Citrus Sinensis ID: 011182

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-
MATRQKLKGKLYHEENGEEEEKLKSAAAMSSDDEEGNEDLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTNTSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSSDKKRIRVRKKKKKEADKIEIEDQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHWNSCMQACARSRGETVEASPSSCYNCGAEGHFARECVSSSKVRKRNIDASTPTFRPHRENKDHSGIKSAPHDLGKVHKRKKTQHEERGIMTSRKSKQRGGWITDDPGDISYGKPKRNHWRSPGTPSSKAHKISAITSGGHFSSPQSSIKRNSHHRFSASRFDSSGSDGIRRGYDWW
ccHHHHHccccccccccccHHHHHccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccHHHHccHHHHHHHHHHccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
ccccccccccEEEccccccccccccccccccccHHHcHHHHHHHHHHHHHHHHHHHcccccccEEEEccccccccccccccccccEEEEccccccccccHHHHHHHHccHHHHHHHHccccHHcHHHHHHcccEccHHHccccHHcHHHHHHHHHcccccHHHHHHHHcccccccHHHHcHHHccccccccccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
matrqklkgklyheengeeeEKLKSAAamssddeegneDLSLKIVEKHMLMRAAkldqddsdsdvvlndntntntsdnsnnknggveavvpgpsgttddviiedvkSSDKKRIRVRKKKKKEADKIEIEDQSVIVRKeeqkvetadngdegvttvEISDNIVLRKllrgpryfdppdrgwqtcyncgeeghmavncrsavkrkkpcfvcgslehgvrqcskaqdcfickkgghrakdcpdkhksgfqnaqvclkcgdsghdmfscrnsyslddlkeVQCYICrcfghlccvnisdavpgevscfrcgqlghtglhwnSCMQACARsrgetveaspsscyncgaeghfarecvssskvrkrnidastptfrphrenkdhsgiksaphdlgkvhkrkktqheergimtsrkskqrggwitddpgdisygkpkrnhwrspgtpsskahkisaitsgghfsspqssikrnshhrfsasrfdssgsdgirrgydww
matrqklkgklyheengeeeeklksaaamssddeegNEDLSLKIVEKHMLMRAAKldqddsdsdvVLNDNtntntsdnsnnknggveavvpgpsgttddviiedvkssdkkrirvrkkkkkeadkieiedqsvivrkeeqkvetadngdegvttveisdnivlrkllrgpryfdppdrGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSlehgvrqcskAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHWNSCMQACARSRGETVEASPSSCYNCGAEGHFARecvssskvrkrnidastptfrphrenkdhsgiksaphdlgkvhkrkktqheergimtsrkskqrggwitddpgdisygkpkrnhwrspgtpssKAHKISAITSGGhfsspqssikrnshhrfsasrfdssgsdgirrgydww
MATRQKLKGKLYHeengeeeeKLKSAAAMSSDDEEGNEDLSLKIVEKHMLMRAAKldqddsdsdvvlndntntntsdnsnnKNGGVEAVVPGPSGTTDDVIIEDvkssdkkrirvrkkkkkeadkieiedQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHWNSCMQACARSRGETVEASPSSCYNCGAEGHFARECVSSSKVRKRNIDASTPTFRPHRENKDHSGIKSAPHDLGKVHKRKKTQHEERGIMTSRKSKQRGGWITDDPGDISYGKPKRNHWRSPGTPSSKAHKISAITSGGHFSSPQSSIKRNSHHRFSASRFDSSGSDGIRRGYDWW
*******************************************************************************************************************************************************VTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNC*****************KPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDC****KSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHWNSCMQACARS**********SCYNCGAEGHFAREC********************************************************************************************************************************************
