-value below 0.001 by BLAST

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	466
359480183	466	PREDICTED: uncharacterized protein LOC10	0.997	0.997	0.770	0.0
297744003	502	unnamed protein product [Vitis vinifera]	0.993	0.922	0.766	0.0
255548385	467	nucleic acid binding protein, putative [	0.997	0.995	0.758	0.0
224064613	461	predicted protein [Populus trichocarpa]	0.989	1.0	0.729	0.0
224130956	464	predicted protein [Populus trichocarpa]	0.993	0.997	0.721	0.0
356572809	463	PREDICTED: uncharacterized protein LOC10	0.991	0.997	0.698	0.0
356505641	463	PREDICTED: uncharacterized protein LOC10	0.991	0.997	0.700	0.0
449528260	467	PREDICTED: uncharacterized LOC101215062	1.0	0.997	0.702	0.0
449460523	467	PREDICTED: uncharacterized protein LOC10	1.0	0.997	0.700	0.0
297838221	478	predicted protein [Arabidopsis lyrata su	0.989	0.964	0.641	1e-149

>gi|359480183|ref|XP_002278072.2| PREDICTED: uncharacterized protein LOC100258835 [Vitis vinifera]

 Score =  758 bits (1957), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/467 (77%), Positives = 411/467 (88%), Gaps = 2/467 (0%)

Query: 1   MAKRPDPDDDDDFSELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTD 60
           MAKRP+PDDDD FSE+YKEYTGPP S  +  Q+KAK +KRS A SDEEEEPRDPNAVPTD
Sbjct: 1   MAKRPEPDDDD-FSEIYKEYTGPPRSTTSNVQDKAKTSKRSHASSDEEEEPRDPNAVPTD 59

Query: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 120
           FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV
Sbjct: 60  FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 119

Query: 121 AARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGD 180
            AR+KHV+ALFTEKVI +IEKDI CKIKM+EKFIIVSGKDRLIL+KG+DAVHK+IKEEG+
Sbjct: 120 PAREKHVKALFTEKVIHKIEKDIGCKIKMEEKFIIVSGKDRLILAKGIDAVHKVIKEEGN 179

Query: 181 QRGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHPVSHNASHFHQRICRQDKVVEDRVRED 240
           ++ +S+SH ++SRSPE+SPVG +  RSESQ+SHP   N + F QR  RQ++VVEDR+R+D
Sbjct: 180 KKASSTSHMNRSRSPERSPVGPRFGRSESQKSHPSPQNIAQFQQRFGRQERVVEDRIRDD 239

Query: 241 VQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDIE 300
           +QK SRGSPQARAYG+DGARGRSSHSKSP +PPY  + +NSYDGHNQS+G YRNDGWD E
Sbjct: 240 MQKLSRGSPQARAYGNDGARGRSSHSKSPAQPPYTGSSYNSYDGHNQSVGVYRNDGWDTE 299

Query: 301 RRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRES 360
           RRGSDMQSG +FEYPA P+TL+ELEL+Y REAM+LGRIRDKEEDEENYKHRE +REMRE+
Sbjct: 300 RRGSDMQSGRKFEYPAAPQTLEELELEYKREAMDLGRIRDKEEDEENYKHREAVREMREN 359

Query: 361 YMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTNSEY 420
           YMKKL  +R  HAKQWEEFLQLD +R   +AR+QMS+SGFGGYKQ +YS YDGSS N  Y
Sbjct: 360 YMKKLAILRGTHAKQWEEFLQLDAERQHQRARQQMSSSGFGGYKQASYSDYDGSSANPHY 419

Query: 421 AGTSYPMDSRGRYPNPMETY-PSRAHDTHGGFQRQRREEFGKAYNRY 466
           AG + PMDSRGRYPNP+E Y PSR HDT+  FQRQRRE+FGKAY+RY
Sbjct: 420 AGANIPMDSRGRYPNPVENYPPSRPHDTYSEFQRQRREDFGKAYHRY 466

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297744003|emb|CBI36973.3| unnamed protein product [Vitis vinifera]

 Score =  748 bits (1931), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/467 (76%), Positives = 409/467 (87%), Gaps = 4/467 (0%)

Query: 1   MAKRPDPDDDDDFSELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTD 60
           MAKRP+PDDDD FSE+YKEYTGPP S  +  Q+KAK +KRS A SDEEEEPRDPNAVPTD
Sbjct: 39  MAKRPEPDDDD-FSEIYKEYTGPPRSTTSNVQDKAKTSKRSHASSDEEEEPRDPNAVPTD 97

Query: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 120
           FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV
Sbjct: 98  FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 157

Query: 121 AARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGD 180
            AR+KHV+ALFTEKVI +IEKDI CKIKM+EKFIIVSGKDRLIL+KG+DAVHK+IKEEG+
Sbjct: 158 PAREKHVKALFTEKVIHKIEKDIGCKIKMEEKFIIVSGKDRLILAKGIDAVHKVIKEEGN 217

Query: 181 QRGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHPVSHNASHFHQRICRQDKVVEDRVRED 240
           ++ +S+SH ++SRSPE+SPVG +  RSESQ+SHP   N + F QR  RQ++VVEDR+R+D
Sbjct: 218 KKASSTSHMNRSRSPERSPVGPRFGRSESQKSHPSPQNIAQFQQRFGRQERVVEDRIRDD 277

Query: 241 VQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDIE 300
           +QK SRGSPQ  AYG+DGARGRSSHSKSP +PPY  + +NSYDGHNQS+G YRNDGWD E
Sbjct: 278 MQKLSRGSPQ--AYGNDGARGRSSHSKSPAQPPYTGSSYNSYDGHNQSVGVYRNDGWDTE 335

Query: 301 RRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRES 360
           RRGSDMQSG +FEYPA P+TL+ELEL+Y REAM+LGRIRDKEEDEENYKHRE +REMRE+
Sbjct: 336 RRGSDMQSGRKFEYPAAPQTLEELELEYKREAMDLGRIRDKEEDEENYKHREAVREMREN 395

Query: 361 YMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTNSEY 420
           YMKKL  +R  HAKQWEEFLQLD +R   +AR+QMS+SGFGGYKQ +YS YDGSS N  Y
Sbjct: 396 YMKKLAILRGTHAKQWEEFLQLDAERQHQRARQQMSSSGFGGYKQASYSDYDGSSANPHY 455

Query: 421 AGTSYPMDSRGRYPNPMETY-PSRAHDTHGGFQRQRREEFGKAYNRY 466
           AG + PMDSRGRYPNP+E Y PSR HDT+  FQRQRRE+FGKAY+RY
Sbjct: 456 AGANIPMDSRGRYPNPVENYPPSRPHDTYSEFQRQRREDFGKAYHRY 502

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255548385|ref|XP_002515249.1| nucleic acid binding protein, putative [Ricinus communis] gi|223545729|gb|EEF47233.1| nucleic acid binding protein, putative [Ricinus communis]

 Score =  680 bits (1755), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 355/468 (75%), Positives = 405/468 (86%), Gaps = 3/468 (0%)

Query: 1   MAKRPDPDDDDDFSELYKEYTGPPGSMVAT-SQEKAKANKRSLAGSDEEEEPRDPNAVPT 59
           MA RPD DDDDDFS++YKEYTGPPGS  A  +Q+++KANKRS AGSDEE+EPRDPNAVPT
Sbjct: 1   MATRPDIDDDDDFSQIYKEYTGPPGSSTANNTQDRSKANKRSHAGSDEEDEPRDPNAVPT 60

Query: 60  DFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFER 119
           DFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFER
Sbjct: 61  DFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFER 120

Query: 120 VAARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEG 179
           V AR+KHV+ALFTEKVIQRIEKDI CK+KM+EKF+IVSGKDRLIL+KGVDAVHK+IK +G
Sbjct: 121 VPAREKHVKALFTEKVIQRIEKDIGCKLKMEEKFLIVSGKDRLILAKGVDAVHKVIKGDG 180

Query: 180 DQRGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHP-VSHNASHFHQRICRQDKVVEDRVR 238
           D +G+SSSH+S+SRSPE+SPVG++LRRSESQRS+     + S + QR  RQDK++EDRVR
Sbjct: 181 DHKGSSSSHRSRSRSPERSPVGSRLRRSESQRSYTGQPRDTSQYQQRFGRQDKILEDRVR 240

Query: 239 EDVQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWD 298
           ED+QKFSRGSPQARAYG+DG R RSSHSKSP  PPYASN + SYDGH+ ++ GYRNDGWD
Sbjct: 241 EDLQKFSRGSPQARAYGNDGGRSRSSHSKSPAHPPYASNSYGSYDGHSHTV-GYRNDGWD 299

Query: 299 IERRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMR 358
            ER+G D+QSG QFEY  FP+TL+ELEL++ REAMELGRIRDK+EDEEN KHRE +REMR
Sbjct: 300 TERQGPDLQSGRQFEYATFPQTLEELELEFNREAMELGRIRDKDEDEENIKHREIVREMR 359

Query: 359 ESYMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTNS 418
           E+YMKKL  +R  HA+QWEEFLQLD QR Q QAR+QM ASGF GYKQ  YS YD SS N 
Sbjct: 360 ENYMKKLAILRGTHARQWEEFLQLDAQRRQQQARQQMPASGFSGYKQPTYSDYDSSSANP 419

Query: 419 EYAGTSYPMDSRGRYPNPMETYPSRAHDTHGGFQRQRREEFGKAYNRY 466
            Y+G   PM+SR RY N +E YPSR HD +G FQRQRRE+FGKAYNRY
Sbjct: 420 HYSGAGLPMESRTRYSNHVENYPSRPHDNYGEFQRQRREDFGKAYNRY 467

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224064613|ref|XP_002301525.1| predicted protein [Populus trichocarpa] gi|222843251|gb|EEE80798.1| predicted protein [Populus trichocarpa]

 Score =  662 bits (1707), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 340/466 (72%), Positives = 385/466 (82%), Gaps = 5/466 (1%)

Query: 1   MAKRPDPDDDDDFSELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTD 60
           MA RP+PD DDDFSE+YKEYTGPP S V+ + ++ K NKRS   SDEEEE  DPNAVPTD
Sbjct: 1   MATRPNPDIDDDFSEIYKEYTGPPSSTVSNAHDREKVNKRSHVDSDEEEETPDPNAVPTD 60

Query: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 120
           FTSREAK WEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV
Sbjct: 61  FTSREAKFWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 120

Query: 121 AARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGD 180
           AARDKH++ALFTEKVIQRIEKD  CKIKM+EKFIIVSGKDRLIL+KGVDAVHK+IK EGD
Sbjct: 121 AARDKHIKALFTEKVIQRIEKDNGCKIKMEEKFIIVSGKDRLILAKGVDAVHKVIKGEGD 180

Query: 181 QRGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHPVSHNASHFHQRICRQDKVVEDRVRED 240
           Q+G+SSSHKS+SRSPE+SPVG++LRRS+SQR HP  H+   +HQR  RQDK++ED  R D
Sbjct: 181 QKGSSSSHKSRSRSPERSPVGSRLRRSDSQRGHP--HDTPQYHQRFGRQDKIMEDH-RGD 237

Query: 241 VQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDIE 300
           + KF+RGSPQ  AYG+DG R  SSHSKSP RP YA N + S+DGH+ S  G+R  GWD E
Sbjct: 238 LHKFARGSPQ--AYGNDGGRSHSSHSKSPARPLYAGNSYGSHDGHSHSTAGFRTTGWDTE 295

Query: 301 RRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRES 360
           RRGSD+QSGH+FEY  FP+TL+ELEL++ REAMEL RI DKEED+ENYKHRETIRE+ E+
Sbjct: 296 RRGSDLQSGHRFEYSTFPQTLEELELEHKREAMELARICDKEEDDENYKHRETIREIGEN 355

Query: 361 YMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTNSEY 420
           YM+KL  +R+ H +QWEEFLQ D Q HQ Q R+  S SGFGGYKQH+YS YD SS    Y
Sbjct: 356 YMQKLAILRSAHTRQWEEFLQQDAQMHQQQPRQPTSVSGFGGYKQHSYSEYDASSATPHY 415

Query: 421 AGTSYPMDSRGRYPNPMETYPSRAHDTHGGFQRQRREEFGKAYNRY 466
           AGTS  MDSR RY N ME Y SR HDT+G FQ  RRE FGKAYNRY
Sbjct: 416 AGTSLTMDSRPRYSNNMENYSSRPHDTYGEFQHPRREAFGKAYNRY 461

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130956|ref|XP_002320966.1| predicted protein [Populus trichocarpa] gi|222861739|gb|EEE99281.1| predicted protein [Populus trichocarpa]

 Score =  661 bits (1705), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 337/467 (72%), Positives = 383/467 (82%), Gaps = 4/467 (0%)

Query: 1   MAKRPDPDDDDDFSELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTD 60
           MA RPDPD DDDFSE+YKEYTGPPGS V ++ + AK NKRS   SDEEEE  DPNAVPTD
Sbjct: 1   MATRPDPDIDDDFSEIYKEYTGPPGSTVNSAHDMAKINKRSHVDSDEEEETPDPNAVPTD 60

Query: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 120
           FTSREAK WEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV
Sbjct: 61  FTSREAKFWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 120

Query: 121 AARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGD 180
           AARDKH++ALFTEKVIQ IEKDI CKIK++EKFIIVSGKDRLIL+KGVDAVHK+IK EGD
Sbjct: 121 AARDKHIKALFTEKVIQGIEKDICCKIKIEEKFIIVSGKDRLILAKGVDAVHKVIKGEGD 180

Query: 181 QRGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHPV-SHNASHFHQRICRQDKVVEDRVRE 239
           Q+G+SSSHKS+SRSPE+SPVG++L  S+SQRS+P   H+ S + QR  RQDK+  DR RE
Sbjct: 181 QKGSSSSHKSRSRSPERSPVGSRLLHSDSQRSYPGHPHDTSRYQQRFGRQDKIKGDR-RE 239

Query: 240 DVQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDI 299
           D+ KFSRGSPQ  AYG+DG R  SS SKSP RP YA N + S+DGH  S  GYR  G DI
Sbjct: 240 DLNKFSRGSPQ--AYGNDGGRSHSSRSKSPARPLYAGNSYGSHDGHGHSTAGYRTAGRDI 297

Query: 300 ERRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRE 359
           ER+GSD+QSGHQF+Y  FP+ L+ELEL+Y R+AMEL RIRDKEEDEENYKHRETIRE+ E
Sbjct: 298 ERQGSDLQSGHQFDYSTFPQMLEELELEYKRDAMELSRIRDKEEDEENYKHRETIREIGE 357

Query: 360 SYMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTNSE 419
           +Y+++L  +R  H +QWEEFL+ + Q HQ Q R+ +S SGFGG+KQH+YS YDGSS N  
Sbjct: 358 NYVQRLAILRGTHTRQWEEFLECNAQMHQQQPRQPISVSGFGGHKQHSYSEYDGSSANPY 417

Query: 420 YAGTSYPMDSRGRYPNPMETYPSRAHDTHGGFQRQRREEFGKAYNRY 466
           YAG S  MDSR R  N ME Y SR HDT+  FQ QRRE FGKAYNRY
Sbjct: 418 YAGNSLHMDSRARCSNDMENYSSRPHDTYDEFQHQRREAFGKAYNRY 464

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572809|ref|XP_003554558.1| PREDICTED: uncharacterized protein LOC100816979 [Glycine max]

 Score =  656 bits (1693), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 326/467 (69%), Positives = 379/467 (81%), Gaps = 5/467 (1%)

Query: 1   MAKRPDPDDDDDFSELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTD 60
           MA RPDPD DDDF ELYKEYTGP G+     QE+AK+NKRS AGSDEEEE RDPNAVPTD
Sbjct: 1   MANRPDPDIDDDFRELYKEYTGPLGTATTNMQERAKSNKRSNAGSDEEEEARDPNAVPTD 60

Query: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 120
           FTSREAKVWEAKSKATERNWKKRKEEEMICK+CGESGHFTQGCPSTLGANRKSQDFFER+
Sbjct: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKLCGESGHFTQGCPSTLGANRKSQDFFERI 120

Query: 121 AARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGD 180
            ARDK+VRALFTEKV+ +IEKD+ CKIKMDEKFIIVSGKDRLIL+KGVDAVHKI +EEGD
Sbjct: 121 PARDKNVRALFTEKVLSKIEKDVGCKIKMDEKFIIVSGKDRLILAKGVDAVHKI-REEGD 179

Query: 181 QRGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHPVSHNASHFHQRICRQDKVVEDRVRED 240
           QRG+SSS  ++SRSPE+SPV  + +RSE QRSH    N S F QR  RQ++ VEDR+R+D
Sbjct: 180 QRGSSSSQMTQSRSPERSPVSARFQRSEPQRSHSGPRNTSQFQQRFGRQERAVEDRIRDD 239

Query: 241 VQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDIE 300
           VQKFSRGSPQARAYG+ GARGRSS S+SP   PY  N +NS+D  NQ+MG YRN+GWD  
Sbjct: 240 VQKFSRGSPQARAYGNSGARGRSSQSRSPRHAPYTGNSYNSFDDRNQNMGAYRNEGWDSH 299

Query: 301 RRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRES 360
           RR S +Q GHQF+Y A P+TL+ELEL+Y  EA EL +IRD+EEDEEN+KHRE IR++RE 
Sbjct: 300 RRESGIQPGHQFDYNASPQTLEELELEYKNEATELMKIRDREEDEENFKHREAIRDLREK 359

Query: 361 YMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTN-SE 419
           YM K++ VR  HAKQ EEFLQLD QR + Q  +QMS SG+ G+KQ ++  YDGS+ N   
Sbjct: 360 YMSKVSLVRVTHAKQLEEFLQLDAQRRRQQVGQQMS-SGYRGFKQQSFPEYDGSTANPPT 418

Query: 420 YAGTSYPMDSRGRYPNPMETYPSRAHDTHGGFQRQRREEFGKAYNRY 466
           YAG++ P++SR R+   METYP+R HD  G F   RR +F KAYNRY
Sbjct: 419 YAGSNIPLESRNRFSGNMETYPNRPHDNFGEF--HRRGDFAKAYNRY 463

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505641|ref|XP_003521598.1| PREDICTED: uncharacterized protein LOC100806099 [Glycine max]

 Score =  654 bits (1686), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 327/467 (70%), Positives = 381/467 (81%), Gaps = 5/467 (1%)

Query: 1   MAKRPDPDDDDDFSELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTD 60
           MA R DPD DDDF ELYKEYTGP GS    +QE+AK+NKRS AGSDEEEE RDPNAVPTD
Sbjct: 1   MANRSDPDIDDDFLELYKEYTGPLGSATTNTQERAKSNKRSNAGSDEEEEARDPNAVPTD 60

Query: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 120
           FTSREAKVWEAKSKATERNWKKRKEEEMICK+CGESGHFTQGCPSTLGANRKSQDFFER+
Sbjct: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKLCGESGHFTQGCPSTLGANRKSQDFFERI 120

Query: 121 AARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGD 180
            ARDK+VRALFTEKV+ +IEKD+ CKIKMDEKFIIVSGKDRLIL+KGVD+VHKI +EEGD
Sbjct: 121 PARDKNVRALFTEKVLSKIEKDVGCKIKMDEKFIIVSGKDRLILAKGVDSVHKI-REEGD 179

Query: 181 QRGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHPVSHNASHFHQRICRQDKVVEDRVRED 240
           QRGTSSS  ++SRSPE+SPV  + +RSE QRSH    N S F QR  RQ++ VEDR+R+D
Sbjct: 180 QRGTSSSQMTRSRSPERSPVSARFQRSEPQRSHSGPRNTSQFQQRFGRQERAVEDRIRDD 239

Query: 241 VQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDIE 300
           VQKFSRGSPQARAYG+ GARGRSS S+SP   PY  N +NS++G NQ+MG YRNDGWD  
Sbjct: 240 VQKFSRGSPQARAYGNSGARGRSSQSRSPRHAPYTGNSYNSFEGRNQNMGAYRNDGWDSH 299

Query: 301 RRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRES 360
           RR S ++ GHQF+Y A P+TL+ELEL+Y  EA EL +IRD+EEDEEN+KHRE IR++RE 
Sbjct: 300 RRESGIRPGHQFDYSASPQTLEELELEYKNEAAELMKIRDREEDEENFKHREAIRDLREK 359

Query: 361 YMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTN-SE 419
           YM K++ VR  HAKQWE FLQLD QR Q QA +QM  SG+ G+KQ ++  YDGS+ N   
Sbjct: 360 YMSKVSLVRDTHAKQWEGFLQLDAQRRQQQAVQQM-PSGYRGFKQQSFPEYDGSTANPPP 418

Query: 420 YAGTSYPMDSRGRYPNPMETYPSRAHDTHGGFQRQRREEFGKAYNRY 466
           YAG++ P++SR R+ + METYP+R HD  G F   RR +F KAYNRY
Sbjct: 419 YAGSNLPLESRNRFSDNMETYPNRPHDNFGEF--HRRGDFAKAYNRY 463

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449528260|ref|XP_004171123.1| PREDICTED: uncharacterized LOC101215062 [Cucumis sativus]

 Score =  651 bits (1679), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 328/467 (70%), Positives = 379/467 (81%), Gaps = 1/467 (0%)

Query: 1   MAKRPDPDDDDDFSELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTD 60
           MA  PD D DDDFSELYKEYTGPP S     QEK   NKRS AGSDEE+EPRDPNAVPTD
Sbjct: 1   MANSPDVDADDDFSELYKEYTGPPRSTTVVPQEKTNTNKRSHAGSDEEDEPRDPNAVPTD 60

Query: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 120
           FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLG++RKSQDFFERV
Sbjct: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGSSRKSQDFFERV 120

Query: 121 AARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGD 180
            ARDKHVRA+FT++VIQ+IEKD+ CKIKMDEKFIIVSGKDRLIL KG+DAV+K+IKE+GD
Sbjct: 121 PARDKHVRAIFTDRVIQKIEKDVGCKIKMDEKFIIVSGKDRLILLKGLDAVNKLIKEDGD 180

Query: 181 QRGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHPVSHNASHFHQRICRQDKVVEDRVRED 240
           Q+G+SSSH S+SRSP++SP G++ +RS+  RSH    NAS F  R  RQ+KVVE+R R+D
Sbjct: 181 QKGSSSSHMSRSRSPDRSPAGSRSQRSDVHRSHSGPTNASQFQPRFSRQEKVVENRARDD 240

Query: 241 VQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDIE 300
           +QK+ R S QAR YG+D  RGRSSHSKSP  PPY+ +   SYD +       R +GWD E
Sbjct: 241 LQKYPRSSVQARTYGNDRVRGRSSHSKSPAHPPYSGSSFGSYDSYQNKNAYGRTEGWDNE 300

Query: 301 RRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRES 360
           RRGSD+QS  QFEYPAFP++L+ELE++Y REA ELG+IRDKEEDEENYK+RETIREMRES
Sbjct: 301 RRGSDLQSSRQFEYPAFPQSLEELEIEYKREATELGKIRDKEEDEENYKNRETIREMRES 360

Query: 361 YMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTNSEY 420
           Y KKLT +R  HAKQW+EFLQLD QR Q Q  +QM+ASGFGGYKQHNYS Y+G S N+ Y
Sbjct: 361 YTKKLTHLRGTHAKQWDEFLQLDAQRRQQQVHQQMAASGFGGYKQHNYSEYEGGSVNAHY 420

Query: 421 AGTSY-PMDSRGRYPNPMETYPSRAHDTHGGFQRQRREEFGKAYNRY 466
            G +   +DSR +Y N ME YPSR H   G FQRQRR+++  AY RY
Sbjct: 421 EGANLAALDSRSKYQNHMENYPSRPHGNFGEFQRQRRDDYENAYKRY 467

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460523|ref|XP_004147995.1| PREDICTED: uncharacterized protein LOC101215062 [Cucumis sativus]

 Score =  647 bits (1670), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 327/467 (70%), Positives = 378/467 (80%), Gaps = 1/467 (0%)

Query: 1   MAKRPDPDDDDDFSELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTD 60
           MA  PD D DDDFSELYKEYTGPP S     QEK   NKRS AGSDEE+EPRDPNAVPTD
Sbjct: 1   MANSPDVDADDDFSELYKEYTGPPRSTTVVPQEKTNTNKRSHAGSDEEDEPRDPNAVPTD 60

Query: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERV 120
           FTSREAKVWEAKSKATERNWKKRKEEEMICK CGESGHFTQGCPSTLG++RKSQDFFERV
Sbjct: 61  FTSREAKVWEAKSKATERNWKKRKEEEMICKRCGESGHFTQGCPSTLGSSRKSQDFFERV 120

Query: 121 AARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGD 180
            ARDKHVRA+FT++VIQ+IEKD+ CKIKMDEKFIIVSGKDRLIL KG+DAV+K+IKE+GD
Sbjct: 121 PARDKHVRAIFTDRVIQKIEKDVGCKIKMDEKFIIVSGKDRLILLKGLDAVNKLIKEDGD 180

Query: 181 QRGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHPVSHNASHFHQRICRQDKVVEDRVRED 240
           Q+G+SSSH S+SRSP++SP G++ +RS+  RSH    NAS F  R  RQ+KVVE+R R+D
Sbjct: 181 QKGSSSSHMSRSRSPDRSPAGSRSQRSDVHRSHSGPTNASQFQPRFSRQEKVVENRARDD 240

