Citrus Sinensis ID: 013049

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
METVNEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLLSTTESTDNRIEPDLEVEEQRAQIGKRINDDGDSIICKLSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKMQSKLRSESSGEQNKDVANSMTSPLELFPTELHRFNGKNYRVWAQQIELLLKQLKVAYVLTDPCPIVTLCPQASSEEVTRVKAAERKWLNDNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDHIKAEEESRSHNKQEEPSKFVELSPAVNFGPRMREMSKKRRESEMDSKTVVCYNCRKKGHVAKHCHNKRLHQEINDNCPC
ccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHccccccccccccccccHHHHHHHHccccccccccccEEEcccccEEEEEcccccEEEEcHHEEccccccccccccccccHHHHHHHHHHcHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccEEEEcccccccccccccccHHHHHHHHHHHHHHHHcHHHHHHHHHHccHHHHHHHHcccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHccccccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
ccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHcHHHHHHHcccccccHHHcccccEEEcccccEEEEEEccccEEEEEEEcccEEEEEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccEHHHHHHcccccccccccHHHHHHHHHHHHHHHcHHHHHcccccccccccccccccHcHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHccccHHHHHHHHHHHcccccccccEEEEEHEEEEEccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHccccHHHHHHHHHccccccHHHHHHHccHHHHHHHHHccccccccccccccEccccccccccccccccccccccccEEEcccccccccHcccccccccccccccc
metvnegrIRQTVMEVLKNSDMEEMTEFKVRVEASERlgidlsdanhKRFIRGVVESFLLSttestdnriepdlEVEEQRAQIGKrinddgdsiickLSNKRTVAIQEFKGRAFVSIREYFrrdgklvptakgIALTSEQWRAFSKSLPAIDEAVVKMQSKLrsessgeqnkdvansmtsplelfptelhrfngkNYRVWAQQIELLLKQLKVAYvltdpcpivtlcpqasseEVTRVKAAERKWLNDNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVYldeefgtkRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDHIKaeeesrshnkqeepskfvelspavnfgprmrEMSKKRresemdsktvvcyncrkkghvakhchnkrlhqeindncpc
metvnegrirqtvmevlknsdmeeMTEFKVRVEASErlgidlsdanhkrFIRGVVESfllsttestdnriepdleVEEQRAQigkrinddgdsiICKLSNKrtvaiqefkgrafvSIREYfrrdgklvptAKGIALTSEQWRAFSKSLPAIDEAVVKMQSKlrsessgeqnkdvanSMTSPLELFPTELHRFNGKNYRVWAQQIELLLKQLKVAYVLTDPCPIVtlcpqasseevTRVKAAERKWLNDNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVyldeefgtkRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDHIKAEEesrshnkqeepskfvelspavnfgprmremskkrresemdsktvvCYNCRKKGHVAkhchnkrlhqeindncpc
METVNEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLLSTTESTDNRIEPDLEVEEQRAQIGKRINDDGDSIICKLSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKMQSKLRSESSGEQNKDVANSMTSPLELFPTELHRFNGKNYRVWAQQIELLLKQLKVAYVLTDPCPIVTLCPQASSEEVTRVKAAERKWLNDNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDHIKAEEESRSHNKQEEPSKFVELSPAVNFGPRMREMSKKRRESEMDSKTVVCYNCRKKGHVAKHCHNKRLHQEINDNCPC
