Citrus Sinensis ID: 012460

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460---
MENSPVTVITSSEEEKEEGNGSKEKNIERGVAAKSKLDEYKEISDLTGFDNLKAMILAESIMKRKKKRNRKKKKKDKTKLDSLYREVADLTGFENLKAMIEAEAPMRRKSSERMRGNLETQFCAQENDTVNVAEEQGQLGEDDGLNKVEETERNGREEKRRRANRAKLDEYEKISDLSGFDNLKAMIEAEAFMRRKKRNRKRKKREIEFCGQEDVSVSAEEEKGQLDKSQPLKVVEVSKPESVLTTEMDGSRHLFIDPAKDNEGASMGEPMPMVRVVGGNDGGNSFEVIDLCLSSTDDDKSVSGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLSDMRLGRRVEDTVSVGPIVGERQQKKRRKKTRVIEAKDKVEDARKENEAKYNVVLRMLLRKPRYFDPPGWNSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQV
cccccEEEEcccHHHHHHccccccHHHHHHHHHHccHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHccccHHHHHHHHHccccccccHHHHccccccHHHHcccccHHHHHHHccccccccccHHHHHHHHcHHHHHHHHHHHcHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHccccEEEccccccccHHHHccccccccccEEEEEcccccEEEEcccccccEEEcccccccccccccccccEEEccccccccccEEEcccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccHHccccccccccccccccccccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccc
cccccEEEEEccccHHccccccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcHHHHHHHHHHHcccccccHHHHcccccHHHHccccccHEHHHHHcccccccccccccccccccHHHHHHHHHHHcHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHcEEEEEccccEEEEcccccccccccccEEEEEEEccccEEEEccccccEEEEccccccccccccccccEEEEEEccccccccEEEEEEEEccccHHHcccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccHHHHHHHHHccccccccccccHHHHHHHccccccccccccccEEccccccccEEEcccccHcccccEEEccccccccccccc
menspvtvitsseeekeegngskekniERGVAAKSKLDeykeisdltgfdnLKAMILAESIMKRKKKRnrkkkkkdktKLDSLYREVADLTGFENLKAMIEAEApmrrkssermrgnletqfcaqendtVNVAeeqgqlgeddglnkveETERNGREEKRRRANRAKldeyekisdlsgfdNLKAMIEAEAFMRRKKRNRKRKKreiefcgqedvsvsaeeekgqldksqplkvvevskpesvlttemdgsrhlfidpakdnegasmgepmpmvrvvggndggnSFEVIDLCLsstdddksvsgvsLERSVEDMGKAVQTtatitgandgvkSVEMNNlyslrleddkplsdmrlgrrvedtvsvgpivgerqqkkrrkktrVIEAKDKVEDARKENEAKYNVVLRMLlrkpryfdppgwnsetcsncgkenhtaatckmqkqnkpcflcgsfkhrwknckqv
menspvtvitsseeekeegngskekniergvaakskldeykeisdltgfdnlkAMILAESimkrkkkrnrkkkkkdktkldslyrevadltgfenlkaMIEAEapmrrkssermRGNLETQFCAQENDTVNVAEEqgqlgeddglnkveeterngreekrrranrakldeyekisdlsgfdnlKAMIEAEAfmrrkkrnrkrkkreiefcgqedvsvsaeeekgqldksqplkvvevskpesvlttemdgsrhlFIDPAKdnegasmgepMPMVRVVGGNDGGNSFEVIDLCLsstdddksvsGVSLERSVEDMGKAVQttatitgandgvksVEMNNLYslrleddkplsdmrlgrrvedtvsvgpivgerqqkkrrkktrvieakdkvedarkeneakynVVLRMLLRKPRYFDPPGWNSETCSNCGKENHTAATCKMQKQNKPCflcgsfkhrwknckqv
MENSPvtvitsseeekeegngskeknieRGVAAKSKLDEYKEISDLTGFDNLKAMILAESIMkrkkkrnrkkkkkdktkLDSLYREVADLTGFENLKAMIEAEAPMRRKSSERMRGNLETQFCAQENDTVNVAEEQGQLGEDDGLNKVeeterngreekrrranrakLDEYEKISDLSGFDNLKAMIEAEAFMrrkkrnrkrkkrEIEFCGQEDVSVSAEEEKGQLDKSQPLKVVEVSKPESVLTTEMDGSRHLFIDPAKDNEGASMGEPMPMVRVVGGNDGGNSFEVIDLCLSSTDDDKSVSGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLSDMRLGRRVEDTVSVGPIVGErqqkkrrkktrVIEAKDKVEDARKENEAKYNVVLRMLLRKPRYFDPPGWNSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQV
******************************************ISDLTGFDNLKAMILA****************************VADLTGFE**************************************************************************************************************************************************************************************V****GGNSFEVIDLCL**********************************************Y***********************************************************KYNVVLRMLLRKPRYFDPPGWNSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKN****
****PVT***************************SKLDEYKEISDLTGFDNLKAMILA************************LYREVADLTGFENLKAMI********************QFCAQENDTVNV**************************************YEKISDLSGFDNLKAMIEA**********************************************************MDGSRHLFID************************GGNSFEVIDLCLSSTD*****SGVSLERSVEDMGK********************************PLSDMRLGRRVEDTVS*************************************************YFDPPGWNSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCK**
***********************EKNIERGVAAKSKLDEYKEISDLTGFDNLKAMILAESIM****************KLDSLYREVADLTGFENLKAMIEAEAPMRRKSSERMRGNLETQFCAQENDTVNVAEEQGQLGEDDGLNKVE**************NRAKLDEYEKISDLSGFDNLKAMIEAEAFMR************IEFCGQ***************KSQPLKVVEVSKPESVLTTEMDGSRHLFIDPAKDNEGASMGEPMPMVRVVGGNDGGNSFEVIDLCLSST******************GKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLSDMRLGRRVEDTVSVGPIVGE************IEAKDKVEDARKENEAKYNVVLRMLLRKPRYFDPPGWNSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQV
*********************SKEKNIERGVAAKSKLDEYKEISDLTGFDNLKAMILAESIMKRKKKRNRKKKKKDKTKLDSLYREVADLTGFENLKAMIEAE**************LETQFCAQENDTVNVAEEQGQ****D*LNKV*********EK****NRAKLDEYEKISDLSGFDNLKAMIEAEAFMRRKKRNRKRKKREIEFCGQEDVSVSAEEEKGQLDKSQPLKVVEVSKPESVLTTEMDGSRHLFIDPAKDNEGASMGEPMPMVRVVGGNDGGNSFEVIDLCLSSTDDDK*VSGVSLERSVEDMGKAVQTTATIT**************************************************************************KYNVVLRMLLRKPRYFDPPGWNSETCSNCGKENHTAATCKMQKQNKPCFLCGSFK*R*K*C***
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MENSPVTVITSSEEEKEEGNGSKEKNIERGVAAKSKLDEYKEISDLTGFDNLKAMILAESIMKRKKKRNRKKKKKDKTKLDSLYREVADLTGFENLKAMIEAEAPMRRKSSERMRGNLETQFCAQENDTVNVAEEQGQLGEDDGLNKVEETERNGREEKRRRANRAKLDEYEKISDLSGFDNLKAMIEAEAFMRRKKRNRKRKKREIEFCGQEDVSVSAEEEKGQLDKSQPLKVVEVSKPESVLTTEMDGSRHLFIDPAKDNEGASMGEPMPMVRVVGGNDGGNSFEVIDLCLSSTDDDKSVSGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLSDMRLGRRVEDTVSVGPIVGERQQKxxxxxxxxxxxxxxxxxxxxxNEAKYNVVLRMLLRKPRYFDPPGWNSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQV
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