**********************************************************************************************************************************************************************LRGPRYFDPPDRGWQTCYNCGEEGHMAVNC********************************KKGGHRAK***************CLKCGDSGHDMFSCRNS******KEVQCYICR*****************VSCFRCGQLGHTGLHWN******************SSCYNCGAEGH*************************************************************************************************************************************************
MATRQKLKGKLYH*************************DLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTNTSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSS*****************IEIEDQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHWNSCMQAC**************CYNCGAEGHFARECVSSSKVRKRNIDASTPTFR*********GIKSAPHD**************************GGWITDDPGDISYGKP*****************ISAITSG****************************DGIRRGYDWW
********************************DEEGNEDLSLKIVEKHMLMRAAKLDQDDSDSDVVL*DN********************PGP****DDV*IED**************************QSVIVRKE*Q*****DN*DEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCF*********RQCSKAQDCF****G****K*CP**********Q*********HDMFSCR******DLKEVQCYIC*CFGHLCCVNISDAVPGEVSCFRC*QLGHTGLHW*********************C*****EGHFARECV*******************************************************************************************************************************************
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MATRQKLKGKLYHEENGEEEEKLKSAAAMSSDDEEGNEDLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTNTSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSSDKKRIRVRKKKKKEADKIEIEDQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHWNSCMQACARSRGETVEASPSSCYNCGAEGHFARECVSSSKVRKRNIDASTPTFRPHRENKDHSGIKSAPHDLGKVHKRKKTQHEERGIMTSRKSKQRGGWITDDPGDISYGKPKRNHWRSPGTPSSKAHKISAITSGGHFSSPQSSIKRNSHHRFSASRFDSSGSDGIRRGYDWW
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query491 2.2.26 [Sep-21-2011]
Q04832271 DNA-binding protein HEXBP yes no 0.344 0.623 0.307 3e-13
O65639299 Cold shock protein 1 OS=A no no 0.329 0.541 0.302 1e-11
P53996178 Cellular nucleic acid-bin yes no 0.256 0.707 0.309 2e-10
Q3T0Q6170 Cellular nucleic acid-bin yes no 0.287 0.829 0.306 2e-10
O42395172 Cellular nucleic acid-bin yes no 0.244 0.697 0.317 3e-10
P62634177 Cellular nucleic acid-bin yes no 0.254 0.706 0.304 4e-10
Q5R5R5177 Cellular nucleic acid-bin yes no 0.254 0.706 0.304 4e-10
P62633177 Cellular nucleic acid-bin yes no 0.254 0.706 0.304 4e-10
P36627179 Cellular nucleic acid-bin yes no 0.299 0.821 0.322 5e-10
Q94C69301 Cold shock domain-contain no no 0.331 0.541 0.278 2e-07
>sp|Q04832|HEXP_LEIMA DNA-binding protein HEXBP OS=Leishmania major GN=HEXBP PE=4 SV=1 Back     alignment and function desciption
 Score = 77.0 bits (188), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 64/208 (30%), Positives = 84/208 (40%), Gaps = 39/208 (18%)