Query: 241 VQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDIE 300
           +QK+ R S QAR YG+D  RGRSSHSKSP  PPY+ +   SYD +       R +GWD E
Sbjct: 241 LQKYPRSSVQARTYGNDRVRGRSSHSKSPAHPPYSGSSFGSYDSYQNKNAYGRTEGWDNE 300

Query: 301 RRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRES 360
           RRGSD+QS  QFEYPAFP++L+ELE++Y REA ELG+IRDKEEDEENYK+RETIREMRES
Sbjct: 301 RRGSDLQSSRQFEYPAFPQSLEELEIEYKREATELGKIRDKEEDEENYKNRETIREMRES 360

Query: 361 YMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHNYSSYDGSSTNSEY 420
           Y KKLT +R  HAKQW+EFLQLD QR Q Q  +QM+ASGFGGYKQHNYS Y+G S N+ Y
Sbjct: 361 YTKKLTHLRGTHAKQWDEFLQLDAQRRQQQVHQQMAASGFGGYKQHNYSEYEGGSVNAHY 420

Query: 421 AGTSY-PMDSRGRYPNPMETYPSRAHDTHGGFQRQRREEFGKAYNRY 466
            G +   +DSR +Y N ME YPSR H   G FQRQRR+++  AY RY
Sbjct: 421 EGANLAALDSRSKYQNHMENYPSRPHGNFGEFQRQRRDDYENAYKRY 467

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297838221|ref|XP_002886992.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297332833|gb|EFH63251.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  534 bits (1376), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 308/480 (64%), Positives = 363/480 (75%), Gaps = 19/480 (3%)

Query: 2   AKRPDPDDDDDFSELYKEYTGPPGSMVA-TSQEKAKANK-RSLAGSDEEEEPRDPNAVPT 59
           + R DP+ DDDFSE+YKEYTGP  ++   T Q+K K  K RS    DEEE+  DPN+VPT
Sbjct: 3   STRSDPELDDDFSEIYKEYTGPASTVTNNTIQDKDKPIKQRSEERCDEEEQLPDPNSVPT 62

Query: 60  DFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFER 119
           DFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQ+FFER
Sbjct: 63  DFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQEFFER 122

Query: 120 VAARDKHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEG 179
           V ARD +VR LFTE+VI+ IE++  CKIKMDEKFIIVSGKDRLIL KGVDAVHK +KE+G
Sbjct: 123 VPARDNNVRVLFTEQVIESIERETGCKIKMDEKFIIVSGKDRLILRKGVDAVHK-VKEDG 181

Query: 180 DQRGTSSSHKSKSRSPEQSPVG-TQLRRSESQRSHPVSHNASHFHQRICRQDKVV----- 233
           + + +S SH+S+SRSP ++ VG  + R SE QR HP SH +S F +R  RQDK V     
Sbjct: 182 EMKSSSVSHRSRSRSPRRTSVGPPRARNSEPQRQHPPSHGSSSFPERSGRQDKFVDNRVR 241

Query: 234 -EDRVREDVQKFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGY 292
            E+R+RE+ +  SRGSPQ  AYGSD AR RS+HSKSPGRP Y S     YD     + GY
Sbjct: 242 EENRIRENQRNVSRGSPQ--AYGSDRARSRSTHSKSPGRPRY-SGWDKPYDRQKSEVSGY 298

Query: 293 RNDGWDIERRG--SDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKH 350
           R++ WD ER G  SD+Q  HQFE P FP+TL+ELEL+YTR+AMEL +  DKEEDEEN KH
Sbjct: 299 RSERWDQERMGGSSDIQVRHQFERPPFPQTLEELELEYTRDAMELEKKCDKEEDEENIKH 358

Query: 351 RETIREMRESYMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQH-NYS 409
           RETIRE+RESYMKKL  +R M+AKQW+EFLQLD QR Q QAR+Q S   +G Y+Q   Y+
Sbjct: 359 RETIRELRESYMKKLAGLRGMNAKQWDEFLQLDAQRRQQQARQQNSGLNYGNYRQFPPYA 418

Query: 410 SYDG--SSTNSEYAGTSYPMDSRGRYPNPMETYPSRAHD-THGGFQRQRREEFGKAYNRY 466
            +D   SS    Y G + PMDS+GRYPN  + Y SR  D  +GGFQRQRRE++GKAYNRY
Sbjct: 419 EFDDGYSSNPPPYGGNNVPMDSKGRYPNHGDNYSSRHQDNNYGGFQRQRREDYGKAYNRY 478

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	466
TAIR|locus:2096004	479	AT3G62330 [Arabidopsis thalian	0.965	0.939	0.604	4.9e-140

TAIR|locus:2096004 AT3G62330 [Arabidopsis thaliana (taxid:3702)]

 Score = 1370 (487.3 bits), Expect = 4.9e-140, P = 4.9e-140
 Identities = 284/470 (60%), Positives = 335/470 (71%)

Query:    13 FSELYKEYTGPPGSMVATS-QEKAKANK-RSLAGSDEEEEPR-DPNAVPTDFTSREAKVW 69
             FSE+YKEYTGP  ++   + Q+K K  K RS    DEEEE   DPN+VPTDFTSREAKVW
Sbjct:    14 FSEIYKEYTGPASAVTNNNIQDKDKPVKQRSEERCDEEEEQLPDPNSVPTDFTSREAKVW 73

Query:    70 EAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQDFFERVAARDKHVRA 129
             EAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQ+FFERV ARD +VR 
Sbjct:    74 EAKSKATERNWKKRKEEEMICKICGESGHFTQGCPSTLGANRKSQEFFERVPARDNNVRV 133

Query:   130 LFTEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIKEEGDQRGTXXXXX 189
             LFTEKV++ IE++ SCKIK+DEKFIIVSGKDRLIL KGVDAVHK+ KE+G+ + +     
Sbjct:   134 LFTEKVMESIERETSCKIKLDEKFIIVSGKDRLILRKGVDAVHKV-KEDGEMKSSSVSHR 192

Query:   190 XXXXXPEQSPVG-TQLRRSESQRSHPVSHNASHFHQR------ICXXXXXXXXXXXXXXX 242
                  P ++ VG ++ R SE QR    SH +S F +R                       
Sbjct:   193 SRSRSPRRTSVGPSRARNSEPQRQQLPSHGSSSFPERSGRQDKFVDNRFREETRVRENQR 252

Query:   243 XFSRGSPQARAYGSDGARGRSSHSKSPGRPPYASNLHNSYDGHNQSMGGYRNDGWDIERR 302
                RGSPQA  YGSD AR RS+HSKSPGRP Y S     YD     + GYR++ WD ER 
Sbjct:   253 NVPRGSPQA--YGSDRARSRSTHSKSPGRPRY-SGWDKPYDRQKPEVSGYRSERWDQERM 309

Query:   303 G--SDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREMRES 360
             G  SD+Q  HQFE P FP+TL+ELEL+YTR+A+EL + RDKEEDEEN KHRETIRE+RES
Sbjct:   310 GGSSDIQVSHQFERPPFPQTLEELELEYTRDALELEKKRDKEEDEENNKHRETIRELRES 369

Query:   361 YMKKLTQVRAMHAKQWEEFLQLDGQRHQHQAREQMSASGFGGYKQHN-YSSYD-GSSTNS 418
             YMKKL  +R M+AKQW++FLQLD QR Q QAR+Q S   +G Y+Q   Y+ +D G S+N 
Sbjct:   370 YMKKLAGLRGMNAKQWDDFLQLDAQRRQQQARQQNSGLSYGNYRQFPPYAEFDDGYSSNP 429

Query:   419 E-YAGTSYPMDSRGRYPNPMETYPSRAHDT-HGGFQRQRREEFGKAYNRY 466
               Y G + PMDS+GRYPN  + Y SR  D  +GGFQRQRREE+GKAYNRY
Sbjct:   430 PPYGGNNMPMDSKGRYPNHGDNYSSRHQDNNYGGFQRQRREEYGKAYNRY 479


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.313   0.129   0.379    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      466       432   0.00086  118 3  11 23  0.46    34
                                                     34  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  613 (65 KB)
  Total size of DFA:  288 KB (2149 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  47.31u 0.19s 47.50t   Elapsed:  00:00:02
  Total cpu time:  47.31u 0.19s 47.50t   Elapsed:  00:00:02
  Start:  Fri May 10 03:33:36 2013   End:  Fri May 10 03:33:38 2013

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion 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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	466
PF13696	32	zf-CCHC_2: Zinc knuckle	94.32
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	93.89
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	93.49
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	86.07
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	85.39
smart00322	69	KH K homology RNA-binding domain.	85.18
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	85.05
PRK13763	180	putative RNA-processing protein; Provisional	84.38
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	83.11
PF13917	42	zf-CCHC_3: Zinc knuckle	82.45
PF13014	43	KH_3: KH domain	80.7
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	80.14

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=94.32  E-value=0.011  Score=42.55  Aligned_cols=20  Identities=40%  Similarity=1.169  Sum_probs=18.5

Q ss_pred             hhhhHhhcCCCCccccCCCC
Q 012298           86 EEMICKICGESGHFTQGCPS  105 (466)
Q Consensus        86 eem~ckicge~ghf~qgcp~  105 (466)
                      +..+|.+|+..|||-+-||.
T Consensus         7 ~~Y~C~~C~~~GH~i~dCP~   26 (32)
T PF13696_consen    7 PGYVCHRCGQKGHWIQDCPT   26 (32)
T ss_pred             CCCEeecCCCCCccHhHCCC
Confidence            45799999999999999998

>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

Probab=93.89  E-value=0.027  Score=49.44  Aligned_cols=46  Identities=22%  Similarity=0.503  Sum_probs=41.8

Q ss_pred             hHHHHHHhhhccccccccccc------------------------eEEeccCc--ceeeecchhhHHHHHHh
Q 012298          132 TEKVIQRIEKDISCKIKMDEK------------------------FIIVSGKD--RLILSKGVDAVHKIIKE  177 (466)
Q Consensus       132 te~vi~~iEkd~gckikm~ek------------------------f~~vsgkD--Rl~l~kgvdaVhk~i~e  177 (466)
                      .+++|.+||+++||+|-+.++                        .|.|++.|  --.|.+++..|..|++.
T Consensus        24 gG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~~   95 (120)
T cd02395          24 RGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLKP   95 (120)
T ss_pred             CChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhcc
Confidence            789999999999999999875                        79999999  89999999999998864

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=93.49  E-value=0.036  Score=34.92  Aligned_cols=17  Identities=47%  Similarity=1.183  Sum_probs=15.6

Q ss_pred             hHhhcCCCCccccCCCC
Q 012298           89 ICKICGESGHFTQGCPS  105 (466)
Q Consensus        89 ~ckicge~ghf~qgcp~  105 (466)
                      +|-.||+.||++.-||.
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            58899999999999995

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

Probab=86.07  E-value=0.34  Score=37.35  Aligned_cols=36  Identities=19%  Similarity=0.500  Sum_probs=27.5

Q ss_pred             hhhhhh--hHHHHHHhhhccccccccccc-eEEeccCcc
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDEK-FIIVSGKDR  161 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~ek-f~~vsgkDR  161 (466)
                      .+..+.  ++.+|..|+..+||+|.+++. .|.|+|.|.
T Consensus        12 ~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~~~   50 (61)
T cd02393          12 KIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDK   50 (61)
T ss_pred             heeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeCCH
Confidence            344444  789999999999999999873 566666654

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=85.39  E-value=0.55  Score=35.07  Aligned_cols=34  Identities=21%  Similarity=0.386  Sum_probs=27.7

Q ss_pred             hhhhhh--hHHHHHHhhhcccccccccc-----ceEEeccC
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDE-----KFIIVSGK  159 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~e-----kf~~vsgk  159 (466)
                      .+..++  .+..|..|++++||+|.+..     .+|.|+|+
T Consensus        10 ~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~   50 (62)
T cd02394          10 LHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP   50 (62)
T ss_pred             HhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC
Confidence            345555  67899999999999999977     57888887

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>smart00322 KH K homology RNA-binding domain

Probab=85.18  E-value=0.52  Score=33.41  Aligned_cols=41  Identities=20%  Similarity=0.390  Sum_probs=30.3

Q ss_pred             hHHHHHHhhhcccccccccc-----ceEEeccCcceeeecchhhHHH
Q 012298          132 TEKVIQRIEKDISCKIKMDE-----KFIIVSGKDRLILSKGVDAVHK  173 (466)
Q Consensus       132 te~vi~~iEkd~gckikm~e-----kf~~vsgkDRl~l~kgvdaVhk  173 (466)
                      .++.|+.|++.+||+|.+..     ..+.|.|. ..-+....+++.+
T Consensus        21 ~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~   66 (69)
T smart00322       21 GGSTIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILE   66 (69)
T ss_pred             CchHHHHHHHHHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHH
Confidence            67899999999999998877     67888887 3444444444443

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=85.05  E-value=0.34  Score=35.96  Aligned_cols=34  Identities=24%  Similarity=0.465  Sum_probs=26.4