No hits with e-value below 0.001 by BLAST

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query463
242068927228 hypothetical protein SORBIDRAFT_05g02241 0.140 0.285 0.569 5e-14
115485975129 Os11g0573200 [Oryza sativa Japonica Grou 0.133 0.480 0.580 1e-13
414591598226 TPA: hypothetical protein ZEAMMB73_14873 0.136 0.278 0.571 5e-13
222616180 800 hypothetical protein OsJ_34326 [Oryza sa 0.131 0.076 0.573 7e-13
224132214 683 predicted protein [Populus trichocarpa] 0.168 0.114 0.5 8e-13
147828626513 hypothetical protein VITISV_005152 [Viti 0.123 0.111 0.573 1e-12
218185703492 hypothetical protein OsI_36043 [Oryza sa 0.131 0.123 0.573 1e-12
359479082481 PREDICTED: uncharacterized protein LOC10 0.123 0.118 0.573 2e-12
357156367464 PREDICTED: uncharacterized protein LOC10 0.131 0.131 0.590 2e-12
357156364476 PREDICTED: uncharacterized protein LOC10 0.131 0.128 0.590 2e-12
>gi|242068927|ref|XP_002449740.1| hypothetical protein SORBIDRAFT_05g022410 [Sorghum bicolor] gi|241935583|gb|EES08728.1| hypothetical protein SORBIDRAFT_05g022410 [Sorghum bicolor] Back     alignment and taxonomy information
 Score = 85.5 bits (210), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query: 399 AKYNVVLRMLLRKPRYFDPPGWNSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWK 458
           A  N+VLR LLR PRYFDP     +TC NC +E H AA C M+K+ KPCF+CG F H  K
Sbjct: 159 ASDNMVLRKLLRIPRYFDPGETLLDTCFNCSEEGHVAANCPMEKRKKPCFVCGLFGHNAK 218

Query: 459 NCKQV 463
            C QV
Sbjct: 219 QCTQV 223

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|115485975|ref|NP_001068131.1| Os11g0573200 [Oryza sativa Japonica Group] gi|113645353|dbj|BAF28494.1| Os11g0573200, partial [Oryza sativa Japonica Group] Back     alignment and taxonomy information
>gi|414591598|tpg|DAA42169.1| TPA: hypothetical protein ZEAMMB73_148737 [Zea mays] Back     alignment and taxonomy information
>gi|222616180|gb|EEE52312.1| hypothetical protein OsJ_34326 [Oryza sativa Japonica Group] 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|147828626|emb|CAN73043.1| hypothetical protein VITISV_005152 [Vitis vinifera] Back     alignment and taxonomy information
>gi|218185703|gb|EEC68130.1| hypothetical protein OsI_36043 [Oryza sativa Indica Group] Back     alignment and taxonomy information
>gi|359479082|ref|XP_002272646.2| PREDICTED: uncharacterized protein LOC100259916 [Vitis vinifera] Back     alignment and taxonomy information
>gi|357156367|ref|XP_003577432.1| PREDICTED: uncharacterized protein LOC100831383 isoform 2 [Brachypodium distachyon] Back     alignment and taxonomy information
>gi|357156364|ref|XP_003577431.1| PREDICTED: uncharacterized protein LOC100831383 isoform 1 [Brachypodium distachyon] 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 ?
Query463
TAIR|locus:2079859 551 AT3G43590 [Arabidopsis thalian 0.343 0.288 0.325 9.9e-12
TAIR|locus:2098164260 AT3G43490 [Arabidopsis thalian 0.161 0.288 0.362 4.5e-08
UNIPROTKB|F1NI84105 CNBP "Cellular nucleic acid-bi 0.101 0.447 0.375 0.00023
TAIR|locus:2079859 AT3G43590 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 188 (71.2 bits), Expect = 9.9e-12, P = 9.9e-12
 Identities = 58/178 (32%), Positives = 90/178 (50%)

Query:   297 DDDKSVSGVSL---ERSVE--DMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS 351
             DDD++   +SL   E+++   D+G  + +  +   ++ GV S  M N    +++  +   
Sbjct:    36 DDDEANEDLSLKILEKALSRRDVGNKLDSDLS---SDSGVVSTVMVNGVKSKVKKSESSK 92

Query:   352 DMRLGRRVEDTVSVGPIVGEXXXXXXXXXXXVI-EAKD-KVE--DARKENEAKYNVVLRM 407
              M+  + +E    + PIV             V  E +D +VE  D  K  E   N+VL+ 
Sbjct:    93 KMKRNK-LEADHEI-PIVWNDQDEEKVVEEIVKGEGEDDEVERSDEPKTEETASNLVLKK 150