Query: 182 TCYNCGEEGHMAVNCRSAV----KRKKPCFVCGSLEHGVRQC--------SKAQDCFICK 229
           +C NCG+EGH A  C  A     +R   CF CG   H  R+C        + A  CF C 
Sbjct: 17  SCRNCGKEGHYARECPEADSKGDERSTTCFRCGEEGHMSRECPNEARSGAAGAMTCFRCG 76

Query: 230 KGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSC-------RNSYSLDDLK------- 275
           + GH ++DCP+  K G      C KCG  GH    C       R  Y     +       
Sbjct: 77  EAGHMSRDCPNSAKPGAAKGFECYKCGQEGHLSRDCPSSQGGSRGGYGQKRGRSGAQGGY 136

Query: 276 --EVQCYICRCFGHLC--CVNISDAV--PGEVSCFRCGQLGHTGLHWNSCMQACARSRGE 329
             +  CY C   GH+   C N        G+ +C++CG  GH         + C   +G 
Sbjct: 137 SGDRTCYKCGDAGHISRDCPNGQGGYSGAGDRTCYKCGDAGHI-------SRDCPNGQGG 189

Query: 330 TVEASPSSCYNCGAEGHFARECVSSSKV 357
              A    CY CG  GH +REC S+   
Sbjct: 190 YSGAGDRKCYKCGESGHMSRECPSAGST 217
Binds to single-stranded DNA located in the 5' hexanucleotide repeat region of the L.major leishmanolysin (GP63) gene.
Leishmania major (taxid: 5664)
>sp|O65639|CSP1_ARATH Cold shock protein 1 OS=Arabidopsis thaliana GN=CSP1 PE=2 SV=1 Back     alignment and function description
>sp|P53996|CNBP_MOUSE Cellular nucleic acid-binding protein OS=Mus musculus GN=Cnbp PE=2 SV=2 Back     alignment and function description
>sp|Q3T0Q6|CNBP_BOVIN Cellular nucleic acid-binding protein OS=Bos taurus GN=CNBP PE=2 SV=1 Back     alignment and function description
>sp|O42395|CNBP_CHICK Cellular nucleic acid-binding protein OS=Gallus gallus GN=CNBP PE=2 SV=1 Back     alignment and function description
>sp|P62634|CNBP_RAT Cellular nucleic acid-binding protein OS=Rattus norvegicus GN=Cnbp PE=2 SV=1 Back     alignment and function description
>sp|Q5R5R5|CNBP_PONAB Cellular nucleic acid-binding protein OS=Pongo abelii GN=CNBP PE=2 SV=1 Back     alignment and function description
>sp|P62633|CNBP_HUMAN Cellular nucleic acid-binding protein OS=Homo sapiens GN=CNBP PE=1 SV=1 Back     alignment and function description
>sp|P36627|BYR3_SCHPO Cellular nucleic acid-binding protein homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=byr3 PE=4 SV=1 Back     alignment and function description
>sp|Q94C69|CSP3_ARATH Cold shock domain-containing protein 3 OS=Arabidopsis thaliana GN=CSP3 PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query491
359479082481 PREDICTED: uncharacterized protein LOC10 0.934 0.954 0.534 1e-126
255573261497 cellular nucleic acid binding protein, p 0.961 0.949 0.5 1e-121
296084007441 unnamed protein product [Vitis vinifera] 0.725 0.807 0.607 1e-120
224132214 683 predicted protein [Populus trichocarpa] 0.918 0.660 0.472 1e-115
356547869529 PREDICTED: uncharacterized protein LOC10 0.934 0.867 0.440 1e-113
356574813533 PREDICTED: uncharacterized protein LOC10 0.926 0.853 0.451 1e-113
224102939 640 predicted protein [Populus trichocarpa] 0.896 0.687 0.441 1e-109
255634708389 unknown [Glycine max] 0.655 0.827 0.487 3e-94
147828626513 hypothetical protein VITISV_005152 [Viti 0.843 0.807 0.448 2e-89
357493439 638 Cellular nucleic acid-binding protein [M 0.665 0.512 0.466 2e-86
>gi|359479082|ref|XP_002272646.2| PREDICTED: uncharacterized protein LOC100259916 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  457 bits (1176), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 274/513 (53%), Positives = 329/513 (64%), Gaps = 54/513 (10%)

Query: 1   MATRQKLKGKLYHEENGEEEEKLKSAAAMSS-DDEEGNEDLSLKIVEKHMLMRAAKLDQD 59
           M  RQK K K+ H+E+ E     +S   +SS DDEE NEDLSLKIVEK M  RA+K D +
Sbjct: 1   MGRRQKPKAKIDHQEDEEGANSSRSVIYLSSSDDEEANEDLSLKIVEKAM-KRASKTDHN 59

Query: 60  DSDSDVVLNDNTNTNTSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSSDKKRIRVRKKK 119
           D+    VL   +      +S ++   V     GP+ T DD  ++  K   +K  R  K  
Sbjct: 60  DA----VLAGRSAVIDLGSSPSEEAEVITDRSGPT-TDDDAEVKSKKKKSRKEKRANKN- 113

Query: 120 KKEADKIEIEDQSVIVRKEEQKVETADNGDEGVTTVEI-----SDNIVLRKLLRGPRYFD 174
                 IE ++++  +  EE+K E+ D   E +  VE      SDNIVLRKLLRGPRYFD
Sbjct: 114 ------IENQEKTDEILMEEKKGES-DKALEILKMVEPYPVEGSDNIVLRKLLRGPRYFD 166

Query: 175 PPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHR 234
           PPD GW  CYNCGEEGH AVNC ++VKRKKPCFVCGSLEH  +QC K QDCFICKKGGHR
Sbjct: 167 PPDSGWGACYNCGEEGHNAVNC-ASVKRKKPCFVCGSLEHNAKQCMKGQDCFICKKGGHR 225

Query: 235 AKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNIS 294
           AKDCP+KH+SG QN+++CLKCGDS HDMFSCRN YS +DLKE+QCYIC+ FGHLCC+N  
Sbjct: 226 AKDCPEKHRSGSQNSKICLKCGDSRHDMFSCRNDYSPEDLKEIQCYICKSFGHLCCINYV 285

Query: 295 DAVPGEVSCFRCGQLGHTGLHWNSCMQACARSRGETVEA-SPSSCYNCGAEGHFARECVS 353
           D  P E SC++CGQLGHTGL       ACAR   ET +  +PSSCY CG +GHF      
Sbjct: 286 DTGPIEPSCYKCGQLGHTGL-------ACARLNAETADVQTPSSCYRCGEQGHF------ 332

