Citrus Sinensis ID: 021122

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-------
MATRQKLKGKLYHEENGEEEEKLKSAAAMSSDDEEGNEDLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTNTSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSSDKKRIRVRKKKKKEADKIEIEDQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLVSW
ccHHHHHccccccccccccHHHHHHHccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHcccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
ccccccccccEEEccccccccccccccccccccHHHcHHHHHHHHHHHHHHHHHHHcccccccEEEEccccccccccccccccccEEEEccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccHHHHcEEEHHHHccccccccccHHHcHccccccHHHHcccccccccccccccccEEcccccccccccccccccccccccEcccccccccccccccccccccccccccccccccccccccccccEccccccccccccccccccccccccccEEEccccccccccccccccccccEEEEccccccccccccc
matrqklkgklyheengeeeEKLKSAAamssddeegneDLSLKIVEKHMLMRAAkldqddsdsdvvlndntntntsdnsnnknggveavvpgpsgttddviiedvkSSDKKRIRVRKKKKKEADKIEIEDQSVIVRKeeqkvetadngdegvttvEISDNIVLRKllrgpryfdppdrgwqtcyncgeeghmavncrsavkrkkpcfvcgslehgvrqcskaqdcfickkgghrakdcpdkhksgfqnaqvclkcgdsghdmfscrnsyslddlkeVQCYICrcfghlccvnisdavpgevscfrcgqlghtglvsw
matrqklkgklyheengeeeeklksaaamssddeegNEDLSLKIVEKHMLMRAAKldqddsdsdvVLNDNtntntsdnsnnknggveavvpgpsgttddviiedvkssdkkrirvrkkkkkeadkieiedqsvivrkeeqkvetadngdegvttveisdnivlrkllrgpryfdppdrGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSlehgvrqcskAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRcgqlghtglvsw
MATRQKLKGKLYHeengeeeeKLKSAAAMSSDDEEGNEDLSLKIVEKHMLMRAAKldqddsdsdvvlndntntntsdnsnnKNGGVEAVVPGPSGTTDDVIIEDvkssdkkrirvrkkkkkeadkieiedQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLVSW
*******************************************************************************************************************************************************VTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNC*****************KPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDC****KSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGL***
***************************************************************************************************************************************************************************YFDPPDRGWQTCYNCGEEGHMAVNC***************LEH***QCSKAQDCFICKKGGHR******************LKCGDSGHDM***********LKEVQCYICRCFG***************SCFRCGQLGHTG*VSW
MATRQKLKGKLYH*************************DLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTNTSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSS*****************IEIEDQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLVSW
********************************DEEGNEDLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDN*****************************************RIRVRKKKKKEADKIEIE****IVRKE*Q************************K******YFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKH******AQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLVSW
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MATRQKLKGKLYHEENGEEEEKLKSAAAMSSDDEEGNEDLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTNTSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSSDKKRIRVRKKKKKEADKIEIEDQSVIVRKEEQKVETADNGDEGVTTVEISDNIVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLVSW
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 ?
Query317 2.2.26 [Sep-21-2011]
Q04832271 DNA-binding protein HEXBP yes no 0.410 0.479 0.306 5e-11
P53996178 Cellular nucleic acid-bin no no 0.362 0.646 0.337 3e-09
O42395172 Cellular nucleic acid-bin yes no 0.343 0.633 0.350 5e-09
P36627179 Cellular nucleic acid-bin yes no 0.372 0.659 0.326 1e-08
P62634177 Cellular nucleic acid-bin yes no 0.359 0.644 0.337 1e-08
Q5R5R5177 Cellular nucleic acid-bin yes no 0.359 0.644 0.337 1e-08
P62633177 Cellular nucleic acid-bin yes no 0.359 0.644 0.337 1e-08
Q3T0Q6170 Cellular nucleic acid-bin yes no 0.340 0.635 0.343 5e-08
Q77373 1435 Gag-Pol polyprotein OS=Hu no no 0.192 0.042 0.415 6e-08
P24740 1428 Gag-Pol polyprotein OS=Hu no no 0.214 0.047 0.358 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 = 68.9 bits (167), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 50/163 (30%), Positives = 68/163 (41%), Gaps = 33/163 (20%)

