Citrus Sinensis ID: 021457

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--
MATRQKLKGKLYHEENGEEEEKLKSAAAMSSDDEEGNEDLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTNTSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSSDKKRIRVRKKKKKEADKIEIEDQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKVCLYFLVQYLAFCIMQSLLVSFKSLEFVCIWYETVVL
cHHHHHcccccccccccccHHHHHHHccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccEEccccccccccccHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEc
ccccccccccEEEcccccccccccEEEEEccccHHHcHHHHHHHHHHHHHHHHHHccccccccEEEEccccccccccccccccccEEEEEccccccccccEEccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHccHHcccccccccccccEEEcccccHHHHHHHccccccccccccccEEEccccccccccccccccccccccEccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccEEEEEccccccEEccccccEEEEEEEEEEEEEEEEEc
matrqklkgklyheengeeeEKLKSAAamssddeegneDLSLKIVEKHMLMRAAkldqddsdsdvvlndntntntsdnsnnknggveavvpgpsgttddviiedvkSSDKKRIRVRKKKKKEADKIEIEDQSVIVRKeeqkvetadngdegvttvEISDNIVLRKllrgpryfdppdrgwqtcyncgeeghmavncrsavkrkkpcfvcgslehgvrqcskaqdcfickkgghrakdcpdkhksgfqnaqvclkcgdsghdmfscrnsyslddLKVCLYFLVQYLAFCIMQSLLVSFKSLEFVCIWYETVVL
matrqklkgklyheengeeeeklksaaamssddeegNEDLSLKIVEKHMLMRAAKldqddsdsdvVLNDNtntntsdnsnnknggveavvpgpsgttddviiedvkssdkkrirvrkkkkkeadkieiedqsvivrkeeqkvetadngdegvttveisdnivlrkllrgpryfdppdrGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSlehgvrqcskAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKVCLYFLVQYLAFCIMQSLLVSFKSLEFVCIWYETVVL
MATRQKLKGKLYHeengeeeeKLKSAAAMSSDDEEGNEDLSLKIVEKHMLMRAAKldqddsdsdvvlndntntntsdnsnnKNGGVEAVVPGPSGTTDDVIIEDvkssdkkrirvrkkkkkeadkieiedQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKVCLYFLVQYLAFCIMQSLLVSFKSLEFVCIWYETVVL
*******************************************************************************************************************************************************VTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNC*****************KPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDC****KSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKVCLYFLVQYLAFCIMQSLLVSFKSLEFVCIWYETVV*
******************************************************************************************************************************************************************************PPDRGWQTCYNCGEEGHMAVNC****K*KKPCFVCGSLEHGVRQCSKAQDCFICKKGGHR******************LKCGDSGHDMFSCRNSYSLDDLKVCLYFLVQYLAFCIMQSL****KSLEFVCIWYETVVL
MATRQKLKGKLYH*************************DLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTNTSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSS*****************IEIEDQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKVCLYFLVQYLAFCIMQSLLVSFKSLEFVCIWYETVVL
*********************KLKSAAAMSSDDEEGNEDLSLKIVEKHMLMRAAKLDQDDSDSDVVL*DN**************G*EA*VPGPSGTTDDVIIEDVKSSD*KRIRVRKKKKKEAD**************************GVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKVCLYFLVQYLAFCIMQSLLVSFKSLEFVCIWYETVVL
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MATRQKLKGKLYHEENGEEEEKLKSAAAMSSDDEEGNEDLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTNTSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSSDKKRIRVRKKKKKEADKIEIEDQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKVCLYFLVQYLAFCIMQSLLVSFKSLEFVCIWYETVVL
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 ?
Query312 2.2.26 [Sep-21-2011]
Q77373 1435 Gag-Pol polyprotein OS=Hu yes no 0.195 0.042 0.415 5e-08
O65639299 Cold shock protein 1 OS=A no no 0.25 0.260 0.340 1e-07
Q8WW36166 Zinc finger CCHC domain-c yes no 0.233 0.439 0.413 1e-07
Q04832 271 DNA-binding protein HEXBP no no 0.253 0.291 0.384 1e-07
P24736493 Gag polyprotein OS=Human no no 0.224 0.141 0.362 2e-07
P24740 1428 Gag-Pol polyprotein OS=Hu no no 0.217 0.047 0.358 4e-07
O41798 1435 Gag-Pol polyprotein OS=Hu no no 0.137 0.029 0.466 2e-06
Q79666 1446 Gag-Pol polyprotein OS=Hu no no 0.195 0.042 0.358 2e-06
Q75002 1439 Gag-Pol polyprotein OS=Hu no no 0.163 0.035 0.444 2e-06
Q8R1J3273 Zinc finger CCHC domain-c yes no 0.298 0.340 0.271 2e-06
>sp|Q77373|POL_HV1AN Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group O (isolate ANT70) GN=gag-pol PE=3 SV=3 Back     alignment and function desciption
 Score = 58.5 bits (140), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 27/65 (41%), Positives = 38/65 (58%), Gaps = 4/65 (6%)