Query: 354 SSKVRKRNIDASTPTFRPHRENKDHSGIKSAPHDLGKVHKRKKTQHEERGIMTSRKSKQR 413
              V KR  + ST + R  +E+KD  G KSAP DLG   KRKK  +EERG +T RK KQR
Sbjct: 333 ---VSKRYSEVSTQSRRFLKEDKDKLGFKSAPKDLGMGRKRKKPWYEERGNITPRKPKQR 389

Query: 414 GGWITDDPGDISYGKPKRNHWRSPGTPSSKAHKISAITSGGHFSSPQSS------IKRN- 466
           GGWIT+DPGD    K K   WRSP TP++K HK   +T+ GH++S QSS        RN 
Sbjct: 390 GGWITEDPGDSPQRKAKVKSWRSPATPTNKNHKRPMLTA-GHYTSSQSSKNTQKFYSRNS 448

Query: 467 --------SHHRFSASRFDSSGSDGIRRGYDWW 491
                   S HRFSASRF SS SD +RR YDWW
Sbjct: 449 TWQGSAKASQHRFSASRFGSSSSDAVRRHYDWW 481

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255573261|ref|XP_002527559.1| cellular nucleic acid binding protein, putative [Ricinus communis] gi|223533051|gb|EEF34811.1| cellular nucleic acid binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|296084007|emb|CBI24395.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224132214|ref|XP_002328213.1| predicted protein [Populus trichocarpa] gi|222837728|gb|EEE76093.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356547869|ref|XP_003542327.1| PREDICTED: uncharacterized protein LOC100780476 [Glycine max] Back     alignment and taxonomy information
>gi|356574813|ref|XP_003555539.1| PREDICTED: uncharacterized protein LOC100794448 [Glycine max] Back     alignment and taxonomy information
>gi|224102939|ref|XP_002312862.1| predicted protein [Populus trichocarpa] gi|222849270|gb|EEE86817.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|255634708|gb|ACU17716.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|147828626|emb|CAN73043.1| hypothetical protein VITISV_005152 [Vitis vinifera] Back     alignment and taxonomy information
>gi|357493439|ref|XP_003617008.1| Cellular nucleic acid-binding protein [Medicago truncatula] gi|355518343|gb|AES99966.1| Cellular nucleic acid-binding protein [Medicago truncatula] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query491
TAIR|locus:2079859551 AT3G43590 [Arabidopsis thalian 0.700 0.624 0.423 6.6e-79
TAIR|locus:2183607254 AT5G36240 [Arabidopsis thalian 0.201 0.389 0.495 3.5e-25
TAIR|locus:2098164260 AT3G43490 [Arabidopsis thalian 0.173 0.326 0.505 5.1e-24
POMBASE|SPAC13D6.02c179 byr3 "zinc finger protein Byr3 0.299 0.821 0.322 8.6e-19
TAIR|locus:2135139299 CSDP1 "cold shock domain prote 0.319 0.525 0.324 1.1e-17
ZFIN|ZDB-GENE-030131-7782243 cnbpb "CCHC-type zinc finger, 0.283 0.572 0.310 1.4e-17
ZFIN|ZDB-GENE-030131-5045163 cnbpa "CCHC-type zinc finger, 0.283 0.852 0.304 1.8e-17
ASPGD|ASPL0000028407171 AN5111 [Emericella nidulans (t 0.313 0.900 0.298 8.4e-17
UNIPROTKB|B4DP17160 CNBP "cDNA FLJ61146, highly si 0.268 0.825 0.322 3.9e-16
CGD|CAL0002417175 GIS2 [Candida albicans (taxid: 0.319 0.897 0.291 6.4e-16
TAIR|locus:2079859 AT3G43590 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 742 (266.3 bits), Expect = 6.6e-79, Sum P(2) = 6.6e-79
 Identities = 154/364 (42%), Positives = 207/364 (56%)

Query:   137 KEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNC 196
             K E + +  +  DE  T  E + N+VL+KLLRG RYFDPPD GW +CY+CGE+GH + NC
Sbjct:   123 KGEGEDDEVERSDEPKTE-ETASNLVLKKLLRGARYFDPPDAGWVSCYSCGEQGHTSFNC 181

Query:   197 RSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCG 256
              +  KR+KPCF+CGSLEHG +QCSK  DC+ICKK GHRAKDCPDK+K+G + A VCL+CG
Sbjct:   182 PTPTKRRKPCFICGSLEHGAKQCSKGHDCYICKKTGHRAKDCPDKYKNGSKGA-VCLRCG 240