************************************RLGIDLSDANHKRFIRGVVESFLLS***************************DDGDSIICKLSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAI*******************************ELFPTELHRFNGKNYRVWAQQIELLLKQLKVAYVLTDPCPIVTLCPQASSEEVTRVKAAERKWLNDNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDHI**********************************************TVVCYNCRKKGHVAKHCHN*************
***********************************************************************************************CKLSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKMQSKLRS*******************LFPTELHRFNGKNYRVWAQQIELLLKQLKVAYVLTDPCP******************AERKWLNDNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDHIK*************************************************YNCRKKGHVAKHCHNKR***********
METVNEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLLSTTESTDNRIEPDLEVEEQRAQIGKRINDDGDSIICKLSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVK*******************SMTSPLELFPTELHRFNGKNYRVWAQQIELLLKQLKVAYVLTDPCPIVTLCPQASSEEVTRVKAAERKWLNDNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDHIKA****************VELSPAVNFGPRM***************TVVCYNCRKKGHVAKHCHNKRLHQEINDNCPC
*ETVNEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLLSTTESTDN**************IGKRINDDGDSIICKLSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKMQSKLRSESSGEQNKDVANSMTSPLELFPTELHRFNGKNYRVWAQQIELLLKQLKVAYVLTDPCPIVTLCPQASSEEVTRVKAAERKWLNDNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDHIKAEEESRSHN************************************TVVCYNCRKKGHVAKHCHN*************
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METVNEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLLSTTESTDNRIEPDLEVEEQRAQIGKRINDDGDSIICKLSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKMQSKLRSESSGEQNKDVANSMTSPLELFPTELHRFNGKNYRVWAQQIELLLKQLKVAYVLTDPCPIVTLCPQASSEEVTRVKAAERKWLNDNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDHIKAEEESRSHNKQEEPSKFVELSPAVNFGPRMREMSKKRRESEMDSKTVVCYNCRKKGHVAKHCHNKRLHQEINDNCPC
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 ?
Query450 2.2.26 [Sep-21-2011]
O65155165 RNA polymerase II transcr no no 0.333 0.909 0.529 5e-38
O65154107 RNA polymerase II transcr no no 0.148 0.626 0.313 3e-07
P87294136 Putative RNA polymerase I yes no 0.144 0.477 0.338 8e-07
Q94045124 Putative RNA polymerase I yes no 0.157 0.572 0.328 2e-06
Q5ZK63126 Activated RNA polymerase yes no 0.148 0.531 0.352 2e-06
Q5R6D0127 Activated RNA polymerase yes no 0.148 0.527 0.352 5e-06
Q4R947127 Activated RNA polymerase N/A no 0.148 0.527 0.352 5e-06
P53999127 Activated RNA polymerase yes no 0.148 0.527 0.352 5e-06
Q63396127 Activated RNA polymerase yes no 0.148 0.527 0.352 9e-06
P11031127 Activated RNA polymerase yes no 0.148 0.527 0.352 1e-05
>sp|O65155|KELP_ARATH RNA polymerase II transcriptional coactivator KELP OS=Arabidopsis thaliana GN=KELP PE=1 SV=1 Back     alignment and function desciption
 Score =  159 bits (402), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 81/153 (52%), Positives = 113/153 (73%), Gaps = 3/153 (1%)