Query: 182 TCYNCGEEGHMAVNC----RSAVKRKKPCFVCGSLEHGVRQC--------SKAQDCFICK 229
           TC+ CGEEGHM+  C    RS       CF CG   H  R C        +K  +C+ C 
Sbjct: 44  TCFRCGEEGHMSRECPNEARSGAAGAMTCFRCGEAGHMSRDCPNSAKPGAAKGFECYKCG 103

Query: 230 KGGHRAKDCPDKH----------------KSGFQNAQVCLKCGDSGHDMFSCRNSY-SLD 272
           + GH ++DCP                   + G+   + C KCGD+GH    C N      
Sbjct: 104 QEGHLSRDCPSSQGGSRGGYGQKRGRSGAQGGYSGDRTCYKCGDAGHISRDCPNGQGGYS 163

Query: 273 DLKEVQCYICRCFGHLC--CVNISDAV--PGEVSCFRCGQLGH 311
              +  CY C   GH+   C N        G+  C++CG+ GH
Sbjct: 164 GAGDRTCYKCGDAGHISRDCPNGQGGYSGAGDRKCYKCGESGH 206
Binds to single-stranded DNA located in the 5' hexanucleotide repeat region of the L.major leishmanolysin (GP63) gene.
Leishmania major (taxid: 5664)
>sp|P53996|CNBP_MOUSE Cellular nucleic acid-binding protein OS=Mus musculus GN=Cnbp PE=2 SV=2 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|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|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|Q3T0Q6|CNBP_BOVIN Cellular nucleic acid-binding protein OS=Bos taurus GN=CNBP PE=2 SV=1 Back     alignment and function description
>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 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

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 ?
Query317
359479082 481 PREDICTED: uncharacterized protein LOC10 0.946 0.623 0.557 3e-85
356547869 529 PREDICTED: uncharacterized protein LOC10 0.917 0.550 0.522 1e-83
356574813 533 PREDICTED: uncharacterized protein LOC10 0.905 0.538 0.524 2e-82
255573261 497 cellular nucleic acid binding protein, p 0.977 0.623 0.533 4e-81
224132214 683 predicted protein [Populus trichocarpa] 0.977 0.453 0.498 4e-79
296084007 441 unnamed protein product [Vitis vinifera] 0.504 0.362 0.776 7e-74
224102939 640 predicted protein [Populus trichocarpa] 0.895 0.443 0.493 2e-73
449532848 425 PREDICTED: DNA-binding protein HEXBP-lik 0.962 0.717 0.506 4e-73
449439166406 PREDICTED: cold shock domain-containing 0.962 0.751 0.506 1e-70
255634708389 unknown [Glycine max] 0.485 0.395 0.729 8e-66
>gi|359479082|ref|XP_002272646.2| PREDICTED: uncharacterized protein LOC100259916 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  321 bits (823), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 179/321 (55%), Positives = 217/321 (67%), Gaps = 21/321 (6%)

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 DAVPGEVSCFRCGQLGHTGLV 315
           D  P E SC++CGQLGHTGL 
Sbjct: 286 DTGPIEPSCYKCGQLGHTGLA 306