Query:   257 DSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHW 316
             D GHDM  C+  YS +DLK+VQCYIC+ FGHLCCV   +++   VSC+RCGQLGH+GL  
Sbjct:   241 DFGHDMILCKYEYSKEDLKDVQCYICKSFGHLCCVEPGNSLSWAVSCYRCGQLGHSGLAC 300

Query:   317 NSCMQACARSRGETVEA-----SPSSCYNCGAEGHFARECVSSSKVR-KRNIDASTPTFR 370
                 +    +   T E        S CY CG EGHFAREC +SS +      ++ T  +R
Sbjct:   301 GRHYEESNENDSATPERLFNSREASECYRCGEEGHFARECPNSSSISTSHGRESQTLCYR 360

Query:   371 PHRENKDHSGIKSAPHDLGKVHKRKK----TQHEERGIMTSRKSKQRGGWITDDPGDISY 426
              +     H   +  P+   +V KR +    T H+ R    ++++ +      +  G    
Sbjct:   361 CN--GSGHFA-RECPNS-SQVSKRDRETSTTSHKSR--KKNKENSEHDSTPHESNGKTKK 414

Query:   427 GKPKRNHWRS-PGT-PSSKAHKISAITSGGHFSSPQSSIKRNSHHRFSASRFDSSGSDGI 484
              K K+ H    P T P  + H+   IT      S Q    R      + S ++ S S  I
Sbjct:   415 KKKKKTHKEEQPQTSPRKRKHRGGWITEEPEEESFQRGKMRRPKSPITPSGYNRSPSTHI 474

Query:   485 RRGY 488
                Y
Sbjct:   475 GHNY 478
GO:0003676 "nucleic acid binding" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0008270 "zinc ion binding" evidence=IEA
TAIR|locus:2183607 AT5G36240 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2098164 AT3G43490 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
POMBASE|SPAC13D6.02c byr3 "zinc finger protein Byr3" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
TAIR|locus:2135139 CSDP1 "cold shock domain protein 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-7782 cnbpb "CCHC-type zinc finger, nucleic acid binding protein b" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-5045 cnbpa "CCHC-type zinc finger, nucleic acid binding protein a" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
ASPGD|ASPL0000028407 AN5111 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
UNIPROTKB|B4DP17 CNBP "cDNA FLJ61146, highly similar to Cellular nucleic acid-binding protein" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
CGD|CAL0002417 GIS2 [Candida albicans (taxid:5476)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00017443001
SubName- Full=Chromosome chr6 scaffold_15, whole genome shotgun sequence; (482 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query491
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 9e-20
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 4e-13
COG5082190 COG5082, AIR1, Arginine methyltransferase-interact 2e-09
COG5082190 COG5082, AIR1, Arginine methyltransferase-interact 2e-06
pfam0009818 pfam00098, zf-CCHC, Zinc knuckle 0.004
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information 
 Score = 85.2 bits (211), Expect = 9e-20
 Identities = 46/175 (26%), Positives = 66/175 (37%), Gaps = 30/175 (17%)

Query: 182 TCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDK 241
            CY CG  GH +  C ++                    +KA+ C+ C + GH +++CP  
Sbjct: 2   VCYRCGGVGHQSRECPNSAPA---------------GAAKARPCYKCGEPGHLSRECPSA 46

Query: 242 HKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLC--CVNISDAVPG 299
                   + C  CG +GH    C  +          CY C   GH+   C N +     
Sbjct: 47  PGGR--GERSCYNCGKTGHLSRECPEAPP--GSGPRSCYNCGQTGHISRECPNRAKGGAA 102

Query: 300 EVSCFRCGQLGHTGLHWNSCMQACARSRGETVEASPSSCYNCGAEGHFARECVSS 354
             +C+ CG  GH       C  A  R  G        +CYNCG  GH +R+C   
Sbjct: 103 RRACYNCGGEGHIS---RDCPNAGKRPGG------DKTCYNCGQTGHLSRDCPDK 148