Query: 13  VMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLLS--TTESTDNRI 70
           V+E+L  SDM+E+TEFKVR  ASE+L IDLS+ +HK F+R VVE FL      E  ++++
Sbjct: 13  VIEILSESDMKEITEFKVRKLASEKLAIDLSEKSHKAFVRSVVEKFLDEERAREYENSQV 72

Query: 71  EPDLEVEEQRAQIG-KRINDDGDSIICKLSNKRTVAIQEFKGRAFVSIREYFRRDGKLVP 129
             + E  ++    G K  +DDGD IIC+LS+KR V IQEFKG++ VSIREY+++DGK +P
Sbjct: 73  NKEEEDGDKDCGKGNKEFDDDGDLIICRLSDKRRVTIQEFKGKSLVSIREYYKKDGKELP 132

Query: 130 TAKGIALTSEQWRAFSKSLPAIDEAVVKMQSKL 162
           T+KGI+LT EQW  F K++PAI+ AV KM+S++
Sbjct: 133 TSKGISLTDEQWSTFKKNMPAIENAVKKMESRV 165
General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. Binds single-stranded DNA.
Arabidopsis thaliana (taxid: 3702)
>sp|O65154|KIWI_ARATH RNA polymerase II transcriptional coactivator KIWI OS=Arabidopsis thaliana GN=KIWI PE=1 SV=1 Back     alignment and function description
>sp|P87294|TCP4_SCHPO Putative RNA polymerase II transcriptional coactivator OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC16A10.02 PE=1 SV=1 Back     alignment and function description
>sp|Q94045|TCP4_CAEEL Putative RNA polymerase II transcriptional coactivator OS=Caenorhabditis elegans GN=T13F2.2 PE=3 SV=1 Back     alignment and function description
>sp|Q5ZK63|TCP4_CHICK Activated RNA polymerase II transcriptional coactivator p15 OS=Gallus gallus GN=SUB1 PE=2 SV=1 Back     alignment and function description
>sp|Q5R6D0|TCP4_PONAB Activated RNA polymerase II transcriptional coactivator p15 OS=Pongo abelii GN=SUB1 PE=2 SV=1 Back     alignment and function description
>sp|Q4R947|TCP4_MACFA Activated RNA polymerase II transcriptional coactivator p15 OS=Macaca fascicularis GN=SUB1 PE=2 SV=1 Back     alignment and function description
>sp|P53999|TCP4_HUMAN Activated RNA polymerase II transcriptional coactivator p15 OS=Homo sapiens GN=SUB1 PE=1 SV=3 Back     alignment and function description
>sp|Q63396|TCP4_RAT Activated RNA polymerase II transcriptional coactivator p15 OS=Rattus norvegicus GN=Sub1 PE=2 SV=3 Back     alignment and function description
>sp|P11031|TCP4_MOUSE Activated RNA polymerase II transcriptional coactivator p15 OS=Mus musculus GN=Sub1 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 ?
Query450
224064265459 predicted protein [Populus trichocarpa] 0.962 0.943 0.543 1e-137
356571246515 PREDICTED: uncharacterized protein LOC10 0.96 0.838 0.464 1e-116
356504175 558 PREDICTED: uncharacterized protein LOC10 0.955 0.770 0.440 1e-110
449433026468 PREDICTED: uncharacterized protein LOC10 0.948 0.912 0.457 1e-103
449478205468 PREDICTED: uncharacterized LOC101205072 0.948 0.912 0.457 1e-103
30678785488 zinc knuckle (CCHC-type) family protein 0.957 0.883 0.413 1e-92
2252849462 contains similarity to gag proteins [Ara 0.906 0.883 0.400 1e-83
16610191 594 PBF68 protein [Nicotiana tabacum] 0.484 0.367 0.432 1e-52
50253454409 At3g43510 [Arabidopsis thaliana] gi|5262 0.675 0.743 0.374 5e-51
7288029421 putative protein [Arabidopsis thaliana] 0.677 0.724 0.362 3e-49
>gi|224064265|ref|XP_002301412.1| predicted protein [Populus trichocarpa] gi|222843138|gb|EEE80685.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  494 bits (1271), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 245/451 (54%), Positives = 331/451 (73%), Gaps = 18/451 (3%)

Query: 8   RIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLLSTTES-- 65
           +I++TV+++LK++ M+E+TEFKVR  A+ERL  DLS   HK+FIRGV+ESFLLST +   
Sbjct: 2   KIQETVIDILKHASMDEITEFKVRATATERLDFDLSHIEHKKFIRGVIESFLLSTMDEEG 61

Query: 66  --TDNRIEPD----LEVEEQRAQIGKRINDDGDSIICKLSNKRTVAIQEFKGRAFVSIRE 119
              +  +  D    L+ E +     K +  DG+ +ICKLS +R+V IQEFKG++FVSIR+
Sbjct: 62  KEANGNVREDTKEALQEEHEEVLTKKEVGTDGNRVICKLSERRSVTIQEFKGKSFVSIRD 121