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|356574813|ref|XP_003555539.1| PREDICTED: uncharacterized protein LOC100794448 [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|296084007|emb|CBI24395.3| unnamed protein product [Vitis vinifera] 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|449532848|ref|XP_004173390.1| PREDICTED: DNA-binding protein HEXBP-like, partial [Cucumis sativus] 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|255634708|gb|ACU17716.1| unknown [Glycine max] 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 ?
Query317
TAIR|locus:2079859 551 AT3G43590 [Arabidopsis thalian 0.555 0.319 0.612 4.2e-69
TAIR|locus:2098164260 AT3G43490 [Arabidopsis thalian 0.268 0.326 0.505 5.6e-25
TAIR|locus:2183607 254 AT5G36240 [Arabidopsis thalian 0.208 0.259 0.560 3.1e-19
ZFIN|ZDB-GENE-030131-7782243 cnbpb "CCHC-type zinc finger, 0.388 0.506 0.337 4.6e-18
ZFIN|ZDB-GENE-030131-5045163 cnbpa "CCHC-type zinc finger, 0.388 0.754 0.324 1.6e-17
UNIPROTKB|B4DP17160 CNBP "cDNA FLJ61146, highly si 0.356 0.706 0.352 2.3e-16
MGI|MGI:88431178 Cnbp "cellular nucleic acid bi 0.343 0.612 0.350 3.7e-16
ASPGD|ASPL0000028407171 AN5111 [Emericella nidulans (t 0.403 0.748 0.331 3.7e-16
POMBASE|SPAC13D6.02c179 byr3 "zinc finger protein Byr3 0.372 0.659 0.326 3.7e-16
UNIPROTKB|E2RPD7179 CNBP "Uncharacterized protein" 0.347 0.614 0.350 7.7e-16
TAIR|locus:2079859 AT3G43590 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 649 (233.5 bits), Expect = 4.2e-69, Sum P(2) = 4.2e-69
 Identities = 109/178 (61%), Positives = 137/178 (76%)

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 DSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGL 314
             D GHDM  C+  YS +DLK+VQCYIC+ FGHLCCV   +++   VSC+RCGQLGH+GL
Sbjct:   241 DFGHDMILCKYEYSKEDLKDVQCYICKSFGHLCCVEPGNSLSWAVSCYRCGQLGHSGL 298
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
TAIR|locus:2183607 AT5G36240 [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
UNIPROTKB|B4DP17 CNBP "cDNA FLJ61146, highly similar to Cellular nucleic acid-binding protein" [Homo sapiens (taxid:9606)] 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
ASPGD|ASPL0000028407 AN5111 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
POMBASE|SPAC13D6.02c byr3 "zinc finger protein Byr3" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
UNIPROTKB|E2RPD7 CNBP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] 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

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query317
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 3e-17
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 4e-09
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 6e-09
COG5082190 COG5082, AIR1, Arginine methyltransferase-interact 1e-06
COG5082190 COG5082, AIR1, Arginine methyltransferase-interact 8e-06
COG5082190 COG5082, AIR1, Arginine methyltransferase-interact 0.001
pfam0009818 pfam00098, zf-CCHC, Zinc knuckle 0.004
smart0034317 smart00343, ZnF_C2HC, zinc finger 0.004
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information 
 Score = 77.2 bits (190), Expect = 3e-17
 Identities = 43/143 (30%), Positives = 61/143 (42%), Gaps = 15/143 (10%)

Query: 182 TCYNCGEEGHMAVNCRSAVK----RKKPCFVCGSLEHGVRQCSKAQD------CFICKKG 231
            CY CG  GH +  C ++      + +PC+ CG   H  R+C  A        C+ C K 
Sbjct: 2   VCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKT 61

Query: 232 GHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLC-- 289
           GH +++CP+         + C  CG +GH    C N           CY C   GH+   
Sbjct: 62  GHLSRECPE--APPGSGPRSCYNCGQTGHISRECPNRAK-GGAARRACYNCGGEGHISRD 118