Length = 148
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] Back     alignment and domain information
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] Back     alignment and domain information
>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 491
PTZ00368148 universal minicircle sequence binding protein (UMS 99.92
PTZ00368148 universal minicircle sequence binding protein (UMS 99.78
COG5082190 AIR1 Arginine methyltransferase-interacting protei 99.77
COG5082190 AIR1 Arginine methyltransferase-interacting protei 99.64
KOG4400261 consensus E3 ubiquitin ligase interacting with arg 99.6
KOG4400261 consensus E3 ubiquitin ligase interacting with arg 99.46
KOG0119554 consensus Splicing factor 1/branch point binding p 98.91
KOG0335 482 consensus ATP-dependent RNA helicase [RNA processi 97.79
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 97.66
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 97.6
PF1369632 zf-CCHC_2: Zinc knuckle 94.73
PF1369632 zf-CCHC_2: Zinc knuckle 94.67
KOG0119 554 consensus Splicing factor 1/branch point binding p 92.73
PF1391742 zf-CCHC_3: Zinc knuckle 92.51
PF1391742 zf-CCHC_3: Zinc knuckle 91.87
smart0034326 ZnF_C2HC zinc finger. 90.86
smart0034326 ZnF_C2HC zinc finger. 90.43
PF1439249 zf-CCHC_4: Zinc knuckle 85.33
KOG0314448 consensus Predicted E3 ubiquitin ligase [Posttrans 81.57
PF1439249 zf-CCHC_4: Zinc knuckle 81.23
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information 
Probab=99.92  E-value=5.3e-25  Score=201.99  Aligned_cols=138  Identities=32%  Similarity=0.872  Sum_probs=100.7

Q ss_pred             cccccccccCccccccccc----ccCCCCcceeecCCCCcccCCCC------ccccccccCCCCCCCCCCccCCCCcCCc
Q 011182          181 QTCYNCGEEGHMAVNCRSA----VKRKKPCFVCGSLEHGVRQCSKA------QDCFICKKGGHRAKDCPDKHKSGFQNAQ  250 (491)
Q Consensus       181 ~~C~~CG~~GH~a~~Cp~~----~~~~~~C~~CG~~GH~a~~Cp~~------~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~  250 (491)
                      ++||+|++.||++++||..    ......|++|+..||++++||..      ..||+|++.||++++||.....  ....
T Consensus         1 ~~C~~C~~~GH~~~~c~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~--~~~~   78 (148)
T PTZ00368          1 MVCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPG--SGPR   78 (148)
T ss_pred             CcCCCCCCCCcCcccCcCCCCCCCCCCccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCcccC--CCCc
Confidence            3699999999999999983    12345788888888888888753      2577777777777777765432  1345


Q ss_pred             ccccCCCCCcCCCCCCCCCCCCccccccccccCCCCcccccCcCCCCCCCcccccCCCCCCCCcccccccccccccCCCC
Q 011182          251 VCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHWNSCMQACARSRGET  330 (491)
Q Consensus       251 ~C~~Cg~~GH~~~dCp~~~~~~~~~~~~C~~Cg~~GHl~c~~~~~~~~~~~~C~~Cg~~GH~~~~~~~~~~~C~~~~~~~  330 (491)
                      .|++|++.||++.+|++.+.                         .....+.||+|++.||+++       +|++...  
T Consensus        79 ~C~~Cg~~GH~~~~C~~~~~-------------------------~~~~~~~C~~Cg~~gH~~~-------~C~~~~~--  124 (148)
T PTZ00368         79 SCYNCGQTGHISRECPNRAK-------------------------GGAARRACYNCGGEGHISR-------DCPNAGK--  124 (148)
T ss_pred             ccCcCCCCCcccccCCCccc-------------------------ccccchhhcccCcCCcchh-------cCCCccc--
Confidence            67777777777777776421                         1123468999999999999       9987421  


Q ss_pred             CCCCCCCcccCCCCCCCcCcCCCc
Q 011182          331 VEASPSSCYNCGAEGHFARECVSS  354 (491)
Q Consensus       331 ~~~~~~~Cy~Cg~~GH~ardCp~~  354 (491)
                      .+.....||+|++.|||+++||.+
T Consensus       125 ~~~~~~~C~~Cg~~gH~~~dCp~~  148 (148)
T PTZ00368        125 RPGGDKTCYNCGQTGHLSRDCPDK  148 (148)
T ss_pred             cCCCCCccccCCCcCcccccCCCC
Confidence            224568999999999999999974