Query:   408 LLRKPRYFDPP--GWNSETCSNCGKENHTAATCKMQ-KQNKPCFLCGSFKHRWKNCKQ 462
             LLR  RYFDPP  GW S  C +CG++ HT+  C    K+ KPCF+CGS +H  K C +
Sbjct:   151 LLRGARYFDPPDAGWVS--CYSCGEQGHTSFNCPTPTKRRKPCFICGSLEHGAKQCSK 206
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|F1NI84 CNBP "Cellular nucleic acid-binding protein" [Gallus gallus (taxid:9031)] 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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 463
PF00607206 Gag_p24: gag gene protein p24 (core nucleocapsid p 99.21
PTZ00368148 universal minicircle sequence binding protein (UMS 98.41
COG5082190 AIR1 Arginine methyltransferase-interacting protei 98.4
PTZ00368148 universal minicircle sequence binding protein (UMS 98.32
COG5082190 AIR1 Arginine methyltransferase-interacting protei 98.2
KOG4400261 consensus E3 ubiquitin ligase interacting with arg 98.17
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 97.71
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 97.66
KOG4400261 consensus E3 ubiquitin ligase interacting with arg 97.59
KOG0119 554 consensus Splicing factor 1/branch point binding p 96.24
PF1369632 zf-CCHC_2: Zinc knuckle 95.04
smart0034326 ZnF_C2HC zinc finger. 94.05
smart0034326 ZnF_C2HC zinc finger. 94.02
PF1369632 zf-CCHC_2: Zinc knuckle 92.63
PF1391742 zf-CCHC_3: Zinc knuckle 92.46
PF1391742 zf-CCHC_3: Zinc knuckle 89.22
KOG0109 346 consensus RNA-binding protein LARK, contains RRM a 88.71
PF1439249 zf-CCHC_4: Zinc knuckle 86.69
KOG0109 346 consensus RNA-binding protein LARK, contains RRM a 85.41
PF1439249 zf-CCHC_4: Zinc knuckle 84.88
COG5222 427 Uncharacterized conserved protein, contains RING Z 84.3
PF1528840 zf-CCHC_6: Zinc knuckle 83.31
PF1528840 zf-CCHC_6: Zinc knuckle 81.03
COG5222 427 Uncharacterized conserved protein, contains RING Z 80.52
PF1478736 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 80.47
>PF00607 Gag_p24: gag gene protein p24 (core nucleocapsid protein); InterPro: IPR000721 The Gag protein from retroviruses, also known as p24, forms the inner protein layer of the nucleocapsid Back     alignment and domain information 
Probab=99.21  E-value=1.7e-12  Score=120.73  Aligned_cols=60  Identities=18%  Similarity=0.313  Sum_probs=52.2

Q ss_pred             cccccchHHHHHHHHHHhhhhccCCCCcccccccccccccCCCCCCcc-ccccccccCCccccCcchhhhHHhhhhhhhh
Q 012460          304 GVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS-DMRLGRRVEDTVSVGPIVGERQQKKRRKKTR  382 (463)
Q Consensus       304 ~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgpe~~~tLe-mMTaCqGVgGgv~~gPs~~Em~QKkkthKaR  382 (463)
                      .++.+++.+++++||+.+|++|||||||++|    |++|++  ++||| ||++|||||+     |.          ||++
T Consensus       146 a~~~~~~~~~~~~~~~~~L~~eNAN~~C~~~----~~~l~~--~~~lee~~~~C~~vg~-----~~----------~k~~  204 (206)
T PF00607_consen  146 AIRREQGENEVKNILIRQLAYENANPDCRRI----IRPLGK--DAPLEEMIRACQGVGG-----PS----------HKAQ  204 (206)
T ss_dssp             HHHCSSSTHHHHHHHHHHHHHHTS-HHHHHH----HHHH-T--TSTHHHHHHHTTTTSS-----TT----------SSSB
T ss_pred             HHhhcccccchhhHHHHHhhhccchHHHHHH----HHccCC--CCCHHHHHHHhhccCC-----Hh----------hhhh
Confidence            3789999999999999999999999999999    999986  77788 9999999996     77          7777