Query: 120 YFRRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKMQS--KLRSESSGEQNKDVANS 177
           ++++DG L+P+  GI LTSEQW A  +++PAI+EA+ KMQS   L  E +G+ +K VA+S
Sbjct: 122 FYQKDGNLLPSKIGICLTSEQWTAIKQNVPAIEEAIAKMQSISGLDVEQNGQISKPVADS 181

Query: 178 MTS--PLELFPTELHRFNGKNYRVWAQQIELLLKQLKVAYVLTDPCPIVTLCPQASSEEV 235
           ++   PLE+   E+ RF+GKNY+ WA Q+E  LKQLK+ YVLT P P +   P AS+EE+
Sbjct: 182 ISQELPLEISRIEVSRFDGKNYQFWAPQMEFFLKQLKIVYVLTVPRPSIATSPPASAEEI 241

Query: 236 TRVKAAERKWLNDNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVYLDEEFGTKR 295
            + KA E+KW ND+++CR +ILN LSD +YY+Y+K+  +AKELWE+LKLVYL EEFGTKR
Sbjct: 242 AQAKATEQKWCNDDHLCRLNILNSLSDSIYYKYAKKIKTAKELWEDLKLVYLYEEFGTKR 301

Query: 296 SQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWKDFCI 355
           SQVKKYIEFQM DEKS+F+Q  ELN IAD+IVAAGM I ENFHVS ++SKLP SWKDFC+
Sbjct: 302 SQVKKYIEFQMVDEKSIFDQLQELNGIADAIVAAGMFIDENFHVSTVISKLPPSWKDFCM 361

Query: 356 KLMRMEYLTFTMLMDHIKAEEESRSHNKQEEPSKFVELSPAVNFGPRMREMSK-----KR 410
           KLM  EYL F +LMD ++AEEESR+ +K  EPS  V        GPR+R+M K     KR
Sbjct: 362 KLMHEEYLPFWILMDRVRAEEESRNQDKLGEPSNHVHSHHPKYLGPRIRDMKKPGLHWKR 421

Query: 411 RESEMD-SKTVVCYNCRKKGHVAKHCHNKRL 440
           R+ E+D +K++ CY C KKGH++KHC +K+ 
Sbjct: 422 RDIEVDNNKSLTCYFCGKKGHISKHCPDKKF 452

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356571246|ref|XP_003553790.1| PREDICTED: uncharacterized protein LOC100800963 [Glycine max] Back     alignment and taxonomy information
>gi|356504175|ref|XP_003520874.1| PREDICTED: uncharacterized protein LOC100818901 [Glycine max] Back     alignment and taxonomy information
>gi|449433026|ref|XP_004134299.1| PREDICTED: uncharacterized protein LOC101205072 [Cucumis sativus] Back     alignment and taxonomy information
>gi|449478205|ref|XP_004155250.1| PREDICTED: uncharacterized LOC101205072 [Cucumis sativus] Back     alignment and taxonomy information
>gi|30678785|ref|NP_567205.2| zinc knuckle (CCHC-type) family protein [Arabidopsis thaliana] gi|26451026|dbj|BAC42619.1| unknown protein [Arabidopsis thaliana] gi|29028884|gb|AAO64821.1| At4g00980 [Arabidopsis thaliana] gi|332656563|gb|AEE81963.1| zinc knuckle (CCHC-type) family protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|2252849|gb|AAB62847.1| contains similarity to gag proteins [Arabidopsis thaliana] gi|7267595|emb|CAB80907.1| AT4g00980 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|16610191|emb|CAD10638.1| PBF68 protein [Nicotiana tabacum] Back     alignment and taxonomy information
>gi|50253454|gb|AAT71929.1| At3g43510 [Arabidopsis thaliana] gi|52627129|gb|AAU84691.1| At3g43510 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|7288029|emb|CAB81791.1| putative protein [Arabidopsis thaliana] 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 ?
Query450
TAIR|locus:2134618488 AT4G00980 [Arabidopsis thalian 0.951 0.877 0.429 2.2e-89
TAIR|locus:2123416165 KELP [Arabidopsis thaliana (ta 0.36 0.981 0.515 1.8e-39
UNIPROTKB|G4NEJ8162 MGG_00780 "Uncharacterized pro 0.186 0.518 0.352 1.1e-09
ASPGD|ASPL0000000236168 AN5806 [Emericella nidulans (t 0.246 0.660 0.300 2.9e-08
TAIR|locus:2184747107 KIWI [Arabidopsis thaliana (ta 0.151 0.635 0.333 3.7e-08
UNIPROTKB|Q5ZK63126 SUB1 "Activated RNA polymerase 0.182 0.650 0.301 4.8e-08
WB|WBGene00011743124 T13F2.2 [Caenorhabditis elegan 0.177 0.645 0.321 6.2e-08
UNIPROTKB|A7YWC6127 SUB1 "Uncharacterized protein" 0.182 0.645 0.333 7.9e-08
UNIPROTKB|J9NRQ9125 SUB1 "Uncharacterized protein" 0.2 0.72 0.288 7.9e-08
UNIPROTKB|E2R6X3127 SUB1 "Uncharacterized protein" 0.182 0.645 0.333 1e-07
TAIR|locus:2134618 AT4G00980 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 892 (319.1 bits), Expect = 2.2e-89, P = 2.2e-89
 Identities = 192/447 (42%), Positives = 277/447 (61%)