Query: 290 CVNISDAVPGEVSCFRCGQLGHT 312
           C N      G+ +C+ CGQ GH 
Sbjct: 119 CPNAGKRPGGDKTCYNCGQTGHL 141

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|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|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 317
PTZ00368148 universal minicircle sequence binding protein (UMS 99.94
PTZ00368148 universal minicircle sequence binding protein (UMS 99.84
COG5082190 AIR1 Arginine methyltransferase-interacting protei 99.83
COG5082190 AIR1 Arginine methyltransferase-interacting protei 99.72
KOG4400261 consensus E3 ubiquitin ligase interacting with arg 99.51
KOG4400261 consensus E3 ubiquitin ligase interacting with arg 99.46
KOG0119 554 consensus Splicing factor 1/branch point binding p 98.82
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 97.78
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 97.7
PF1369632 zf-CCHC_2: Zinc knuckle 96.24
PF1369632 zf-CCHC_2: Zinc knuckle 95.17
PF1391742 zf-CCHC_3: Zinc knuckle 94.77
PF1391742 zf-CCHC_3: Zinc knuckle 92.97
smart0034326 ZnF_C2HC zinc finger. 92.83
KOG0119 554 consensus Splicing factor 1/branch point binding p 92.71
smart0034326 ZnF_C2HC zinc finger. 91.6
KOG0109346 consensus RNA-binding protein LARK, contains RRM a 89.63
KOG0314 448 consensus Predicted E3 ubiquitin ligase [Posttrans 88.77
KOG0314 448 consensus Predicted E3 ubiquitin ligase [Posttrans 86.92
PF1528840 zf-CCHC_6: Zinc knuckle 86.57
COG5222 427 Uncharacterized conserved protein, contains RING Z 86.53
COG5222 427 Uncharacterized conserved protein, contains RING Z 86.34
COG5176269 MSL5 Splicing factor (branch point binding protein 85.19
PF1439249 zf-CCHC_4: Zinc knuckle 84.02
KOG0109 346 consensus RNA-binding protein LARK, contains RRM a 83.84
PF1439249 zf-CCHC_4: Zinc knuckle 82.91
PF1478736 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 81.72
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information 
Probab=99.94  E-value=4.1e-27  Score=202.68  Aligned_cols=133  Identities=32%  Similarity=0.824  Sum_probs=111.8

Q ss_pred             cccccccccCccccccccc----ccCCCCcccccCCCCCcccCCCC------ccccccccCCCCCCCCCCCCCCCCCCCc
Q 021122          181 QTCYNCGEEGHMAVNCRSA----VKRKKPCFVCGSLEHGVRQCSKA------QDCFICKKGGHRAKDCPDKHKSGFQNAQ  250 (317)
Q Consensus       181 ~~C~~CG~~GH~a~~Cp~~----~~~~~~C~~CG~~GH~a~~Cp~~------~~C~~C~~~GH~ar~Cp~~~~~~~~~~~  250 (317)
                      +.||+|++.||++++||..    ......||+|+..||++++||..      ..|++|++.||++++||+....  ....
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            4699999999999999973    12346899999999999999974      3699999999999999997643  2457


Q ss_pred             ccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCc--ccCCCCCCCCCccccCCCCCCcccCCC
Q 021122          251 VCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLC--CVNISDAVPGEVSCFRCGQLGHTGLVS  316 (317)
Q Consensus       251 ~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~--C~~~~~~~~~~~~C~~Cg~~GH~~~d~  316 (317)
                      .||+|++.||++++||..+.. ......||+|++.||++  |+.........++||+|++.|||+.|+
T Consensus        79 ~C~~Cg~~GH~~~~C~~~~~~-~~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~dC  145 (148)
T PTZ00368         79 SCYNCGQTGHISRECPNRAKG-GAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDC  145 (148)
T ss_pred             ccCcCCCCCcccccCCCcccc-cccchhhcccCcCCcchhcCCCccccCCCCCccccCCCcCcccccC
Confidence            899999999999999997643 33567899999999999  776544455678999999999999986

>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
>PF13696 zf-CCHC_2: Zinc knuckle Back     alignment and domain information
>PF13696 zf-CCHC_2: Zinc knuckle 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
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>smart00343 ZnF_C2HC zinc finger 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
>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
>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
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only] Back     alignment and domain information
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification] 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
>PF14392 zf-CCHC_4: Zinc knuckle Back     alignment and domain information
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A 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 ?
Query317
2m3z_A55 Nmr Solution Structure Of Hiv-1 Nucleocapsid Protei 2e-04
1f6u_A56 Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bou 2e-04
1a1t_A55 Structure Of The Hiv-1 Nucleocapsid Protein Bound T 2e-04
1aaf_A55 Nucleocapsid Zinc Fingers Detected In Retroviruses: 3e-04
2l4l_A45 Structural Insights Into The Ctar Dna Recognition B 3e-04
2exf_A44 Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7( 4e-04
1bj6_A42 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTUR 4e-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 = 43.5 bits (101), Expect = 2e-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|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|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|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 ?
Query317
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 3e-11
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 7e-09
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 1e-07
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 4e-10
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 7e-07
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 1e-09
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 4e-07
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 1e-08
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 3e-04
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 6e-08
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 4e-06
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 4e-06
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 5e-06
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 3e-04
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 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 = 59.0 bits (142), Expect = 3e-11
 Identities = 31/150 (20%), Positives = 45/150 (30%), Gaps = 53/150 (35%)