Q ss_pred             chhhhhh--hHHHHHHhhhccccccccccc----eEEecc
Q 012298          125 KHVRALF--TEKVIQRIEKDISCKIKMDEK----FIIVSG  158 (466)
Q Consensus       125 k~vr~lf--te~vi~~iEkd~gckikm~ek----f~~vsg  158 (466)
                      ..+..++  .+..|..||+++||+|.+.++    .|.|+|
T Consensus         9 ~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G   48 (60)
T PF00013_consen    9 SLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG   48 (60)
T ss_dssp             HHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE
T ss_pred             HHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe
Confidence            3444555  788999999999999999874    666666

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>PRK13763 putative RNA-processing protein; Provisional

Probab=84.38  E-value=0.69  Score=42.62  Aligned_cols=44  Identities=20%  Similarity=0.222  Sum_probs=38.6

Q ss_pred             hHHHHHHhhhccccccccccceEEeccCcceeeecchhhHHHHHH
Q 012298          132 TEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIK  176 (466)
Q Consensus       132 te~vi~~iEkd~gckikm~ekf~~vsgkDRl~l~kgvdaVhk~i~  176 (466)
                      .+++|..||..+||+|-++++.|.|.| |-.-+....++|..||+
T Consensus       113 ~G~~~k~ie~~t~~~i~i~~~~v~i~G-~~~~~~~A~~~I~~li~  156 (180)
T PRK13763        113 GGKTRRIIEELTGVDISVYGKTVAIIG-DPEQVEIAREAIEMLIE  156 (180)
T ss_pred             CcHHHHHHHHHHCcEEEEcCCEEEEEe-CHHHHHHHHHHHHHHHc
Confidence            678999999999999999999999998 77777777888888883

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=83.11  E-value=0.7  Score=42.19  Aligned_cols=51  Identities=20%  Similarity=0.326  Sum_probs=43.7

Q ss_pred             hhhhhh--hHHHHHHhhhccccccccccc--eEEe--ccCcceeeecchhhHHHHHH
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDEK--FIIV--SGKDRLILSKGVDAVHKIIK  176 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~ek--f~~v--sgkDRl~l~kgvdaVhk~i~  176 (466)
                      .|.++.  ++++|..|++.+||+|.|+++  -|.|  .+.|-..+.|+.+.|..+..
T Consensus         8 kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~   64 (172)
T TIGR03665         8 RIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGR   64 (172)
T ss_pred             HhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence            455555  799999999999999999985  8888  88999999999999988654

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=82.45  E-value=0.38  Score=36.29  Aligned_cols=18  Identities=44%  Similarity=1.224  Sum_probs=16.9

Q ss_pred             hhHhhcCCCCccccCCCC
Q 012298           88 MICKICGESGHFTQGCPS  105 (466)
Q Consensus        88 m~ckicge~ghf~qgcp~  105 (466)
                      -+|.-||+.||+|-=||.
T Consensus         5 ~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    5 VRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CcCcccCCCCcchhhCCC
Confidence            479999999999999997

>PF13014 KH_3: KH domain

Probab=80.70  E-value=1.2  Score=31.67  Aligned_cols=20  Identities=20%  Similarity=0.380  Sum_probs=18.2

Q ss_pred             hHHHHHHhhhcccccccccc
Q 012298          132 TEKVIQRIEKDISCKIKMDE  151 (466)
Q Consensus       132 te~vi~~iEkd~gckikm~e  151 (466)
                      .+.+|..|++++||+|++..
T Consensus         9 ~G~~I~~I~~~tg~~I~i~~   28 (43)
T PF13014_consen    9 GGSTIKEIREETGAKIQIPP   28 (43)
T ss_pred             CChHHHHHHHHhCcEEEECC
Confidence            46889999999999999887

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=80.14  E-value=0.97  Score=41.30  Aligned_cols=44  Identities=20%  Similarity=0.191  Sum_probs=38.2

Q ss_pred             hHHHHHHhhhccccccccccceEEeccCcceeeecchhhHHHHHH
Q 012298          132 TEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIK  176 (466)
Q Consensus       132 te~vi~~iEkd~gckikm~ekf~~vsgkDRl~l~kgvdaVhk~i~  176 (466)
                      .+++|..||..+||+|-+.++.|.|+| +---+.....+|..||+
T Consensus       107 ~G~t~~~ie~~t~~~i~i~~~~v~i~G-~~~~~~~A~~~i~~li~  150 (172)
T TIGR03665       107 GGKTRRIIEELTGVSISVYGKTVGIIG-DPEQVQIAREAIEMLIE  150 (172)
T ss_pred             CcHHHHHHHHHHCCeEEEcCCEEEEEC-CHHHHHHHHHHHHHHHc
Confidence            678999999999999999999999999 66666677778888883

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

---

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	466
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06

>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 = 47.9 bits (113), Expect = 5e-06
 Identities = 50/448 (11%), Positives = 111/448 (24%), Gaps = 125/448 (27%)

Query: 8   DDDDDF--SELYKEYTGPPGSMVATSQEKAKANKRSLAGSDEEEEPRDPNAVPTDFTSRE 65
             +  F  S +  E   P        +++ +                D         SR 
Sbjct: 88  RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY-------------NDNQVFAKYNVSRL 134

Query: 66  AKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGC-PSTLGANRKSQDFFERVAARD 124
               + +         + +  + +  I G       G   + +  +              
Sbjct: 135 QPYLKLRQAL-----LELRPAKNVL-IDG-----VLGSGKTWVALD----------VCLS 173

Query: 125 KHVRALFTEKVIQRIEKDISCKIKMDEKFIIVSGK---DRLILSKGVDAVHKIIKEEGDQ 181
             V+     K+                 F +          +L      +++I     D 
Sbjct: 174 YKVQCKMDFKI-----------------FWLNLKNCNSPETVLEMLQKLLYQI-----DP 211

Query: 182 RGTSSSHKSKSRSPEQSPVGTQLRRSESQRSHP--------VSHN--ASHFHQRICR--- 228
             TS S  S +       +  +LRR    + +         V +    + F+   C+   
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS-CKILL 270

Query: 229 --QDKVVEDRVREDVQKFSRGSPQARAYGSDGARG---RSSHSKSPGRPPYA---SNLHN 280
             + K V D +             +     D  +    +    +    P      +    
Sbjct: 271 TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL 330

Query: 281 SYDGHNQSMGGYRNDGW---DIERRGSDMQSGHQFEYPA-----------FP-------K 319
           S    +   G    D W   + ++  + ++S      PA           FP        
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTI 390

Query: 320 TLDEL--ELDYTREAMELGRIRDK---EEDEENYKHRETIREMRESYMKKLTQVRAMHAK 374
            L  +  ++  +   + + ++      E+  +       I  +      KL    A+H  
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS--IPSIYLELKVKLENEYALHRS 448

Query: 375 -----------QWEEFL--QLDGQRHQH 389
                        ++ +   LD   + H
Sbjct: 449 IVDHYNIPKTFDSDDLIPPYLDQYFYSH 476

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	466
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	95.01
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	94.98
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	94.84
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	94.62
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	94.35
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	94.17
1we8_A	104	Tudor and KH domain containing protein; structural	94.17
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	93.89
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	93.76
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	93.74
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	93.71
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	93.66
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	93.51
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	93.44
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	93.12
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	92.93
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	92.77
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	92.02
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	91.92
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	91.45
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	90.36
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	89.5
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	89.07
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	89.01
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	88.9
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	88.52
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	87.99
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	87.71
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	87.49
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	87.02
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	86.96
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	86.69
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	86.51
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	86.04
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	85.77
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	85.47
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	84.68
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	84.3
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	84.13
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	83.56
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	83.2
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	83.19
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	82.22
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	81.2
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	80.28

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=95.01  E-value=0.0077  Score=51.94  Aligned_cols=46  Identities=24%  Similarity=0.415  Sum_probs=41.0

Q ss_pred             hHHHHHHhhhccccccccccc-----------------------eEEeccCcceeeecchhhHHHHHHh
Q 012298          132 TEKVIQRIEKDISCKIKMDEK-----------------------FIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       132 te~vi~~iEkd~gckikm~ek-----------------------f~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      .+++|.+||+++||||.+.++                       .|.|++.|.-.|.+++.-|++|+++
T Consensus        31 ~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           31 RGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQ   99 (131)
T ss_dssp             SSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHHHHHHHHHHHHTT
T ss_pred             CcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHHHHHHHHHHHHHHhc
Confidence            789999999999999999652                       7889999999999999999999854

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.98  E-value=0.011  Score=50.65  Aligned_cols=51  Identities=12%  Similarity=0.146  Sum_probs=42.7

Q ss_pred             hhhhh--hHHHHHHhhhcccccccccc-----------------ceEEeccCcceeeecchhhHHHHHHh
Q 012298          127 VRALF--TEKVIQRIEKDISCKIKMDE-----------------KFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       127 vr~lf--te~vi~~iEkd~gckikm~e-----------------kf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      |..++  .+++|.+|++++||||-+..                 -.|.|++.|--.|.+++.-|..||.+
T Consensus        30 ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~~Ie~Ll~~   99 (119)
T 2yqr_A           30 KEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKKLCENLLQT   99 (119)
T ss_dssp             HHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             eeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHHHHHHHhhc
Confidence            34444  88999999999999999963                 37889999999999999988888865

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=94.84  E-value=0.014  Score=46.53  Aligned_cols=62  Identities=18%  Similarity=0.323  Sum_probs=48.9

Q ss_pred             HHHhhhcccchhhhhh--hHHHHHHhhhccccccccccc-------eEEeccCcceeeecchhhHHHHHHhh
Q 012298          116 FFERVAARDKHVRALF--TEKVIQRIEKDISCKIKMDEK-------FIIVSGKDRLILSKGVDAVHKIIKEE  178 (466)
Q Consensus       116 ffeRv~ardk~vr~lf--te~vi~~iEkd~gckikm~ek-------f~~vsgkDRl~l~kgvdaVhk~i~e~  178 (466)
                      +.++|.-=...|..+.  .+++|..|++++||+|.+++.       .|.|+|. .--+.++...|..+|.+.
T Consensus        15 ~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~-~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           15 MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT-PESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             EEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEEC-HHHHHHHHHHHHHHHHHT
T ss_pred             EEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHHHhc
Confidence            3445555556777777  689999999999999999984       7888887 667788888899988763

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1

Probab=94.62  E-value=0.0061  Score=48.81  Aligned_cols=64  Identities=11%  Similarity=0.269  Sum_probs=49.7

Q ss_pred             hHHHHhhhcccchhhhhh--hHHHHHHhhhccccccccccc---------eEEeccCcceeeecchhhHHHHHHhh
Q 012298          114 QDFFERVAARDKHVRALF--TEKVIQRIEKDISCKIKMDEK---------FIIVSGKDRLILSKGVDAVHKIIKEE  178 (466)
Q Consensus       114 ~dffeRv~ardk~vr~lf--te~vi~~iEkd~gckikm~ek---------f~~vsgkDRl~l~kgvdaVhk~i~e~  178 (466)
                      ..+.++|.--...|..+.  .+++|..|++++||+|.+++.         .|.|+| +.-.+.+++..|..+|.+.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           13 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG-DPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEE-CTTTHHHHHHHHHHHHCCC
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHHhcc
Confidence            344555555556677776  789999999999999999763         477888 7778888999999988663

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=94.35  E-value=0.011  Score=46.23  Aligned_cols=52  Identities=13%  Similarity=0.285  Sum_probs=41.9

Q ss_pred             chhhhhh--hHHHHHHhhhccccccccccc---------eEEeccCcceeeecchhhHHHHHHh
Q 012298          125 KHVRALF--TEKVIQRIEKDISCKIKMDEK---------FIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       125 k~vr~lf--te~vi~~iEkd~gckikm~ek---------f~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      ..|..+.  .+++|..|++++||+|.+++.         .|.|+| +.-.+.+++..|..+++|
T Consensus        23 ~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           23 GKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG-DPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             TTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEE-CHHHHHHHHHHHHHHHTC
T ss_pred             hheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHhcC
Confidence            5566666  799999999999999999874         277788 777778888888887753

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=94.17  E-value=0.018  Score=46.25  Aligned_cols=55  Identities=22%  Similarity=0.302  Sum_probs=44.9

Q ss_pred             cchhhhhh--hHHHHHHhhhcccccccccc-----ceEEeccCcceeeecchhhHHHHHHhhc
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMDE-----KFIIVSGKDRLILSKGVDAVHKIIKEEG  179 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~e-----kf~~vsgkDRl~l~kgvdaVhk~i~e~~  179 (466)
                      ...++.+.  ++++|..|+.++||+|.+++     ..|.|+|. .--+.++.+.+..++.+..
T Consensus        25 ~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~~~~~V~I~G~-~e~v~~A~~~I~~i~~~~~   86 (94)
T 2cte_A           25 KEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGT-KEGIEKARHEVLLISAEQD   86 (94)
T ss_dssp             TTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEEC-HHHHHHHHHHHHHHHHHHH
T ss_pred             hHHeeeeECCCChhHHHHHHHHCCEEEeCCCCCCCCeEEEEEC-HHHHHHHHHHHHHHhhccc
Confidence            34555665  68999999999999999974     58889998 8888889999999887644