Query:     1 METVNEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLL 60
             ME V   +I +TV  +L  SDM++MTEFK+R++AS +LGIDLS  NHK+ +R V+E FLL
Sbjct:    12 MEIVATQKIEETVKSILSESDMDQMTEFKLRLDASAKLGIDLSGTNHKKLVRDVLEVFLL 71

Query:    61 STT-ES-TDNRIEPDLEVEEQRAQIGKRINDDGDSIICKLSNKRTVAIQEFKGRAFVSIR 118
             ST  E+     + P     E  +     +  + +  ICKLS K+   +Q ++G+ F+SI 
Sbjct:    72 STPGEALVPETVAP--AKNETVSVAAASVGGEDERFICKLSEKQNATVQRYRGQPFLSIG 129

Query:   119 EYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKMQSKLRSESSGEQNKDVANSM 178
                +  GK     +G  L++ QW    K+  AI++ + + QSKL+SE++   +   A   
Sbjct:   130 S--QEHGKAF---RGAHLSTNQWSVIKKNFAAIEDGIKQCQSKLKSEAARNGDTSEAVDK 184

Query:   179 TSPLELFPTELHRFNGKNYRVWAQQIELLLKQLKVAYVLTDPCPIV--TLCPQASSEEVT 236
              S       ++ RF+GK+Y  WA Q+EL LKQLK+ YVL++PCP +  +  P+ +  E+T
Sbjct:   185 DSSHGFSVIKISRFDGKSYLYWASQMELFLKQLKLTYVLSEPCPSIGSSQGPETNPREIT 244

Query:   237 RVKAAERKWLNDNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVYLDEEFGTKRS 296
             R  A  +KWL D+ +C  H++N LSDHLY +YS++   AKELW+ELK VY  +E  +KRS
Sbjct:   245 RADATGKKWLRDDYLCYTHLMNSLSDHLYRRYSQKFKHAKELWDELKWVYQCDESKSKRS 304

Query:   297 QVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWKDFCIK 356
             QV+KYIEF+M +E+ + EQ    NKIADSIV+AGM + E FHVS I+SK P SW+ FC +
Sbjct:   305 QVRKYIEFRMVEERPILEQVQVFNKIADSIVSAGMFLDEAFHVSTIISKFPPSWRGFCTR 364