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

Query: 241 KHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCC---------- 290
                   A  C KC + GH    C + +     K+VQC +C+   H             
Sbjct: 41  -------KAIQCSKCDEVGHYRSQCPHKW-----KKVQCTLCKSKKHSKERCPSIWRAYI 88

Query: 291 -------VNISDAVPGEVSCFRCGQLGHTG 313
                            + C+ CG  GH G
Sbjct: 89  LVDDNEKAKPKVLPFHTIYCYNCGGKGHFG 118
>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
>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
>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
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Length = 39 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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query317
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 99.93
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 99.75
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 99.49
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 99.4
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 99.19
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 99.15
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 99.08
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 99.04
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 99.03
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 98.94
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 98.92
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 98.91
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 98.86
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 98.85
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 98.84
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 98.83
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 98.83
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 98.83
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 98.8
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 98.78
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 98.63
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 98.55
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 97.6
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 97.48
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 97.48
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 97.45
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 97.16
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 97.13
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 97.01
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 96.84
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 96.77
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 96.52
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
Probab=99.93  E-value=1.4e-25  Score=186.71  Aligned_cols=117  Identities=28%  Similarity=0.572  Sum_probs=94.6

Q ss_pred             ccccccccccCcccccccccccCCCCcccccCC-CCCcccCCCCccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCC
Q 021122          180 WQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSL-EHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDS  258 (317)
Q Consensus       180 ~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~-GH~a~~Cp~~~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~  258 (317)
                      ...||+|++.||++++||..     .||+||+. ||++++||....||+|++.||++++||..+.     ...||+|++.
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            35799999999999999985     89999998 9999999988899999999999999998653     4789999999


Q ss_pred             CcCCCCCCCCCCCCCccCccccccCCCCcCcccCCCCCCCCCccccCCCCCCcccCCC
Q 021122          259 GHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLVS  316 (317)
Q Consensus       259 GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~C~~~~~~~~~~~~C~~Cg~~GH~~~d~  316 (317)
                      ||++++||..|+.|.+...       .+-.   .+.......+.||+||+.|||+.|+
T Consensus        74 GH~~~~Cp~~~~~y~~~~~-------~~~~---~~~~~~~~~~~Cy~Cg~~GH~a~dC  121 (124)
T 2lli_A           74 KHSKERCPSIWRAYILVDD-------NEKA---KPKVLPFHTIYCYNCGGKGHFGDDC  121 (124)
T ss_dssp             CCCTTTCCCSTTSCCSSSC-------CCCC---CCSCCCCCCCCTTTTSSSCTTTTTS
T ss_pred             CcchhhCCCccccccccCc-------cccc---cccccCCCCCCcCCCCCCCcCcccC
Confidence            9999999999976543210       0000   0011112468999999999999986
>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
>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
>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
>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
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia 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
>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
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma 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
>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
>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
>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
>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
>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
>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
>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 317
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 5e-07
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 3e-05
d1nc8a_29 g.40.1.1 (A:) HIV nucleocapsid {Human immunodefici 0.004
>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 = 43.7 bits (103), Expect = 5e-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
>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 ?
Query317
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 99.09
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 99.09
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 97.8
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 97.02
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 95.12
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 94.31
d1a6bb_40 Zinc finger protein ncp10 {Moloney murine leukemia 93.83
d1a6bb_40 Zinc finger protein ncp10 {Moloney murine leukemia 92.24
>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=99.09  E-value=3.5e-11  Score=80.42  Aligned_cols=39  Identities=41%  Similarity=0.985  Sum_probs=32.1

Q ss_pred             ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCC
Q 021122          223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRN  267 (317)
Q Consensus       223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~  267 (317)
                      +.||+|++.||++++||.+.      ...||+||+.||++++||.
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~------~~~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPR------KKGCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCC------CSSCSSSCCSSSCTTTCCS
T ss_pred             CccccCCCcCcCcccCcCCC------cCccccCCCCCeecccCCC
Confidence            57888888888888888753      2579999999999999985
>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
>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