Query: 174 DPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCF--ICKKG 231
           +P  +G   C+NCG+EGH+A NCR+   RKK C+ CG   H ++ C   +  F  I   G
Sbjct: 387 NPIRKGTIKCFNCGKEGHIARNCRAP--RKKGCWKCGQEGHQMKDCRNGKQFFRQILASG 444

Query: 232 GHRAK 236
           GH A+
Sbjct: 445 GHEAR 449
Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 2
>sp|O65639|CSP1_ARATH Cold shock protein 1 OS=Arabidopsis thaliana GN=CSP1 PE=2 SV=1 Back     alignment and function description
>sp|Q8WW36|ZCH13_HUMAN Zinc finger CCHC domain-containing protein 13 OS=Homo sapiens GN=ZCCHC13 PE=2 SV=1 Back     alignment and function description
>sp|Q04832|HEXP_LEIMA DNA-binding protein HEXBP OS=Leishmania major GN=HEXBP PE=4 SV=1 Back     alignment and function description
>sp|P24736|GAG_HV1U4 Gag polyprotein OS=Human immunodeficiency virus type 1 group M subtype A (isolate U455) GN=gag PE=1 SV=3 Back     alignment and function description
>sp|P24740|POL_HV1U4 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M subtype A (isolate U455) GN=gag-pol PE=1 SV=3 Back     alignment and function description
>sp|O41798|POL_HV19N Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M subtype G (isolate 92NG083) GN=gag-pol PE=3 SV=3 Back     alignment and function description
>sp|Q79666|POL_HV1MV Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group O (isolate MVP5180) GN=gag-pol PE=3 SV=3 Back     alignment and function description
>sp|Q75002|POL_HV1ET Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M subtype C (isolate ETH2220) GN=gag-pol PE=3 SV=3 Back     alignment and function description
>sp|Q8R1J3|ZCHC9_MOUSE Zinc finger CCHC domain-containing protein 9 OS=Mus musculus GN=Zcchc9 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 ?
Query312
359479082 481 PREDICTED: uncharacterized protein LOC10 0.881 0.571 0.518 9e-66
356547869 529 PREDICTED: uncharacterized protein LOC10 0.839 0.495 0.487 2e-64
255573261 497 cellular nucleic acid binding protein, p 0.871 0.547 0.512 8e-63
224132214 683 predicted protein [Populus trichocarpa] 0.923 0.421 0.461 3e-61
356574813 533 PREDICTED: uncharacterized protein LOC10 0.791 0.463 0.5 3e-61
449532848 425 PREDICTED: DNA-binding protein HEXBP-lik 0.887 0.651 0.478 1e-57
224102939 640 predicted protein [Populus trichocarpa] 0.839 0.409 0.454 1e-55
449439166406 PREDICTED: cold shock domain-containing 0.887 0.682 0.478 3e-55
296084007 441 unnamed protein product [Vitis vinifera] 0.432 0.306 0.729 7e-55
297815456 556 hypothetical protein ARALYDRAFT_323091 [ 0.708 0.397 0.448 5e-48
>gi|359479082|ref|XP_002272646.2| PREDICTED: uncharacterized protein LOC100259916 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  256 bits (654), Expect = 9e-66,   Method: Compositional matrix adjust.
 Identities = 154/297 (51%), Positives = 190/297 (63%), Gaps = 22/297 (7%)