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] Back     alignment and domain information
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] Back     alignment and domain information
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification] Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>PF13696 zf-CCHC_2: Zinc knuckle Back     alignment and domain information
>PF13696 zf-CCHC_2: Zinc knuckle Back     alignment and domain information
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>PF13917 zf-CCHC_3: Zinc knuckle Back     alignment and domain information
>PF13917 zf-CCHC_3: Zinc knuckle Back     alignment and domain information
>smart00343 ZnF_C2HC zinc finger Back     alignment and domain information
>smart00343 ZnF_C2HC zinc finger Back     alignment and domain information
>PF14392 zf-CCHC_4: Zinc knuckle Back     alignment and domain information
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PF14392 zf-CCHC_4: Zinc knuckle Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query491
1a1t_A55 Structure Of The Hiv-1 Nucleocapsid Protein Bound T 4e-04
2m3z_A55 Nmr Solution Structure Of Hiv-1 Nucleocapsid Protei 4e-04
1f6u_A56 Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bou 4e-04
1aaf_A55 Nucleocapsid Zinc Fingers Detected In Retroviruses: 8e-04
>pdb|1A1T|A Chain A, Structure Of The Hiv-1 Nucleocapsid Protein Bound To The Sl3 Psi-Rna Recognition Element, Nmr, 25 Structures Length = 55 Back     alignment and structure 
Iteration: 1

 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 29/41 (70%), Gaps = 2/41 (4%)
Query: 183 CYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQ 223
           C+NCG+EGH+A NCR+   RKK C+ CG   H ++ C++ Q
Sbjct: 15  CFNCGKEGHIAKNCRAP--RKKGCWKCGKEGHQMKDCTERQ 53
>pdb|2M3Z|A Chain A, Nmr Solution Structure Of Hiv-1 Nucleocapsid Protein In Complex With An Inhibitor Displaying A 2 Inhibitors:1 Nc Stoichiometry Length = 55 Back     alignment and structure
>pdb|1F6U|A Chain A, Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bound To Stem-Loop Sl2 Of The Psi-Rna Packaging Signal. Implications For Genome Recognition Length = 56 Back     alignment and structure
>pdb|1AAF|A Chain A, Nucleocapsid Zinc Fingers Detected In Retroviruses: Exafs Studies On Intact Viruses And The Solution-State Structure Of The Nucleocapsid Protein From Hiv-1 Length = 55 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query491
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 6e-15
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 2e-08
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 2e-07
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 2e-05
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 2e-09
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 2e-06
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 9e-05
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 6e-09
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 1e-06
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 2e-05
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 5e-08
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 2e-07
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 7e-06
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 7e-06
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 7e-06
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 2e-05
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 4e-04
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 4e-04
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124 Back     alignment and structure
 Score = 70.2 bits (171), Expect = 6e-15
 Identities = 35/171 (20%), Positives = 51/171 (29%), Gaps = 54/171 (31%)

Query: 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPD 240
             C NC + GH+  +C         C  CG+                     H ++ CP 
Sbjct: 5   PKCNNCSQRGHLKKDCP-----HIICSYCGA------------------TDDHYSRHCP- 40

Query: 241 KHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGE 300
                   A  C KC + GH    C + +     K+VQC +C+   H       +  P  
Sbjct: 41  -------KAIQCSKCDEVGHYRSQCPHKW-----KKVQCTLCKSKKH-----SKERCPSI 83

Query: 301 VSCFRCGQLGHTGLHWNSCMQACARSRGETVEASPSSCYNCGAEGHFAREC 351
              +                                 CYNCG +GHF  +C
Sbjct: 84  WRAYILVDDNEKAKPKVLP-------------FHTIYCYNCGGKGHFGDDC 121
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124 Back     alignment and structure
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124 Back     alignment and structure
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124 Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61 Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61 Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61 Back     alignment and structure
>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 Length = 60 Back     alignment and structure
>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 Length = 60 Back     alignment and structure
>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 Length = 60 Back     alignment and structure
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74 Back     alignment and structure
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63 Back     alignment and structure
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Length = 39 Back     alignment and structure
>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 Length = 55 Back     alignment and structure
>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 Length = 49 Back     alignment and structure
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Length = 83 Back     alignment and structure
>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* Length = 148 Back     alignment and structure
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Length = 37 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query491
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 99.87
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 99.87
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 99.43
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 99.27
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 99.07
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 99.03
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 98.94
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 98.92
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 98.92
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 98.9
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 98.87
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 98.84
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 98.8
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 98.8
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 98.78
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 98.76
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 98.75
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 98.72
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 98.71
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 98.69
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 98.53
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 98.48
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 97.54
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 97.37
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 97.36
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 97.36
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 97.29
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 97.03
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 96.96
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 96.6
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 96.12
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 95.95
2db3_A 434 ATP-dependent RNA helicase VASA; DEAD-BOX, protein 89.31
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
Probab=99.87  E-value=1.9e-22  Score=178.59  Aligned_cols=81  Identities=32%  Similarity=0.742  Sum_probs=74.2