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=94.17  E-value=0.014  Score=47.41  Aligned_cols=54  Identities=20%  Similarity=0.364  Sum_probs=43.5

Q ss_pred             cchhhhhh--hHHHHHHhhhcccccccccc---------ceEEeccCcceeeecchhhHHHHHHhh
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMDE---------KFIIVSGKDRLILSKGVDAVHKIIKEE  178 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~e---------kf~~vsgkDRl~l~kgvdaVhk~i~e~  178 (466)
                      ...|..+.  .+++|..|++++||+|.+++         ..|.|+|.+. -+.+++..|..+|.++
T Consensus        23 ~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~-~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           23 QRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQK-EVAAAKHLILEKVSED   87 (104)
T ss_dssp             TTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHH-HHHHHHHHHHHHHHHH
T ss_pred             hhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHH-HHHHHHHHHHHHHhhC
Confidence            34566666  58999999999999999984         6788889887 4688888888888654

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=93.89  E-value=0.0099  Score=45.45  Aligned_cols=53  Identities=13%  Similarity=0.229  Sum_probs=40.4

Q ss_pred             chhhhhh--hHHHHHHhhhcccccccccc-------ceEEeccCcceeeecchhhHHHHHHhh
Q 012298          125 KHVRALF--TEKVIQRIEKDISCKIKMDE-------KFIIVSGKDRLILSKGVDAVHKIIKEE  178 (466)
Q Consensus       125 k~vr~lf--te~vi~~iEkd~gckikm~e-------kf~~vsgkDRl~l~kgvdaVhk~i~e~  178 (466)
                      ..|..+.  ++++|..|..++||+|.+++       ..|.|+|. .--+.++...|..+|.++
T Consensus        14 ~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A           14 DLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGS-AASISLAQYLINVRLSSE   75 (76)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEEC-HHHHHHHHHHHHHHHTTC
T ss_pred             HHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeC-HHHHHHHHHHHHHHHHcc
Confidence            4566666  68999999999999999985       67778886 555666777777776554

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=93.76  E-value=0.042  Score=44.83  Aligned_cols=55  Identities=15%  Similarity=0.284  Sum_probs=45.9

Q ss_pred             chhhhhh--hHHHHHHhhhcc-ccccccccc-----eEEeccCcceeeecchhhHHHHHHhhcC
Q 012298          125 KHVRALF--TEKVIQRIEKDI-SCKIKMDEK-----FIIVSGKDRLILSKGVDAVHKIIKEEGD  180 (466)
Q Consensus       125 k~vr~lf--te~vi~~iEkd~-gckikm~ek-----f~~vsgkDRl~l~kgvdaVhk~i~e~~~  180 (466)
                      +.++.+.  .+++|..|+.++ ||+|.+++.     -|.|+|++. .+.++.+.+..++.+-..
T Consensus        26 ~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g~~~~~V~I~G~~~-~v~~A~~~I~~iv~e~e~   88 (95)
T 2ctj_A           26 KLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSS-DVEKAKKQLLHLAEEKQT   88 (95)
T ss_dssp             HHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHH-HHHHHHHHHHHHHHHHSC
T ss_pred             HHHhhhCCCCchhHHHHHHHcCCCEEEeCCCCCCcceEEEEcCHH-HHHHHHHHHHHHHhhhhh
Confidence            3455665  789999999999 999999874     799999999 889999999998876443

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=93.74  E-value=0.015  Score=44.07  Aligned_cols=51  Identities=10%  Similarity=0.185  Sum_probs=36.4

Q ss_pred             hhhhhh--hHHHHHHhhhcccccccccc----------ceEEeccCcceeeecchhhHHHHHHh
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDE----------KFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~e----------kf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      .|..+.  .+++|..|++.+||+|.+++          ..|.|+|. .--+.++...|..+|.|
T Consensus        13 ~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A           13 LVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS-PAATQAAQYLISQRVTY   75 (76)
T ss_dssp             THHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEES-HHHHHHHHHHHHHHCC-
T ss_pred             HcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeC-HHHHHHHHHHHHHHHhc
Confidence            455555  58999999999999999986          37777886 44555555566555544

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=93.71  E-value=0.027  Score=44.49  Aligned_cols=55  Identities=16%  Similarity=0.323  Sum_probs=42.9

Q ss_pred             cchhhhhh--hHHHHHHhhhcccccccccc-------ceEEeccCcceeeecchhhHHHHHHhhc
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMDE-------KFIIVSGKDRLILSKGVDAVHKIIKEEG  179 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~e-------kf~~vsgkDRl~l~kgvdaVhk~i~e~~  179 (466)
                      ...|..+.  .+++|..|++++||+|++++       ..|.|+|. .--+.+++..|..+|++..
T Consensus        22 ~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~-~e~v~~A~~~I~~~i~e~~   85 (89)
T 1j5k_A           22 KDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-QDQIQNAQYLLQNSVKQYS   85 (89)
T ss_dssp             HHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEE-HHHHHHHHHHHHHHHHHHC
T ss_pred             hhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHHhhh
Confidence            34566666  68999999999999999987       57778887 5556677778888887653

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1

Probab=93.66  E-value=0.018  Score=44.75  Aligned_cols=54  Identities=13%  Similarity=0.227  Sum_probs=40.2

Q ss_pred             chhhhhh--hHHHHHHhhhcccccccccc-------ceEEeccCcceeeecchhhHHHHHHhhc
Q 012298          125 KHVRALF--TEKVIQRIEKDISCKIKMDE-------KFIIVSGKDRLILSKGVDAVHKIIKEEG  179 (466)
Q Consensus       125 k~vr~lf--te~vi~~iEkd~gckikm~e-------kf~~vsgkDRl~l~kgvdaVhk~i~e~~  179 (466)
                      ..|..+.  .+++|..|.+++||+|.+++       ..|.|+|.. --+.+++..|..+|.++.
T Consensus        15 ~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~-~~v~~A~~~I~~~i~~~~   77 (82)
T 1wvn_A           15 NLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSA-ASISLAQYLINARLSSEK   77 (82)
T ss_dssp             GGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECH-HHHHHHHHHHHHHTC---
T ss_pred             HhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHHhhh
Confidence            4566666  68999999999999999986       377788876 556667777777776653

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=93.51  E-value=0.034  Score=43.25  Aligned_cols=55  Identities=16%  Similarity=0.301  Sum_probs=43.5

Q ss_pred             chhhhhh--hHHHHHHhhhccccccccccc-------eEEeccCcceeeecchhhHHHHHHhhcC
Q 012298          125 KHVRALF--TEKVIQRIEKDISCKIKMDEK-------FIIVSGKDRLILSKGVDAVHKIIKEEGD  180 (466)
Q Consensus       125 k~vr~lf--te~vi~~iEkd~gckikm~ek-------f~~vsgkDRl~l~kgvdaVhk~i~e~~~  180 (466)
                      ..|..+.  .+++|..|+.++||+|.+++.       .|.|+|. .--+.++...|..+|++.++
T Consensus        16 ~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~i~~~~g   79 (82)
T 1zzk_A           16 DLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-QDQIQNAQYLLQNSVKQYSG   79 (82)
T ss_dssp             TTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEEC-HHHHHHHHHHHHHHHHHHHS
T ss_pred             HhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHhccC
Confidence            4566666  689999999999999999874       7888885 56667778888888877654

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=93.44  E-value=0.014  Score=47.94  Aligned_cols=54  Identities=9%  Similarity=0.219  Sum_probs=43.4

Q ss_pred             chhhhhh--hHHHHHHhhhcccccccccc----------ceEEeccCcceeeecchhhHHHHHHhhc
Q 012298          125 KHVRALF--TEKVIQRIEKDISCKIKMDE----------KFIIVSGKDRLILSKGVDAVHKIIKEEG  179 (466)
Q Consensus       125 k~vr~lf--te~vi~~iEkd~gckikm~e----------kf~~vsgkDRl~l~kgvdaVhk~i~e~~  179 (466)
                      ..|..+.  .+++|..|++++||+|++++          ..|.|+| +.-.+.+++..|..+|.+..
T Consensus        16 ~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G-~~e~v~~A~~~I~~~i~e~~   81 (107)
T 2hh2_A           16 HKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRG-SPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             GGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEES-CHHHHHHHHHHHHHHSCSCC
T ss_pred             HHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEEC-CHHHHHHHHHHHHHHHhccc
Confidence            4566666  58999999999999999986          4788888 77777888888888887654

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=93.12  E-value=0.017  Score=44.29  Aligned_cols=52  Identities=15%  Similarity=0.358  Sum_probs=36.7

Q ss_pred             chhhhhh--hHHHHHHhhhccccccccccc-----eEEeccCcceeeecchhhHHHHHHh
Q 012298          125 KHVRALF--TEKVIQRIEKDISCKIKMDEK-----FIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       125 k~vr~lf--te~vi~~iEkd~gckikm~ek-----f~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      ..+..+.  ++++|..|..++||+|.+++.     .|.|+|. .-.+.+++..|..+|.|
T Consensus        14 ~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~~~er~v~I~G~-~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A           14 KEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGP-TNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEEC-HHHHHHHHHHHHHHHHC
T ss_pred             hHeeeEECCCCHHHHHHHHHHCCEEEEecCCCCcEEEEEEeC-HHHHHHHHHHHHHHHhc
Confidence            4455555  789999999999999999986     5666665 44445555556665544

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=92.93  E-value=0.042  Score=45.52  Aligned_cols=54  Identities=13%  Similarity=0.308  Sum_probs=42.6

Q ss_pred             cchhhhhh--hHHHHHHhhhcccccccccc-------ceEEeccCcceeeecchhhHHHHHHhh
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMDE-------KFIIVSGKDRLILSKGVDAVHKIIKEE  178 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~e-------kf~~vsgkDRl~l~kgvdaVhk~i~e~  178 (466)
                      ...|..+.  .+++|..|++++||+|.+++       ..|.|+|. .-.+.++...|.++|.+.
T Consensus        19 ~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~-~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           19 RHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGP-PDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             TTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESS-HHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeC-HHHHHHHHHHHHHHHhcc
Confidence            34555665  68999999999999999974       26888887 566778888888888663

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=92.77  E-value=0.054  Score=42.42  Aligned_cols=55  Identities=11%  Similarity=0.179  Sum_probs=43.4

Q ss_pred             hhhhhh--hHHHHHHhhhcccccccccc----------ceEEeccCcceeeecchhhHHHHHHhhcCC
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDE----------KFIIVSGKDRLILSKGVDAVHKIIKEEGDQ  181 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~e----------kf~~vsgkDRl~l~kgvdaVhk~i~e~~~~  181 (466)
                      .|..+.  ++++|..|++.+||+|.+++          ..|.|+|. .-.+.++...|..+|.+....
T Consensus        13 ~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~~~~   79 (87)
T 1ec6_A           13 LVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS-PAATQAAQYLISQRVTYEQGV   79 (87)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhccccc
Confidence            445555  68999999999999999986          37888887 567778888888888775443

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=91.92  E-value=0.056  Score=44.44  Aligned_cols=51  Identities=16%  Similarity=0.264  Sum_probs=41.1

Q ss_pred             hhhhhh--hHHHHHHhhhccccccccccc-----eEEeccCcceeeecchhhHHHHHHh
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDEK-----FIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~ek-----f~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      .++.+.  ++++|..|+.++||+|.+++.     .|.|+|.+ --+.+....+..++++
T Consensus        27 ~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~~~~~V~I~G~~-e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           27 LHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLA-ANLDRAKAGLLERVKE   84 (104)
T ss_dssp             HHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECH-HHHHHHHHHHHHHHHH
T ss_pred             HccceeCCCchHHHHHHHHHCCEEEecCCCCCcceEEEEcCH-HHHHHHHHHHHHHHhh
Confidence            445554  799999999999999999986     89999987 5567777777777655

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=91.45  E-value=0.066  Score=43.38  Aligned_cols=58  Identities=14%  Similarity=0.255  Sum_probs=45.0

Q ss_pred             cchhhhhh--hHHHHHHhhhccccccccccc------eEEeccCcceeeecchhhHHHHHHhhcCCC
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMDEK------FIIVSGKDRLILSKGVDAVHKIIKEEGDQR  182 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~ek------f~~vsgkDRl~l~kgvdaVhk~i~e~~~~~  182 (466)
                      ...++.+.  .+++|..|+.++||+|++.+.      .|.|+|.. --+.+...++..+++|-...-
T Consensus        25 ~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~~~~~V~I~G~~-e~v~~A~~~I~~i~~e~~~~~   90 (95)
T 2ctm_A           25 HRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLP-ENVEEAIDHILNLEEEYLADS   90 (95)
T ss_dssp             TTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCH-HHHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHccccCCCCcchHHHHHHHHCCeEEecCCCCCCCcEEEEEcCH-HHHHHHHHHHHHHHHHHHHHh
Confidence            34556665  789999999999999999886      78889986 446778888888887654433