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 AKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLK-VCLYFLVQYLAFCIM 290
           AKDCP+KH+SG QN+++CLKCGDS HDMFSCRN YS +DLK +  Y    +   C +
Sbjct: 226 AKDCPEKHRSGSQNSKICLKCGDSRHDMFSCRNDYSPEDLKEIQCYICKSFGHLCCI 282

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356547869|ref|XP_003542327.1| PREDICTED: uncharacterized protein LOC100780476 [Glycine max] Back     alignment and taxonomy information
>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|224132214|ref|XP_002328213.1| predicted protein [Populus trichocarpa] gi|222837728|gb|EEE76093.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356574813|ref|XP_003555539.1| PREDICTED: uncharacterized protein LOC100794448 [Glycine max] Back     alignment and taxonomy information
>gi|449532848|ref|XP_004173390.1| PREDICTED: DNA-binding protein HEXBP-like, partial [Cucumis sativus] 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|449439166|ref|XP_004137358.1| PREDICTED: cold shock domain-containing protein 3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|296084007|emb|CBI24395.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|297815456|ref|XP_002875611.1| hypothetical protein ARALYDRAFT_323091 [Arabidopsis lyrata subsp. lyrata] gi|297321449|gb|EFH51870.1| hypothetical protein ARALYDRAFT_323091 [Arabidopsis lyrata subsp. lyrata] 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 ?
Query312
TAIR|locus:2079859 551 AT3G43590 [Arabidopsis thalian 0.490 0.277 0.557 6.9e-53
TAIR|locus:2098164260 AT3G43490 [Arabidopsis thalian 0.272 0.326 0.505 5.6e-25
UNIPROTKB|Q8WW36166 ZCCHC13 "Zinc finger CCHC doma 0.233 0.439 0.413 2.1e-13
ASPGD|ASPL0000028407171 AN5111 [Emericella nidulans (t 0.275 0.502 0.336 5.6e-13
SGD|S000005199153 GIS2 "Translational activator 0.294 0.601 0.319 8.6e-12
UNIPROTKB|B4DP17160 CNBP "cDNA FLJ61146, highly si 0.266 0.518 0.369 8.6e-12
UNIPROTKB|O42395172 CNBP "Cellular nucleic acid-bi 0.266 0.482 0.369 8.6e-12
MGI|MGI:88431178 Cnbp "cellular nucleic acid bi 0.243 0.426 0.375 8.6e-12
UNIPROTKB|E2RPD7179 CNBP "Uncharacterized protein" 0.243 0.424 0.375 8.6e-12
UNIPROTKB|F8WFK2179 Cnbp "Cellular nucleic acid-bi 0.243 0.424 0.375 8.6e-12
TAIR|locus:2079859 AT3G43590 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 495 (179.3 bits), Expect = 6.9e-53, Sum P(2) = 6.9e-53
 Identities = 87/156 (55%), Positives = 111/156 (71%)