Query:   357 LMRMEYLTFTMLMDHIKAEEES-RSHNK--QEEP---SKFVELSPAVNFGPR-MREMSKK 409
             LM  EYL   MLM+ +KAEEE  R+  K     P   S  +E +P++    R  + +  K
Sbjct:   365 LMEEEYLPVWMLMERVKAEEELLRNGAKGVTYRPATGSSQMERTPSLGTTHRGSQSVGWK 424

Query:   410 RRESEMDSKTV-VCYNCRKKGHVAKHC 435
             R+E E D + + VC NC +KGH+AKHC
Sbjct:   425 RKEPERDERVIIVCDNCGRKGHLAKHC 451
GO:0003676 "nucleic acid binding" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0008150 "biological_process" evidence=ND
GO:0008270 "zinc ion binding" evidence=IEA
TAIR|locus:2123416 KELP [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|G4NEJ8 MGG_00780 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)] Back     alignment and assigned GO terms
ASPGD|ASPL0000000236 AN5806 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
TAIR|locus:2184747 KIWI [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q5ZK63 SUB1 "Activated RNA polymerase II transcriptional coactivator p15" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
WB|WBGene00011743 T13F2.2 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
UNIPROTKB|A7YWC6 SUB1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|J9NRQ9 SUB1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|E2R6X3 SUB1 "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

Your Input:
gw1.II.823.1
hypothetical protein (459 aa)
(Populus trichocarpa)
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 ?
Query450
pfam0222981 pfam02229, PC4, Transcriptional Coactivator p15 (P 2e-23
pfam14227115 pfam14227, UBN2_2, gag-polypeptide of LTR copia-ty 6e-13
pfam0876654 pfam08766, DEK_C, DEK C terminal domain 2e-10
pfam14223119 pfam14223, UBN2, gag-polypeptide of LTR copia-type 1e-07
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 0.003
>gnl|CDD|216939 pfam02229, PC4, Transcriptional Coactivator p15 (PC4) Back     alignment and domain information 
 Score = 93.1 bits (232), Expect = 2e-23
 Identities = 32/81 (39%), Positives = 52/81 (64%)

Query: 75  EVEEQRAQIGKRINDDGDSIICKLSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGI 134
            V++ +++   + +D    I  +LS  R V + EFKG+  V IREY+ +DG+++P  KGI
Sbjct: 1   PVKKSKSEESSKGSDAEGDIFFELSKNRRVTVSEFKGKTLVDIREYYEKDGEMLPGKKGI 60

Query: 135 ALTSEQWRAFSKSLPAIDEAV 155
           +LT EQW A  + +P ID+A+
Sbjct: 61  SLTLEQWNALKEHIPEIDDAI 81

p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain. Length = 81
>gnl|CDD|222609 pfam14227, UBN2_2, gag-polypeptide of LTR copia-type Back     alignment and domain information
>gnl|CDD|204056 pfam08766, DEK_C, DEK C terminal domain Back     alignment and domain information
>gnl|CDD|222605 pfam14223, UBN2, gag-polypeptide of LTR copia-type Back     alignment and domain information
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 450
KOG2712108 consensus Transcriptional coactivator [Transcripti 99.96
PF14244152 UBN2_3: gag-polypeptide of LTR copia-type 99.85
PF0222956 PC4: Transcriptional Coactivator p15 (PC4); InterP 99.85
PF14227119 UBN2_2: gag-polypeptide of LTR copia-type 99.77
PF14223119 UBN2: gag-polypeptide of LTR copia-type 99.71
PF0876654 DEK_C: DEK C terminal domain; InterPro: IPR014876 99.52
KOG2266594 consensus Chromatin-associated protein Dek and rel 98.61
PF1396127 DUF4219: Domain of unknown function (DUF4219) 98.45
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 98.16
PF03564145 DUF1759: Protein of unknown function (DUF1759); In 97.98
PF1369632 zf-CCHC_2: Zinc knuckle 97.13
PF0373296 Retrotrans_gag: Retrotransposon gag protein ; Inte 96.89
PF1391742 zf-CCHC_3: Zinc knuckle 95.56
smart0034326 ZnF_C2HC zinc finger. 95.31
PF1478736 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 94.67
PF1528840 zf-CCHC_6: Zinc knuckle 93.86
PF1439249 zf-CCHC_4: Zinc knuckle 93.69
COG5082190 AIR1 Arginine methyltransferase-interacting protei 91.68
COG5222 427 Uncharacterized conserved protein, contains RING Z 89.93
COG5082190 AIR1 Arginine methyltransferase-interacting protei 89.78
PTZ00368148 universal minicircle sequence binding protein (UMS 89.29
KOG0109 346 consensus RNA-binding protein LARK, contains RRM a 88.23
COG444372 Uncharacterized protein conserved in bacteria [Fun 84.5
PF14893331 PNMA: PNMA 81.83
KOG1946240 consensus RNA polymerase I transcription factor UA 80.15
>KOG2712 consensus Transcriptional coactivator [Transcription] Back     alignment and domain information 
Probab=99.96  E-value=2.4e-30  Score=202.96  Aligned_cols=72  Identities=43%  Similarity=0.802  Sum_probs=69.2