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=90.36  E-value=0.085  Score=46.52  Aligned_cols=45  Identities=22%  Similarity=0.459  Sum_probs=37.5

Q ss_pred             hHHHHHHhhhccccccccccc-------------------------eEEeccCcce-----eeecchhhHHHHHH
Q 012298          132 TEKVIQRIEKDISCKIKMDEK-------------------------FIIVSGKDRL-----ILSKGVDAVHKIIK  176 (466)
Q Consensus       132 te~vi~~iEkd~gckikm~ek-------------------------f~~vsgkDRl-----~l~kgvdaVhk~i~  176 (466)
                      .+.+|.+||+++||||.+..+                         .|.||+.|--     .|.+++.-|.+++.
T Consensus        26 rG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           26 RGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             THHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHHHHHSS
T ss_pred             CcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchhhHHHHHHHHHHHHHHHCC
Confidence            788999999999999988752                         7889988864     67788888888774

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=89.50  E-value=0.17  Score=42.68  Aligned_cols=57  Identities=7%  Similarity=0.158  Sum_probs=45.3

Q ss_pred             cchhhhhh--hHHHHHHhhhccccccccccc---------eEEeccCcceeeecchhhHHHHHHhhcCC
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMDEK---------FIIVSGKDRLILSKGVDAVHKIIKEEGDQ  181 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~ek---------f~~vsgkDRl~l~kgvdaVhk~i~e~~~~  181 (466)
                      ...+..+.  .+++|..|..++||+|.+.+.         .|.|+| +.--+.++...|..+|++-..+
T Consensus        93 ~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~~~~~  160 (163)
T 3krm_A           93 ASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIG-HFYASQMAQRKIRDILAQVKQQ  160 (163)
T ss_dssp             TTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEE-CHHHHHHHHHHHHHHHHHHTC-
T ss_pred             hhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHHHHHHHh
Confidence            45566665  799999999999999999876         788888 6667788888888888775443

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=89.07  E-value=0.068  Score=40.94  Aligned_cols=27  Identities=26%  Similarity=0.774  Sum_probs=21.1

Q ss_pred             hhhhhhhhhhHhhcCCCCccccCCCCc
Q 012298           80 WKKRKEEEMICKICGESGHFTQGCPST  106 (466)
Q Consensus        80 wkkrkeeem~ckicge~ghf~qgcp~t  106 (466)
                      |.++.-....|-+||+.|||+.-||.-
T Consensus        16 ~~~~~~~~~~C~~Cge~GH~ardCp~~   42 (56)
T 1u6p_A           16 RRRSQLDRDQCAYCKEKGHWAKDCPKK   42 (56)
T ss_dssp             CCSTTCCTTBCSSSCCBSSCGGGCTTC
T ss_pred             cCCCCCCCCcceeCCCCCcccccCcCC
Confidence            344444456799999999999999973

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=89.01  E-value=0.11  Score=37.59  Aligned_cols=21  Identities=33%  Similarity=0.879  Sum_probs=18.5

Q ss_pred             hhhHhhcCCCCccccCCCCcc
Q 012298           87 EMICKICGESGHFTQGCPSTL  107 (466)
Q Consensus        87 em~ckicge~ghf~qgcp~tL  107 (466)
                      ...|-+||+.||++.-||.-.
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSC
T ss_pred             CCeeeECCCCCcchhhCcCCc
Confidence            468999999999999999754

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=88.90  E-value=0.17  Score=42.50  Aligned_cols=53  Identities=15%  Similarity=0.257  Sum_probs=41.8

Q ss_pred             cchhhhhh--hHHHHHHhhhccccccccc--------cceEEeccCcceeeecchhhHHHHHHh
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMD--------EKFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~--------ekf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      ...+..+.  .+++|..|...+||+|.++        +..|.|+| +.--+.+++..|..+|.|
T Consensus        97 ~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A           97 ASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAG-IPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             HHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEE-CHHHHHHHHHHHHHHHHH
T ss_pred             hhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Confidence            45666666  6899999999999999997        46788888 566667777777777765

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=88.52  E-value=0.17  Score=42.24  Aligned_cols=53  Identities=15%  Similarity=0.343  Sum_probs=41.7

Q ss_pred             cchhhhhh--hHHHHHHhhhccccccccc-------cceEEeccCcceeeecchhhHHHHHHh
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMD-------EKFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~-------ekf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      ...+..+.  .+++|..|++++||+|.+.       +..|.|+|. .--+.++...|..+|++
T Consensus        99 ~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~i~~  160 (164)
T 2jvz_A           99 RHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGP-PDRCEHAARIINDLLQS  160 (164)
T ss_dssp             TTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEESC-HHHHHHHHHHHHHHHHH
T ss_pred             hhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEcC-HHHHHHHHHHHHHHHhh
Confidence            34566666  6899999999999999998       468888887 55677777888887765

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=87.99  E-value=0.13  Score=35.25  Aligned_cols=18  Identities=39%  Similarity=1.012  Sum_probs=15.8

Q ss_pred             hhHhhcCCCCccccCCCC
Q 012298           88 MICKICGESGHFTQGCPS  105 (466)
Q Consensus        88 m~ckicge~ghf~qgcp~  105 (466)
                      ..|-+||+.||++..||+
T Consensus        20 ~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           20 KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             TTCSSCCCTTGGGGTTCC
T ss_pred             CeEccCCCcCCccCcCcC
Confidence            479999999999999985

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=87.71  E-value=0.22  Score=42.63  Aligned_cols=52  Identities=12%  Similarity=0.330  Sum_probs=39.9

Q ss_pred             hhhhhh--hHHHHHHhhhcccccccccc-------ceEEeccCcceeeecchhhHHHHHHhh
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDE-------KFIIVSGKDRLILSKGVDAVHKIIKEE  178 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~e-------kf~~vsgkDRl~l~kgvdaVhk~i~e~  178 (466)
                      .|..+.  .+++|.+|++++||+|.+++       .+|.|+|. .--+.++...|.+++.+.
T Consensus        13 ~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~~~~~   73 (174)
T 1j4w_A           13 AVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP-PDRAQHAAEIITDLLRSV   73 (174)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEEC-HHHHHHHHHHHHHHHHHH
T ss_pred             heeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeC-HHHHHHHHHHHHHHHHhc
Confidence            444454  78999999999999999974       37788887 445667777788888764

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=87.49  E-value=0.18  Score=40.82  Aligned_cols=55  Identities=22%  Similarity=0.271  Sum_probs=41.9

Q ss_pred             cchhhhhh--hHHHHHHhhhccccccccccc--------eEEeccCcceeeecchhhHHHHHHhhc
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMDEK--------FIIVSGKDRLILSKGVDAVHKIIKEEG  179 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~ek--------f~~vsgkDRl~l~kgvdaVhk~i~e~~  179 (466)
                      ...|..+.  .+++|..|..++||+|.+.+.        .|.|+|. .-.+.++...+..++++-.
T Consensus        25 ~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~-~e~v~~A~~~I~~iv~e~e   89 (97)
T 2ctl_A           25 PKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGY-EKNTEAARDAILRIVGELE   89 (97)
T ss_dssp             TTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESC-HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHHHHHH
Confidence            34556666  689999999999999999764        6888887 4456677777777776543

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=87.02  E-value=0.11  Score=43.56  Aligned_cols=54  Identities=15%  Similarity=0.362  Sum_probs=38.8

Q ss_pred             cchhhhhh--hHHHHHHhhhccccccccccc-----eEEeccCcceeeecchhhHHHHHHhh
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMDEK-----FIIVSGKDRLILSKGVDAVHKIIKEE  178 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~ek-----f~~vsgkDRl~l~kgvdaVhk~i~e~  178 (466)
                      ...+..+.  .+.+|.+|++++||+|.+++.     +|.|+|. .--+.++...|..++.+.
T Consensus        13 ~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~e~   73 (160)
T 2jzx_A           13 GKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGP-TNAIFKAFAMIIDKLEED   73 (160)
T ss_dssp             HHHHHHHHCGGGHHHHHHHHHHCSEEEEECCTTTEEEEEEEEE-HHHHHHHHHHHHHHHHHH
T ss_pred             hhheeeeECCCcHHHHHHHHHHCCEEEEcCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHhh
Confidence            34555565  789999999999999999875     7778886 333445555566666553

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=86.96  E-value=0.18  Score=34.89  Aligned_cols=18  Identities=33%  Similarity=0.647  Sum_probs=16.3

Q ss_pred             hhHhhcCCCCccccCCCC
Q 012298           88 MICKICGESGHFTQGCPS  105 (466)
Q Consensus        88 m~ckicge~ghf~qgcp~  105 (466)
                      ..|-+||+.||++..||.
T Consensus        22 ~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           22 EGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             SSCTTTCCSSSCTTTSCC
T ss_pred             CccccCCCCCCccCcCcC
Confidence            589999999999999983

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.69  E-value=0.2  Score=38.27  Aligned_cols=20  Identities=35%  Similarity=1.065  Sum_probs=17.7

Q ss_pred             hhhHhhcCCCCccccCCCCc
Q 012298           87 EMICKICGESGHFTQGCPST  106 (466)
Q Consensus        87 em~ckicge~ghf~qgcp~t  106 (466)
                      -.+|-.||+.||+.+-||+.
T Consensus         7 ~~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            7 GYTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             SCCCTTTCCTTSCGGGCSGG
T ss_pred             CCccccCCCcCcccccCCCC
Confidence            35799999999999999964

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=86.51  E-value=0.24  Score=36.79  Aligned_cols=21  Identities=24%  Similarity=0.635  Sum_probs=18.9

Q ss_pred             hhHhhcCCCCccccCCCCccc
Q 012298           88 MICKICGESGHFTQGCPSTLG  108 (466)
Q Consensus        88 m~ckicge~ghf~qgcp~tLG  108 (466)
                      .+|-+||+.||++..||+...
T Consensus        31 ~~C~~Cg~~GH~ar~C~~~~~   51 (60)
T 1cl4_A           31 GLCPRCKRGKHWANECKSKTD   51 (60)
T ss_dssp             CSCSSCSSCSSCSTTCCCTTS
T ss_pred             cceeECCCCCCccCcCCCccc
Confidence            689999999999999998754

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=86.04  E-value=0.22  Score=41.59  Aligned_cols=51  Identities=16%  Similarity=0.315  Sum_probs=36.3

Q ss_pred             hhhhhh--hHHHHHHhhhcccccccccc---------ceEEeccCcceeeecchhhHHHHHHh
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDE---------KFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~e---------kf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      .+..+.  .+.+|..|++++||+|.+..         .+|.|+| +.-.+.++..+|..++.+
T Consensus        12 ~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~ii~e   73 (164)
T 2jvz_A           12 KAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG-DPYKVQQACEMVMDILRE   73 (164)
T ss_dssp             CHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEE-CHHHHHHHHHHHHHHTTC
T ss_pred             heeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Confidence            445555  68999999999999999853         3777787 444455666666666644

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=85.77  E-value=0.21  Score=33.01  Aligned_cols=19  Identities=32%  Similarity=0.833  Sum_probs=17.0

Q ss_pred             hhHhhcCCCCccccCCCCc
Q 012298           88 MICKICGESGHFTQGCPST  106 (466)
Q Consensus        88 m~ckicge~ghf~qgcp~t  106 (466)
                      +.|-.||+.||++.-||..
T Consensus         7 ~~C~nCgk~GH~ar~C~~p   25 (29)
T 1nc8_A            7 IRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CBCTTTSCBSSCGGGCCSS
T ss_pred             CEEEECCccccCHhHCccc
Confidence            6799999999999999863

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=85.47  E-value=0.35  Score=41.40  Aligned_cols=58  Identities=16%  Similarity=0.275  Sum_probs=42.1

Q ss_pred             hhhcccchhhhhh--hHHHHHHhhhccccccccccc---------eEEeccCcceeeecchhhHHHHHHh
Q 012298          119 RVAARDKHVRALF--TEKVIQRIEKDISCKIKMDEK---------FIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       119 Rv~ardk~vr~lf--te~vi~~iEkd~gckikm~ek---------f~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      +|.--...+..+.  .+++|..|...+||+|.+...         .|.|+|.. -.+.++...|..+|+|
T Consensus       107 ~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~-~~v~~A~~~I~~~i~e  175 (178)
T 2anr_A          107 KIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEP-EQNRKAVELIIQKIQE  175 (178)
T ss_dssp             EEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEESSH-HHHHHHHHHHHHHHHS
T ss_pred             EEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHHh
Confidence            3333344556666  789999999999999999754         77888876 4556677777777765