Q ss_pred             hh
Q 012460          383 VI  384 (463)
Q Consensus       383 VL  384 (463)
                      ++
T Consensus       205 ~l  206 (206)
T PF00607_consen  205 AL  206 (206)
T ss_dssp             BH
T ss_pred             cC
Confidence            54

This protein performs highly complex orchestrated tasks during the assembly, budding, maturation and infection stages of the viral replication cycle. During viral assembly, the proteins form membrane associations and self-associations that ultimately result in budding of an immature virion from the infected cell. Gag precursors also function during viral assembly to selectively bind and package two plus strands of genomic RNA. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.; GO: 0016032 viral reproduction; PDB: 1BMX_A 1SJH_C 1SJE_C 1U57_A 1FGL_B 1G03_A 2XT1_A 2JO0_A 2L6E_A 2HJL_C ....
>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
>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
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones] 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
>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
>PF13696 zf-CCHC_2: 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
>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
>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
>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
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [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
>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 ?
Query463
2a51_A39 Structure Of The (13-51) Domain Of The Nucleocapsid 1e-04
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid Protein Ncp8 From Sivlhoest Length = 39 Back     alignment and structure 
Iteration: 1

 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/39 (46%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 424 TCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
           TC NCGK  HTA  C+  +Q + C+ CGS +HR+  C +
Sbjct: 2   TCFNCGKPGHTARMCRQPRQ-EGCWNCGSKEHRFAQCPK 39

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query463
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 9e-10
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 1e-08
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 2e-06
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 6e-05
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 3e-06
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 8e-06
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 1e-05
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 2e-05
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 6e-04
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 7e-04
>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
 Score = 53.8 bits (129), Expect = 9e-10
 Identities = 15/38 (39%), Positives = 18/38 (47%)

Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
           C NCG  +H A  CK+  Q K C  C S  H   +C  
Sbjct: 10  CYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPL 47
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74 Back     alignment and structure
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124 Back     alignment and structure
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124 Back     alignment and structure
>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
>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
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61 Back     alignment and structure
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Length = 39 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
>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 ?
Query463
1baj_A101 GAG polyprotein; capsid, HIV-1 assembly protein, v 99.79
3ds4_A86 HIV-1 capsid protein; HIV, mutant, polyprotein, co 99.74
2jyl_A105 Capsid protein P24 (Ca); HIV-1, carboxy-terminal, 99.68
1qrj_B199 HTLV-I capsid protein; retrovirus, two-domain prot 99.57
1eoq_A96 GAG polyprotein capsid protein P27; virus/viral pr 99.45
3h47_A231 Ca, capsid protein P24; hexamer, engineered disulf 99.41
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 99.41
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 99.36
1eia_A207 EIAV capsid protein P26; viral capsid, HIV, lentiv 99.35
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 99.3
3gv2_A342 Ca, fusion protein consisting of capsid protein P2 99.3
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 99.23
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 99.23
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 99.2
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 99.19
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 99.17
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 99.16
1d1d_A262 Protein (capsid protein); two independent domains 99.06
3g21_A77 GAG polyprotein, capsid protein; alpha-helical bun 98.98
1u57_A48 GAG polyprotein, HIV-1; particle assembly, viral p 98.85
3g1g_A87 GAG polyprotein, capsid protein; alpha-helical bun 98.84
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 98.77
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 98.72
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 98.69
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 98.36
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 98.14
3tir_A226 ROUS sarcoma virus capsid protein P27; viral capsi 98.05
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 97.97
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 97.81
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 97.59
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 97.49
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 97.33
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 97.29
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 97.21
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 97.07
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 96.99
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 96.73
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 96.69
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 96.56
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 96.5
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 96.43
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 96.43
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 96.14
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 96.13
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 94.59
>1baj_A GAG polyprotein; capsid, HIV-1 assembly protein, viral protein; 2.60A {Human immunodeficiency virus 1} SCOP: a.28.3.1 Back     alignment and structure
Probab=99.79  E-value=4.1e-21  Score=160.63  Aligned_cols=67  Identities=21%  Similarity=0.240  Sum_probs=45.1