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 DSGHDMFSCRNSYSLDDLK-VCLYFLVQYLAFCIMQ 291
             D GHDM  C+  YS +DLK V  Y    +   C ++
Sbjct:   241 DFGHDMILCKYEYSKEDLKDVQCYICKSFGHLCCVE 276
GO:0003676 "nucleic acid binding" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0008270 "zinc ion binding" evidence=IEA
TAIR|locus:2098164 AT3G43490 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q8WW36 ZCCHC13 "Zinc finger CCHC domain-containing protein 13" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
ASPGD|ASPL0000028407 AN5111 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
SGD|S000005199 GIS2 "Translational activator for mRNAs with internal ribosome entry sites" [Saccharomyces cerevisiae (taxid:4932)] 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
UNIPROTKB|O42395 CNBP "Cellular nucleic acid-binding protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
MGI|MGI:88431 Cnbp "cellular nucleic acid binding protein" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|E2RPD7 CNBP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F8WFK2 Cnbp "Cellular nucleic acid-binding protein" [Rattus norvegicus (taxid:10116)] 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 ?
Query312
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 8e-15
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 1e-14
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 4e-13
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 1e-10
COG5082190 COG5082, AIR1, Arginine methyltransferase-interact 6e-08
COG5082190 COG5082, AIR1, Arginine methyltransferase-interact 2e-04
pfam0009818 pfam00098, zf-CCHC, Zinc knuckle 0.001
smart0034317 smart00343, ZnF_C2HC, zinc finger 0.001
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information 
 Score = 70.2 bits (172), Expect = 8e-15
 Identities = 32/95 (33%), Positives = 45/95 (47%), Gaps = 10/95 (10%)

Query: 175 PPDRGWQTCYNCGEEGHMAVNCRSAVKRKKP--CFVCGSLEHGVRQCSKAQD-------C 225
           P  RG ++CYNCG+ GH++  C  A     P  C+ CG   H  R+C            C
Sbjct: 47  PGGRGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGGAARRAC 106

Query: 226 FICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGH 260
           + C   GH ++DCP+  K      + C  CG +GH
Sbjct: 107 YNCGGEGHISRDCPNAGKRP-GGDKTCYNCGQTGH 140

Length = 148
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information
>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
>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 312
PTZ00368148 universal minicircle sequence binding protein (UMS 99.88
PTZ00368148 universal minicircle sequence binding protein (UMS 99.86
COG5082190 AIR1 Arginine methyltransferase-interacting protei 99.84
COG5082190 AIR1 Arginine methyltransferase-interacting protei 99.59
KOG4400261 consensus E3 ubiquitin ligase interacting with arg 99.47
KOG4400261 consensus E3 ubiquitin ligase interacting with arg 99.34
KOG0119 554 consensus Splicing factor 1/branch point binding p 99.11
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 97.81
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 97.78
COG5176269 MSL5 Splicing factor (branch point binding protein 97.6
PF1369632 zf-CCHC_2: Zinc knuckle 96.29
PF1369632 zf-CCHC_2: Zinc knuckle 95.86
KOG0119 554 consensus Splicing factor 1/branch point binding p 94.61
PF1391742 zf-CCHC_3: Zinc knuckle 94.43
PF1391742 zf-CCHC_3: Zinc knuckle 94.34
smart0034326 ZnF_C2HC zinc finger. 92.74
smart0034326 ZnF_C2HC zinc finger. 92.52
KOG0314 448 consensus Predicted E3 ubiquitin ligase [Posttrans 91.7
KOG0314 448 consensus Predicted E3 ubiquitin ligase [Posttrans 89.75
COG5222 427 Uncharacterized conserved protein, contains RING Z 88.34
PF1439249 zf-CCHC_4: Zinc knuckle 86.67
PF1439249 zf-CCHC_4: Zinc knuckle 86.11
KOG0109 346 consensus RNA-binding protein LARK, contains RRM a 85.13
PF1528840 zf-CCHC_6: Zinc knuckle 83.87
PF1528840 zf-CCHC_6: Zinc knuckle 82.51
COG5222 427 Uncharacterized conserved protein, contains RING Z 81.24
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information 
Probab=99.88  E-value=4.8e-23  Score=177.13  Aligned_cols=114  Identities=27%  Similarity=0.605  Sum_probs=95.6