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=84.68  E-value=0.14  Score=39.05  Aligned_cols=35  Identities=20%  Similarity=0.395  Sum_probs=28.0

Q ss_pred             hhhhhh--hHHHHHHhhhccccccccccc-----eEEeccCc
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDEK-----FIIVSGKD  160 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~ek-----f~~vsgkD  160 (466)
                      .++.+.  .+++|..|+.++||+|.+++.     -|.|+|..
T Consensus        15 ~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g~~~~~V~I~G~~   56 (71)
T 1vig_A           15 FHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDP   56 (71)
T ss_dssp             HHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEESS
T ss_pred             HhhhhcCCCCccHHHHHHHHCCEEEECCCCCcccEEEEEcCH
Confidence            445555  788999999999999999875     67777763

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=84.30  E-value=0.36  Score=41.27  Aligned_cols=53  Identities=15%  Similarity=0.268  Sum_probs=35.1

Q ss_pred             cchhhhhh--hHHHHHHhhhccccccccccc----------eEEeccCcceeeecchhhHHHHHHh
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMDEK----------FIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~ek----------f~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      .+.+..+.  .+.+|..|++++||+|++++.          +|.|+|. .--+.+....|.+++.+
T Consensus        14 ~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~-~~~v~~A~~~I~~~~~~   78 (178)
T 2anr_A           14 SYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT-IEALNAVHGFIAEKIRE   78 (178)
T ss_dssp             HHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEEC-HHHHHHHHHHHHHHHTC
T ss_pred             hhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeC-HHHHHHHHHHHHHHHhc
Confidence            34555665  789999999999999999753          6777775 22233444444454533

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=84.13  E-value=0.25  Score=36.08  Aligned_cols=18  Identities=33%  Similarity=0.783  Sum_probs=14.2

Q ss_pred             hhHhhcCCCCccccCCCC
Q 012298           88 MICKICGESGHFTQGCPS  105 (466)
Q Consensus        88 m~ckicge~ghf~qgcp~  105 (466)
                      ..|-.||+.||++..||.
T Consensus        34 ~~C~~Cg~~GH~~~~C~~   51 (55)
T 1a1t_A           34 KGCWKCGKEGHQMKDCTE   51 (55)
T ss_dssp             CBCTTTCCBSSCGGGCSS
T ss_pred             CEeCCCCCcCCccCCCcC
Confidence            468888888888888875

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=83.56  E-value=0.29  Score=33.80  Aligned_cols=18  Identities=33%  Similarity=0.822  Sum_probs=16.3

Q ss_pred             hHhhcCCCCccccCCCCc
Q 012298           89 ICKICGESGHFTQGCPST  106 (466)
Q Consensus        89 ~ckicge~ghf~qgcp~t  106 (466)
                      .|-.||+.||++..||..
T Consensus         2 ~C~~Cg~~GH~a~~C~~~   19 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQP   19 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSC
T ss_pred             eeeccCCCCcccccCCCC
Confidence            588999999999999974

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=83.20  E-value=0.28  Score=36.85  Aligned_cols=21  Identities=24%  Similarity=0.613  Sum_probs=18.2

Q ss_pred             hhhHhhcCCCCccccCCCCcc
Q 012298           87 EMICKICGESGHFTQGCPSTL  107 (466)
Q Consensus        87 em~ckicge~ghf~qgcp~tL  107 (466)
                      ..+|-+||+.||++..||..-
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~   50 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCRKRD   50 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCCCCC
T ss_pred             CCeeCCCCCCCCCcCCCcCCC
Confidence            367999999999999999753

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=83.19  E-value=0.27  Score=35.54  Aligned_cols=18  Identities=39%  Similarity=0.949  Sum_probs=15.5

Q ss_pred             hhHhhcCCCCccccCCCC
Q 012298           88 MICKICGESGHFTQGCPS  105 (466)
Q Consensus        88 m~ckicge~ghf~qgcp~  105 (466)
                      ..|-+||+.||++..||.
T Consensus        28 ~~C~~Cg~~GH~~~~C~~   45 (49)
T 2ec7_A           28 QGCWKCGKTGHVMAKCPE   45 (49)
T ss_dssp             CSCSSSCCSSCCGGGCCS
T ss_pred             CeeCcCCCcCCccCCCcC
Confidence            469999999999999986

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=82.22  E-value=0.39  Score=41.89  Aligned_cols=26  Identities=19%  Similarity=0.520  Sum_probs=17.7

Q ss_pred             hhhHhhcCCCCccccCCCCccccCCc
Q 012298           87 EMICKICGESGHFTQGCPSTLGANRK  112 (466)
Q Consensus        87 em~ckicge~ghf~qgcp~tLGanrk  112 (466)
                      ...|.+||+.||+...||........
T Consensus       119 ~~~C~~Cg~~GH~~r~Cp~~~~~~~~  144 (148)
T 3ts2_A          119 PKKCHFCQSINHMVASCPLKAQQGPS  144 (148)
T ss_dssp             CCCCTTTCCSSCCGGGCTTTTC----
T ss_pred             CCcccccCCcCCEeccCcCCCCCCCc
Confidence            35799999999999999876554333

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.20  E-value=0.42  Score=36.27  Aligned_cols=19  Identities=26%  Similarity=0.768  Sum_probs=17.6

Q ss_pred             hhHhhcCCCCccccCCCCc
Q 012298           88 MICKICGESGHFTQGCPST  106 (466)
Q Consensus        88 m~ckicge~ghf~qgcp~t  106 (466)
                      .+|-+||+.||++..||..
T Consensus        30 ~~C~~Cg~~GH~ar~Cp~~   48 (63)
T 2cqf_A           30 KKCHFCQSISHMVASCPLK   48 (63)
T ss_dssp             SCCTTTCCSSSCTTTCTGG
T ss_pred             CccCCcCCcCCccCcCCCc
Confidence            6899999999999999975

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=80.28  E-value=0.54  Score=34.27  Aligned_cols=22  Identities=27%  Similarity=0.815  Sum_probs=19.1

Q ss_pred             hhhhhHhhcCCCCccccCCCCc
Q 012298           85 EEEMICKICGESGHFTQGCPST  106 (466)
Q Consensus        85 eeem~ckicge~ghf~qgcp~t  106 (466)
                      .....|-.||+.||++..||..
T Consensus        10 ~~~~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           10 RKTVKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             GGTCBCTTTCCBSSCGGGCSSC
T ss_pred             CCCcceeeeCCCCcChhhcCCC
Confidence            3457899999999999999975

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	466
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	95.63
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	92.75
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	91.7
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	90.82
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	90.25
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	89.26
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	89.18
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	89.14
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	88.93
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	88.31
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	88.05
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	87.57
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	87.24
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	85.01
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	84.78
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	82.68
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	82.56
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	81.31
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	81.23

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=95.63  E-value=0.0018  Score=48.53  Aligned_cols=52  Identities=17%  Similarity=0.257  Sum_probs=36.0

Q ss_pred             hhhhhh--hHHHHHHhhhcccccccccc-ceEEeccCcceeeecchhhHHHHHHh
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDE-KFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~e-kf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      .|..++  .+++|..|+.++||+|.+++ .-|.|+|.|...+.+..++|.+|+.|
T Consensus        11 ~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~g~v~I~g~~~~~v~~A~~~I~~i~~e   65 (69)
T d2je6i3          11 KVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENE   65 (69)
T ss_dssp             GHHHHHCGGGHHHHHHHTTC---CEECTTSEEEC-----CTTCCTHHHHTTTTTT
T ss_pred             hccceECCchhHHHHHHHHHCCEEEEcCCCEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            345555  78999999999999999976 48999999999999999999886644

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=92.75  E-value=0.022  Score=44.89  Aligned_cols=46  Identities=20%  Similarity=0.255  Sum_probs=42.1

Q ss_pred             hHHHHHHhhhccccccccccc-eEEeccCcceeeecchhhHHHHHHh
Q 012298          132 TEKVIQRIEKDISCKIKMDEK-FIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       132 te~vi~~iEkd~gckikm~ek-f~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      ++++|..|+.++||+|-+++. -|.|+|+|.-.+.+.+.+|+.|..|
T Consensus        19 gG~~ik~i~~~t~~~I~I~d~G~V~I~g~~~~~~~~A~~~I~~I~~e   65 (87)
T d2z0sa2          19 KMSMLKTLEEKTECKIFVARNGRIHLECPNEDLEAIAVMAIKIIDEE   65 (87)
T ss_dssp             GGHHHHHHHHHHCCEEEEETTTEEEEECSCHHHHHHHHHHHHHHHHC
T ss_pred             CCcHHHHHHHHHCCEEEECCCcEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            799999999999999999885 8999999999999999999997655

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.70  E-value=0.025  Score=42.27  Aligned_cols=52  Identities=23%  Similarity=0.309  Sum_probs=41.0

Q ss_pred             chhhhhh--hHHHHHHhhhcccccccc-----ccceEEeccCcceeeecchhhHHHHHHh
Q 012298          125 KHVRALF--TEKVIQRIEKDISCKIKM-----DEKFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       125 k~vr~lf--te~vi~~iEkd~gckikm-----~ekf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      ..+..++  .+..|..|++++||+|.+     .+.+|.|+|..- -+.+++..+..+++|
T Consensus        19 ~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G~~~-~v~~A~~~I~~iv~e   77 (81)
T d2ctea1          19 EHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKE-GIEKARHEVLLISAE   77 (81)
T ss_dssp             TTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEECHH-HHHHHHHHHHHHHHH
T ss_pred             HHHhhccCCCChhHHHHHHHhCCEEEECCCCCCCCEEEEEeCHH-HHHHHHHHHHHHHHH
Confidence            3455555  678999999999999998     346888888765 577888888888765

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=90.82  E-value=0.047  Score=44.10  Aligned_cols=50  Identities=14%  Similarity=0.191  Sum_probs=37.3

Q ss_pred             hhhhhh---hHHHHHHhhhccccccccccce-EEeccCcceeeecchhhHHHHHHh
Q 012298          126 HVRALF---TEKVIQRIEKDISCKIKMDEKF-IIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       126 ~vr~lf---te~vi~~iEkd~gckikm~ekf-~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      ++|.++   ++++|..||..+||+|-++++= ++++..|.  +..+.+||..||++
T Consensus        22 R~~GrIIG~gGktik~Ie~~Tg~~I~I~d~~v~iig~~e~--i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          22 RIKGRIIGEGGRARRTIEEMTDTYINVGEYEVAIIGDYER--AMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECSSEEEEEEEHHH--HHHHHHHHHHHHTT
T ss_pred             HHhcceeCCCcHHHHHHHHHHCCeEEEeCCeEEEEECchh--HHHHHHHHHHHHcC
Confidence            345555   8999999999999999999874 44444554  46677888888854

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.25  E-value=0.031  Score=43.39  Aligned_cols=73  Identities=19%  Similarity=0.320  Sum_probs=51.0

Q ss_pred             ccccCCchhHHHHhhhcccchhhhhh--hHHHHHHhhhccccccccccc---------eEEeccCcceeeecchhhHHHH
Q 012298          106 TLGANRKSQDFFERVAARDKHVRALF--TEKVIQRIEKDISCKIKMDEK---------FIIVSGKDRLILSKGVDAVHKI  174 (466)
Q Consensus       106 tLGanrks~dffeRv~ardk~vr~lf--te~vi~~iEkd~gckikm~ek---------f~~vsgkDRl~l~kgvdaVhk~  174 (466)
                      +-|.-..+.-.+|+|.--...|..+.  .+..|..|+.++||+|.+...         .|.|+| ..--+.+++..|.++
T Consensus         5 s~~~~~~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~   83 (104)
T d1we8a_           5 SSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISG-TQKEVAAAKHLILEK   83 (104)
T ss_dssp             CCCCCSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEE-EHHHHHHHHHHHHHH
T ss_pred             CCCccCCCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEe-CHHHHHHHHHHHHHH
Confidence            34445556666777666666777777  789999999999999998543         455666 333456677777777


Q ss_pred             HHhhc
Q 012298          175 IKEEG  179 (466)
Q Consensus       175 i~e~~  179 (466)
                      |++..
T Consensus        84 i~e~~   88 (104)
T d1we8a_          84 VSEDE   88 (104)
T ss_dssp             HHHHH
T ss_pred             HhCcH
Confidence            76644

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=89.26  E-value=0.1  Score=40.38  Aligned_cols=52  Identities=17%  Similarity=0.242  Sum_probs=37.5

Q ss_pred             hhhhhh--hHHHHHHhhhcccccccccc--ceEEeccCcceeeecchhhHHHHHHh
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDE--KFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~e--kf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      .|..+.  ++++|..|++++||+|.+++  ..+.+.+.+=-....++..+..+|++
T Consensus        13 ~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g~v~i~~~~~~~~~~a~~~a~~iI~a   68 (84)
T d1tuaa1          13 RLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKA   68 (84)
T ss_dssp             GHHHHHCGGGHHHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHH
T ss_pred             HcCeeecCCchhHHHHHHHHCCEEEEEcCCCeEEEecCCccccHHHHHHHHHHHHH
Confidence            344454  79999999999999999964  46777666555555666666666654