Q ss_pred             cccccccchHHHHHHHHHHhhhhccCCCCcccccccccccccCCCCCCcc-ccccccccCCccccCcchhhhHHhhhhhh
Q 012460          302 VSGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS-DMRLGRRVEDTVSVGPIVGERQQKKRRKK  380 (463)
Q Consensus       302 ~q~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgpe~~~tLe-mMTaCqGVgGgv~~gPs~~Em~QKkkthK  380 (463)
                      +.+|++||++++||+|||+||++||||||||+|    |++||+  +++|+ ||++||||||     |+          ||
T Consensus        25 ~k~l~~e~~~~~vK~~~~~tL~~qnanp~Ck~~----lk~l~~--~~~l~e~~~ac~~vg~-----p~----------~k   83 (101)
T 1baj_A           25 YKTLRAEQASQEVKNWMTETLLVQNANPDCKTI----LKALGP--GATLEEMMTACQGVGG-----PG----------HK   83 (101)
T ss_dssp             HHHHHHTTCCHHHHHHHHHTHHHHTSCHHHHHH----HHHHCS--SCCHHHHHHHC------------------------
T ss_pred             HHHHHHhhccHHHHHHHhhhHHHHhhchhhhHH----HHccCC--CCCHHHHHHhccccCC-----cc----------hh
Confidence            345899999999999999999999999999999    999987  56778 9999999995     88          99


Q ss_pred             hhhhhhhhc
Q 012460          381 TRVIEAKDK  389 (463)
Q Consensus       381 aRVLAEams  389 (463)
                      ++|+|++|+
T Consensus        84 a~~laea~~   92 (101)
T 1baj_A           84 ARVLAEAMS   92 (101)
T ss_dssp             ---------
T ss_pred             hHHHHHHHH
Confidence            999999874
>3ds4_A HIV-1 capsid protein; HIV, mutant, polyprotein, complex(viral protein/peptide), mainly alpha; 1.12A {Human immunodeficiency virus 1} PDB: 3dph_A 1a43_A 2xt1_A 2buo_A 3lry_A 2kod_A 3ds1_A 3dtj_A 3ds0_A 3ds5_A 3ds2_A 3ds3_A 2jo0_A 2jyg_A 2xxm_A 2xv6_A 2ont_A 1aum_A 1a8o_A 4arg_B ... Back     alignment and structure
>2jyl_A Capsid protein P24 (Ca); HIV-1, carboxy-terminal, dimerization domain, CTD, 3D- NMR, capsid protein (Ca), double mutant; NMR {Human immunodeficiency virus 1} PDB: 2k1c_A* 2l6e_A* Back     alignment and structure
>1qrj_B HTLV-I capsid protein; retrovirus, two-domain protein, alpha helical protein, heteronuclear spectroscopy; NMR {Human t-cell lymphotrophic virus TYPE1} SCOP: a.28.3.1 a.73.1.1 Back     alignment and structure
>1eoq_A GAG polyprotein capsid protein P27; virus/viral protein; NMR {Rous sarcoma virus - prague C} SCOP: a.28.3.1 Back     alignment and structure
>3h47_A Ca, capsid protein P24; hexamer, engineered disulfide bonds, viral protein; 1.90A {Human immunodeficiency virus type 1} PDB: 3h4e_A 2lf4_A 3mge_A 3p05_A 3p0a_A 3dik_A 3nte_A 1e6j_P 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
>1eia_A EIAV capsid protein P26; viral capsid, HIV, lentivirus, viral protein; 2.70A {Equine infectious anemia virus} SCOP: a.28.3.1 a.73.1.1 PDB: 2eia_A 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
>3gv2_A Ca, fusion protein consisting of capsid protein P24, carbon dioxide-concentrating mechanism...; hexameric retroviral capsid; 7.00A {Human immunodeficiency virus type 1} Back     alignment and structure
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} 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
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; 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
>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
>1d1d_A Protein (capsid protein); two independent domains helical bundles, virus/viral protein; NMR {Rous sarcoma virus} SCOP: a.28.3.1 a.73.1.1 Back     alignment and structure
>3g21_A GAG polyprotein, capsid protein; alpha-helical bundle, virion, viral protein, retrovirus; 0.90A {Rous sarcoma virus} PDB: 3g1i_A 3g28_A 3g29_A 3g26_A 3g0v_A Back     alignment and structure
>1u57_A GAG polyprotein, HIV-1; particle assembly, viral protein; NMR {Human immunodeficiency virus 1} Back     alignment and structure
>3g1g_A GAG polyprotein, capsid protein; alpha-helical bundle, virion, viral protein, retrovirus; 2.01A {Rous sarcoma virus} 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
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>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
>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
>3tir_A ROUS sarcoma virus capsid protein P27; viral capsid protein, viral protein; 4.10A {Rous sarcoma virus} PDB: 2x8q_A 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
>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
>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
>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
>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
>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
>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
>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
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} 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
>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
>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
>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
>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