Q ss_pred             ccccccccccccccccCCccccc--CCCccccCCCCCcCccccccC------cccccccCCCCCCCCCCCCCCCCCcccc
Q 021457          179 GWQTCYNCGEEGHMAVNCRSAVK--RKKPCFVCGSLEHGVRQCSKA------QDCFICKKGGHRAKDCPDKHKSGFQNAQ  250 (312)
Q Consensus       179 ~~~~C~~CG~~GH~a~~Cp~~~~--~~~~C~~CG~~GH~a~~Cp~~------~~C~~Cg~~GH~ardCp~~~~~~~~~~~  250 (312)
                      +...||+|++.||++++||.+..  ....||+|+..||++.+||+.      ..|++|++.||++++||+.... .....
T Consensus        26 ~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~-~~~~~  104 (148)
T PTZ00368         26 KARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKG-GAARR  104 (148)
T ss_pred             CCccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCCcccc-cccch
Confidence            35789999999999999998631  345799999999999999874      3799999999999999997643 23456


Q ss_pred             cccccccCCCCccCCCCCCCCCCCCCccccccCCCCcCcCCCcC
Q 021457          251 VCLKCGDSGHDMFSCRNSYSLDDLKVCLYFLVQYLAFCIMQSLL  294 (312)
Q Consensus       251 ~C~~Cg~~GH~a~dCp~~~~~~~~~~~~Cy~Cg~~GH~~~eC~~  294 (312)
                      .||+|++.||++++||..|.. ....+.||+|++.|||+.+||.
T Consensus       105 ~C~~Cg~~gH~~~~C~~~~~~-~~~~~~C~~Cg~~gH~~~dCp~  147 (148)
T PTZ00368        105 ACYNCGGEGHISRDCPNAGKR-PGGDKTCYNCGQTGHLSRDCPD  147 (148)
T ss_pred             hhcccCcCCcchhcCCCcccc-CCCCCccccCCCcCcccccCCC
Confidence            899999999999999997542 3346899999999999999996

>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
>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
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification] 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
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only] Back     alignment and domain information
>PF14392 zf-CCHC_4: Zinc knuckle Back     alignment and domain information
>PF14392 zf-CCHC_4: Zinc knuckle Back     alignment and domain information
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only] Back     alignment and domain information
>PF15288 zf-CCHC_6: Zinc knuckle Back     alignment and domain information
>PF15288 zf-CCHC_6: Zinc knuckle Back     alignment and domain information
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only] 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 ?
Query312
2m3z_A55 Nmr Solution Structure Of Hiv-1 Nucleocapsid Protei 9e-05
1a1t_A55 Structure Of The Hiv-1 Nucleocapsid Protein Bound T 9e-05
1f6u_A56 Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bou 9e-05
1aaf_A55 Nucleocapsid Zinc Fingers Detected In Retroviruses: 1e-04
2l4l_A45 Structural Insights Into The Ctar Dna Recognition B 2e-04
2exf_A44 Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7( 2e-04
1bj6_A42 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTUR 2e-04
>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 
Iteration: 1

 Score = 44.3 bits (103), Expect = 9e-05,   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|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
>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
>pdb|2L4L|A Chain A, Structural Insights Into The Ctar Dna Recognition By The Hiv-1 Nucleocapsid Protein: Role Of Sugar Deoxyriboses In The Binding Polarity Of Nc Length = 45 Back     alignment and structure
>pdb|2EXF|A Chain A, Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7(12-55)) Complexed With The Dna (-) Primer Binding Site Length = 44 Back     alignment and structure
>pdb|1BJ6|A Chain A, 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES Length = 42 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 ?
Query312
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 7e-17
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 3e-09
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 1e-04
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 8e-12
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 4e-08
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 5e-11
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 3e-08
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 5e-10
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 3e-05
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 2e-09
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 2e-04
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 3e-07
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 5e-04
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 4e-07
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 7e-04
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 5e-07
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 7e-04
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 2e-05
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 8e-05
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 9e-05
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 2e-04
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124 Back     alignment and structure
 Score = 74.8 bits (183), Expect = 7e-17
 Identities = 27/98 (27%), Positives = 35/98 (35%), Gaps = 11/98 (11%)

Query: 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLE-HGVRQCSKAQDCFICKKGGHRAKDCP 239
             C NC + GH+  +C         C  CG+ + H  R C KA  C  C + GH    CP
Sbjct: 5   PKCNNCSQRGHLKKDCP-----HIICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCP 59