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.18  E-value=0.079  Score=40.67  Aligned_cols=50  Identities=22%  Similarity=0.361  Sum_probs=38.8

Q ss_pred             hhhhh--hHHHHHHhhhccccccccccc-eEEeccCcceeeecchhhHHHHHHh
Q 012298          127 VRALF--TEKVIQRIEKDISCKIKMDEK-FIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       127 vr~lf--te~vi~~iEkd~gckikm~ek-f~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      |..+.  .+++|..|..++||+|.+++. -|.|+|. .--+.+...+|..++.|
T Consensus        12 ig~IIG~gG~~I~~I~~~tg~~I~i~~~g~v~I~G~-~e~v~~A~~~I~~i~~e   64 (84)
T d2ba0a3          12 VPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWVNGD-RRKVSIAEEAIYLIEQE   64 (84)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEECTTSEEEEESC-HHHHHHHHHHHHHHHHC
T ss_pred             cceeeCCcHHHHHHHHHHHCCEEEECCCCEEEEEeC-HHHHHHHHHHHHHHHHh
Confidence            44444  789999999999999999764 7788884 45667777788777655

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.14  E-value=0.075  Score=39.07  Aligned_cols=58  Identities=17%  Similarity=0.338  Sum_probs=43.0

Q ss_pred             hhcccchhhhhh--hHHHHHHhhhcccccccccc-------ceEEeccCcceeeecchhhHHHHHHhh
Q 012298          120 VAARDKHVRALF--TEKVIQRIEKDISCKIKMDE-------KFIIVSGKDRLILSKGVDAVHKIIKEE  178 (466)
Q Consensus       120 v~ardk~vr~lf--te~vi~~iEkd~gckikm~e-------kf~~vsgkDRl~l~kgvdaVhk~i~e~  178 (466)
                      |+--...+..+.  .+..|..|+.++||+|.+..       ..|.|+|. .--+.++.+.|..+|.|+
T Consensus        12 i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1          12 YKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT-PESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             EEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEEC-HHHHHHHHHHHHHHHHHT
T ss_pred             EEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHcc
Confidence            333344555555  78999999999999998853       47888884 456678888888888763

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.93  E-value=0.021  Score=42.64  Aligned_cols=62  Identities=10%  Similarity=0.249  Sum_probs=41.2

Q ss_pred             HHHhhhcccchhhhhh--hHHHHHHhhhccccccccccc---------eEEeccCcceeeecchhhHHHHHHhh
Q 012298          116 FFERVAARDKHVRALF--TEKVIQRIEKDISCKIKMDEK---------FIIVSGKDRLILSKGVDAVHKIIKEE  178 (466)
Q Consensus       116 ffeRv~ardk~vr~lf--te~vi~~iEkd~gckikm~ek---------f~~vsgkDRl~l~kgvdaVhk~i~e~  178 (466)
                      +.++|.--...+..+.  .+.+|.+|+.++||+|.+...         .|.|+|. .--+.++...|..+|+|.
T Consensus         8 ~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~e~   80 (81)
T d1x4ma1           8 AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGD-PYKVQQAKEMVLELIRDQ   80 (81)
T ss_dssp             EEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEEC-TTTHHHHHHHHHHHHCCC
T ss_pred             EEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHhc
Confidence            3344444445666666  678999999999999998543         3555553 245566666777777654

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.31  E-value=0.097  Score=37.89  Aligned_cols=50  Identities=18%  Similarity=0.353  Sum_probs=33.2

Q ss_pred             hhhhhh--hHHHHHHhhhcccccccccc-------ceEEeccCcceeeecchhhHHHHHH
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDE-------KFIIVSGKDRLILSKGVDAVHKIIK  176 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~e-------kf~~vsgkDRl~l~kgvdaVhk~i~  176 (466)
                      .|-.+.  .+..|..|+.++||+|++.+       +.|.|+|. .--+.++...|..+|+
T Consensus        14 ~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~-~~~v~~A~~~I~~~i~   72 (75)
T d1zzka1          14 LAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-QDQIQNAQYLLQNSVK   72 (75)
T ss_dssp             TGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEEC-HHHHHHHHHHHHHHHH
T ss_pred             hcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeC-HHHHHHHHHHHHHHHH
Confidence            344555  78999999999999999964       36777774 3334444444444443

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.05  E-value=0.088  Score=39.17  Aligned_cols=52  Identities=15%  Similarity=0.349  Sum_probs=38.0

Q ss_pred             chhhhhh--hHHHHHHhhhcccccccccc------ceEEeccCcceeeecchhhHHHHHHh
Q 012298          125 KHVRALF--TEKVIQRIEKDISCKIKMDE------KFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       125 k~vr~lf--te~vi~~iEkd~gckikm~e------kf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      +.++.+.  .+..|..|++++||+|.+..      ..|.|+|.-- -+.++.+.+..+++|
T Consensus        19 ~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~~v~I~G~~~-~V~~A~~~I~~i~~e   78 (81)
T d2ctma1          19 RVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPE-NVEEAIDHILNLEEE   78 (81)
T ss_dssp             TTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHH-HHHHHHHHHHHHHHH
T ss_pred             HHHhhccCCCCccHHHHHHHhCCEEEeCCccCCCCCEEEEeCCHH-HHHHHHHHHHHHHHH
Confidence            4455565  67899999999999999832      4677777543 356777777777655

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.57  E-value=0.14  Score=37.18  Aligned_cols=47  Identities=21%  Similarity=0.423  Sum_probs=32.8

Q ss_pred             chhhhhh--hHHHHHHhhhcccccccccc-----ceEEeccCcceeeecchhhHHHHHH
Q 012298          125 KHVRALF--TEKVIQRIEKDISCKIKMDE-----KFIIVSGKDRLILSKGVDAVHKIIK  176 (466)
Q Consensus       125 k~vr~lf--te~vi~~iEkd~gckikm~e-----kf~~vsgkDRl~l~kgvdaVhk~i~  176 (466)
                      +.++.++  .+.+|+.|++++||+|.+..     ..|.|+|.     ..+|++..+.|.
T Consensus        14 ~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~v~I~G~-----~~~v~~A~~~I~   67 (71)
T d1viga_          14 KFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGD-----PQGVQQAKRELL   67 (71)
T ss_dssp             SHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEES-----SHHHHHHHHHHH
T ss_pred             HHhcccCCCCCchHHHHHHHhCCEEEeCCCCCCCCEEEEECC-----HHHHHHHHHHHH
Confidence            3445555  68899999999999999943     46667774     345555555554

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.24  E-value=0.085  Score=39.27  Aligned_cols=51  Identities=20%  Similarity=0.281  Sum_probs=35.7

Q ss_pred             hhhhhh--hHHHHHHhhhcccccccccc--------ceEEeccCcceeeecchhhHHHHHHh
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDE--------KFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~e--------kf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      .+..+.  .+..|..|++.+||+|.+..        ..|.|+|. .--+.+..+.|+++|++
T Consensus        20 ~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~-~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1          20 YHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGY-EKNTEAARDAILRIVGE   80 (84)
T ss_dssp             THHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESC-HHHHHHHHHHHHHHHHH
T ss_pred             HHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECC-HHHHHHHHHHHHHHHHh
Confidence            344444  67899999999999999843        37888886 33445566666666654

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.01  E-value=0.19  Score=36.41  Aligned_cols=50  Identities=12%  Similarity=0.354  Sum_probs=33.5

Q ss_pred             hhhhhh--hHHHHHHhhhcccccccccc-------ceEEeccCcceeeecchhhHHHHHH
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDE-------KFIIVSGKDRLILSKGVDAVHKIIK  176 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~e-------kf~~vsgkDRl~l~kgvdaVhk~i~  176 (466)
                      .|-.+.  .+..|..|++++||+|.+..       +.|.|+|. .--+.++...|..+|.
T Consensus        13 ~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~   71 (74)
T d1j4wa1          13 AVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP-PDRAQHAAEIITDLLR   71 (74)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEEC-HHHHHHHHHHHHHHHH
T ss_pred             HCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeC-HHHHHHHHHHHHHHHH
Confidence            344444  78999999999999999853       36667764 3344555555555553

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.78  E-value=0.18  Score=38.09  Aligned_cols=45  Identities=16%  Similarity=0.296  Sum_probs=34.3

Q ss_pred             hHHHHHHhhhccccccccc-----cceEEeccCcceeeecchhhHHHHHHh
Q 012298          132 TEKVIQRIEKDISCKIKMD-----EKFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       132 te~vi~~iEkd~gckikm~-----ekf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      .+..|..|++++||+|.+.     +..|.|+|. .--+.++...|.+++++
T Consensus        28 ~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G~-~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1          28 KGSGIRKMMDEFEVNIHVPAPELQSDIIAITGL-AANLDRAKAGLLERVKE   77 (91)
T ss_dssp             SSHHHHHHHHHTCCEEECCCTTTTCCEEEEEEC-HHHHHHHHHHHHHHHHH
T ss_pred             CchhHHHHHHHhCCEEEECCCCCCcceEEEECC-HHHHHHHHHHHHHHHHH
Confidence            7889999999999999994     347777884 44666666666666654

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.68  E-value=0.25  Score=35.71  Aligned_cols=37  Identities=16%  Similarity=0.433  Sum_probs=27.4

Q ss_pred             cchhhhhh--hHHHHHHhhhccccccccccceEEeccCcceee
Q 012298          124 DKHVRALF--TEKVIQRIEKDISCKIKMDEKFIIVSGKDRLIL  164 (466)
Q Consensus       124 dk~vr~lf--te~vi~~iEkd~gckikm~ekf~~vsgkDRl~l  164 (466)
                      .+.+-.+.  .+..|..|+.++||+|++.+.    +.+||++.
T Consensus        12 ~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~----~~~er~v~   50 (71)
T d2axya1          12 GKEVGSIIGKKGESVKKMREESGARINISEG----NCPERIIT   50 (71)
T ss_dssp             HHHHHHHHCGGGHHHHHHHHHHCCEEEECSS----CCSEEEEE
T ss_pred             HHHcCeEECCCChhHHHHHHHhCCEEEEcCC----CCCcceEE
Confidence            34555555  789999999999999998774    34555553

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=82.56  E-value=0.16  Score=34.77  Aligned_cols=18  Identities=33%  Similarity=0.783  Sum_probs=16.1

Q ss_pred             hhHhhcCCCCccccCCCC
Q 012298           88 MICKICGESGHFTQGCPS  105 (466)
Q Consensus        88 m~ckicge~ghf~qgcp~  105 (466)
                      +.|-.||+.||++.-||.
T Consensus        23 ~~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1          23 KGCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             SSCSSSCCSSSCTTTCCS
T ss_pred             CccccCCCCCeecccCCC
Confidence            459999999999999995

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=81.31  E-value=0.15  Score=36.84  Aligned_cols=35  Identities=17%  Similarity=0.480  Sum_probs=14.3

Q ss_pred             hhhhhh--hHHHHHHhhhccccccccccc-eEEeccCc
Q 012298          126 HVRALF--TEKVIQRIEKDISCKIKMDEK-FIIVSGKD  160 (466)
Q Consensus       126 ~vr~lf--te~vi~~iEkd~gckikm~ek-f~~vsgkD  160 (466)
                      .|..++  ++++|..|+.++||+|.+++. -|.|+|+|
T Consensus        13 kig~vIG~GG~~Ik~I~~~tga~I~i~ddg~v~I~a~~   50 (54)
T d1e3ha4          13 KIGEVIGPKRQMINQIQEDTGAEITIEDDGTIYIGAAD   50 (54)
T ss_dssp             --------------CHHHHSCCCC--------CCCCBS
T ss_pred             HeeEEECCccHHHHHHHHHHCCEEEEeCCeEEEEEecC
Confidence            345555  789999999999999999654 77777766

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.23  E-value=0.24  Score=40.49  Aligned_cols=46  Identities=22%  Similarity=0.377  Sum_probs=38.2

Q ss_pred             hHHHHHHhhhcccccccccc-----------------------ceEEeccCcceeeecchhhHHHHHHh
Q 012298          132 TEKVIQRIEKDISCKIKMDE-----------------------KFIIVSGKDRLILSKGVDAVHKIIKE  177 (466)
Q Consensus       132 te~vi~~iEkd~gckikm~e-----------------------kf~~vsgkDRl~l~kgvdaVhk~i~e  177 (466)
                      .+..+.+||+++||||.+-.                       -.|.||+.+--.|++++..|.++|+.
T Consensus        27 rG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          27 RGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQ   95 (122)
T ss_dssp             SSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHHHHHHHHHHHHTT
T ss_pred             CCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhHHHHHHHHHHHHHh
Confidence            56788899999999998732                       27888888888888999999999954