Q ss_pred             ccccccccccCcccccccccccCCCCcceeecC-CCCcccCCCCccccccccCCCCCCCCCCccCCCCcCCcccccCCCC
Q 011182          180 WQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSL-EHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDS  258 (491)
Q Consensus       180 ~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~-GH~a~~Cp~~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~C~~Cg~~  258 (491)
                      .+.||+|++.||++++||..     .|++||+. ||++++||....||+|++.||++++||....     ...|++|++.
T Consensus         4 ~~~C~~C~~~GH~~~~Cp~~-----~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~-----~~~C~~Cg~~   73 (124)
T 2lli_A            4 APKCNNCSQRGHLKKDCPHI-----ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWK-----KVQCTLCKSK   73 (124)
T ss_dssp             SSCCSSCSSSSCCTTTTTSC-----CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCC-----CCSSSSSCSS
T ss_pred             CCcccCCCCCCcCcccCcCC-----cCcCCCCcCCccCcccCCcccccccCCCCCccccCcCccc-----CccCCCCCcC
Confidence            46799999999999999995     89999998 9999999988899999999999999998643     4789999999


Q ss_pred             CcCCCCCCCCCC
Q 011182          259 GHDMFSCRNSYS  270 (491)
Q Consensus       259 GH~~~dCp~~~~  270 (491)
                      ||++++||..|.
T Consensus        74 GH~~~~Cp~~~~   85 (124)
T 2lli_A           74 KHSKERCPSIWR   85 (124)
T ss_dssp             CCCTTTCCCSTT
T ss_pred             CcchhhCCCccc
Confidence            999999998764
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Back     alignment and structure
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Back     alignment and structure
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Back     alignment and structure
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Back     alignment and structure
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Back     alignment and structure
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Back     alignment and structure
>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 Back     alignment and structure
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Back     alignment and structure
>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 Back     alignment and structure
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>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 Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Back     alignment and structure
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>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 Back     alignment and structure
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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* Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 491
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 9e-07
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 6e-05
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 0.002
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42 Back     information, alignment and structure

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]

 Score = 43.3 bits (102), Expect = 9e-07
 Identities = 20/41 (48%), Positives = 28/41 (68%), Gaps = 2/41 (4%)

Query: 183 CYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQ 223
           C+NCG+EGH A NCR+   RKK C+ CG   H ++ C++ Q
Sbjct: 4   CFNCGKEGHTARNCRA--PRKKGCWKCGKEGHQMKDCTERQ 42
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42 Back     information, alignment and structure
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query491
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 99.01
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 99.0
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 97.84
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 97.29
d1a6bb_40 Zinc finger protein ncp10 {Moloney murine leukemia 95.52
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 93.84
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 93.55
d1a6bb_40 Zinc finger protein ncp10 {Moloney murine leukemia 93.24
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Back     information, alignment and structure
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=99.01  E-value=9.7e-11  Score=82.89  Aligned_cols=40  Identities=43%  Similarity=1.094  Sum_probs=35.7

Q ss_pred             cccccCCCCCCCCcccccccccccccCCCCCCCCCCCcccCCCCCCCcCcCCCc
Q 011182          301 VSCFRCGQLGHTGLHWNSCMQACARSRGETVEASPSSCYNCGAEGHFARECVSS  354 (491)
Q Consensus       301 ~~C~~Cg~~GH~~~~~~~~~~~C~~~~~~~~~~~~~~Cy~Cg~~GH~ardCp~~  354 (491)
                      +.||+|++.||++.       +||..+       ...||+|++.||++++||++
T Consensus         2 i~C~~Cg~~GH~~~-------~Cp~~~-------~~~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1           2 VKCFNCGKEGHTAR-------NCRAPR-------KKGCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             CCCTTTCCSSSCTT-------TCSSCC-------CSSCSSSCCSSSCTTTCCSS
T ss_pred             CccccCCCcCcCcc-------cCcCCC-------cCccccCCCCCeecccCCCC
Confidence            78999999999999       999743       35799999999999999975
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Back     information, alignment and structure
>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]} Back     information, alignment and structure
>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]} Back     information, alignment and structure
>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]} Back     information, alignment and structure
>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]} Back     information, alignment and structure
>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]} Back     information, alignment and structure
>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]} Back     information, alignment and structure