Query: 240 DKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKVC 277
            K K        C  C    H    C + +    L   
Sbjct: 60  HKWKK-----VQCTLCKSKKHSKERCPSIWRAYILVDD 92
>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
>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
>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
>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
>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
>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
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Length = 39 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
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query312
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 99.94
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 99.78
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 99.56
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 99.52
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 99.34
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 99.24
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 99.09
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 99.08
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 99.07
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 99.05
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 99.03
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 99.0
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 98.99
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 98.98
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 98.94
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 98.93
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 98.93
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 98.9
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 98.9
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 98.89
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 98.69
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 98.68
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 97.61
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 97.54
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 97.5
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 97.41
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 97.34
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 97.32
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 97.06
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 97.04
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 96.67
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 96.49
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
Probab=99.94  E-value=6.9e-27  Score=194.42  Aligned_cols=105  Identities=25%  Similarity=0.504  Sum_probs=94.2

Q ss_pred             cccccccccccccccCCcccccCCCccccCCCC-CcCccccccCcccccccCCCCCCCCCCCCCCCCCcccccccccccC
Q 021457          180 WQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSL-EHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDS  258 (312)
Q Consensus       180 ~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~-GH~a~~Cp~~~~C~~Cg~~GH~ardCp~~~~~~~~~~~~C~~Cg~~  258 (312)
                      ...||+|++.||++++||..     .||+||+. ||++++||....||+|++.||++++||..+.     ...||+|++.
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            46799999999999999985     79999998 9999999998899999999999999998753     4689999999


Q ss_pred             CCCccCCCCCCCC--------------CCCCCccccccCCCCcCcCCCcC
Q 021457          259 GHDMFSCRNSYSL--------------DDLKVCLYFLVQYLAFCIMQSLL  294 (312)
Q Consensus       259 GH~a~dCp~~~~~--------------~~~~~~~Cy~Cg~~GH~~~eC~~  294 (312)
                      ||++++||..|..              .....+.||+|++.|||+.+||+
T Consensus        74 GH~~~~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A           74 KHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CCCTTTCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCC
T ss_pred             CcchhhCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcC
Confidence            9999999998752              11246899999999999999996
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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

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 312
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 4e-08
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 4e-06
d1nc8a_29 g.40.1.1 (A:) HIV nucleocapsid {Human immunodefici 9e-04
>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 = 46.8 bits (111), Expect = 4e-08
 Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 21/59 (35%)

Query: 183 CYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDK 241
           C+NCG+EGH A NCR+  K+                      C+ C K GH+ KDC ++
Sbjct: 4   CFNCGKEGHTARNCRAPRKKG---------------------CWKCGKEGHQMKDCTER 41
>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
>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 29 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 ?
Query312
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 99.15
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 99.13
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 97.81
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 97.66
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 95.16
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 95.12
d1a6bb_40 Zinc finger protein ncp10 {Moloney murine leukemia 94.67
d1a6bb_40 Zinc finger protein ncp10 {Moloney murine leukemia 93.62
>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=99.15  E-value=1.2e-11  Score=83.14  Aligned_cols=38  Identities=42%  Similarity=1.024  Sum_probs=19.5

Q ss_pred             ccccccCCCCCCCCCCCCCCCCCcccccccccccCCCCccCCCC
Q 021457          224 DCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRN  267 (312)
Q Consensus       224 ~C~~Cg~~GH~ardCp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~  267 (312)
                      .||+|++.||++++||...      ...||+||+.||++++||+
T Consensus         3 ~C~~Cg~~GH~~~~Cp~~~------~~~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1           3 KCFNCGKEGHTARNCRAPR------KKGCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             CCTTTCCSSSCTTTCSSCC------CSSCSSSCCSSSCTTTCCS
T ss_pred             ccccCCCcCcCcccCcCCC------cCccccCCCCCeecccCCC
Confidence            4555555555555555431      2345555555555555554
>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
>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
>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]} Back     information, alignment and structure