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 463
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 2e-06
>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 = 42.5 bits (100), Expect = 2e-06
 Identities = 17/38 (44%), Positives = 23/38 (60%), Gaps = 1/38 (2%)

Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
           C NCGKE HTA  C+   + K C+ CG   H+ K+C +
Sbjct: 4   CFNCGKEGHTARNCR-APRKKGCWKCGKEGHQMKDCTE 40

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query463
d2eiaa175 EIAV capsid protein p26 {Equine infectious anemia 99.62
d1qrjb184 HTLV-I capsid protein {Human T-cell leukemia virus 99.61
d1a8oa_70 HIV capsid protein, dimerisation domain {Human imm 99.47
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 99.33
d1d1da180 RSV capsid protein {Rous sarcoma virus [TaxId: 118 99.05
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 98.57
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 96.92
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 96.9
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 95.93
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 95.57
d1a6bb_40 Zinc finger protein ncp10 {Moloney murine leukemia 83.46
>d2eiaa1 a.28.3.1 (A:148-222) EIAV capsid protein p26 {Equine infectious anemia virus [TaxId: 11665]} Back     information, alignment and structure
class: All alpha proteins
fold: Acyl carrier protein-like
superfamily: Retrovirus capsid dimerization domain-like
family: Retrovirus capsid protein C-terminal domain
domain: EIAV capsid protein p26
species: Equine infectious anemia virus [TaxId: 11665]

Probab=99.62  E-value=2.8e-17  Score=129.88  Aligned_cols=53  Identities=25%  Similarity=0.353  Sum_probs=49.1

Q ss_pred             cccccccchHHHHHHHHHHhhhhccCCCCcccccccccccccCCCCCCcc-ccccccccC
Q 012460          302 VSGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS-DMRLGRRVE  360 (463)
Q Consensus       302 ~q~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgpe~~~tLe-mMTaCqGVg  360 (463)
                      ...|+++++++++|+||++||++||||||||+|    |++|++  ++||+ ||+||||||
T Consensus        22 ~~a~~~~~~~~~~k~~~~~~L~~qNANpdCk~i----Lr~l~~--~~tLeemm~aCq~VG   75 (75)
T d2eiaa1          22 LSQIKSEGHPQEISKFLTDTLTIQNANEECRNA----MRHLRP--EDTLEEKMYACRDIG   75 (75)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHTSCTTTTTT----TTTCCT--TSCHHHHHHHTSSCC
T ss_pred             HHHHHhhcCcHhHHHHHHHHHhHhcCCHHHHHH----HHhcCC--CCCHHHHHHHhccCC
Confidence            446899999999999999999999999999999    999987  67778 999999998
>d1qrjb1 a.28.3.1 (B:131-214) HTLV-I capsid protein {Human T-cell leukemia virus type 1 [TaxId: 11908]} Back     information, alignment and structure
>d1a8oa_ a.28.3.1 (A:) HIV capsid protein, dimerisation domain {Human immunodeficiency virus type 1 [TaxId: 11676]} Back     information, alignment and structure
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Back     information, alignment and structure
>d1d1da1 a.28.3.1 (A:151-230) RSV capsid protein {Rous sarcoma virus [TaxId: 11886]} 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
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} 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