Q ss_pred             CCCCceEEEcCCceeeEEeeecCceeEeeEeEEecCCcccCCCcccccCHHHHHHHHhhhhHHHHHHHHhcc
Q 013049           89 DDGDSIICKLSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKMQS  160 (450)
Q Consensus        89 ~~~d~~~~~~~~~~~~~~~~~~g~~~~~ir~~~~~~~~~~p~~kgi~l~~~~~~~l~~~~~~i~~~~~~~~~  160 (450)
                      +.++.++|.|+++|||||++|+|+.||||||||.+||+|+|||||||||.+||+.|++.+++|++||..+++
T Consensus        36 ~s~~~~i~~l~~~RrVtV~eFkGk~~VdIREyY~kdG~mlPgkKGISLs~~qW~~Lk~~~~eId~Al~~l~s  107 (108)
T KOG2712|consen   36 DSEDDNIFNLGKNRRVTVREFKGKILVDIREYYVKDGKMLPGKKGISLSLEQWSKLKEHIEEIDKALRKLSS  107 (108)
T ss_pred             CcCccceeecCCceEEehhhcCCceEEehhHhhhccCccccCccccccCHHHHHHHHHHHHHHHHHHHHhcc
Confidence            567789999999999999999999999999999999999999999999999999999999999999998875

>PF14244 UBN2_3: gag-polypeptide of LTR copia-type Back     alignment and domain information
>PF02229 PC4: Transcriptional Coactivator p15 (PC4); InterPro: IPR003173 p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain [] Back     alignment and domain information
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type Back     alignment and domain information
>PF14223 UBN2: gag-polypeptide of LTR copia-type Back     alignment and domain information
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease Back     alignment and domain information
>KOG2266 consensus Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics] Back     alignment and domain information
>PF13961 DUF4219: Domain of unknown function (DUF4219) 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
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function Back     alignment and domain information
>PF13696 zf-CCHC_2: Zinc knuckle Back     alignment and domain information
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes 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
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A Back     alignment and domain information
>PF15288 zf-CCHC_6: Zinc knuckle Back     alignment and domain information
>PF14392 zf-CCHC_4: Zinc knuckle 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
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only] 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
>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
>COG4443 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PF14893 PNMA: PNMA Back     alignment and domain information
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription] 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 ?
Query450
4agh_A158 Structural Features Of Ssdna Binding Protein Mosub1 4e-09
1pcf_A66 Human Transcriptional Coactivator Pc4 C-Terminal Do 3e-06
>pdb|4AGH|A Chain A, Structural Features Of Ssdna Binding Protein Mosub1 From Magnaporthe Oryzae Length = 158 Back     alignment and structure 
Iteration: 1

 Score = 59.7 bits (143), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 39/55 (70%)
Query: 98  LSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAID 152
           +S+KR V I +FK   F++IREY+   G++ P  KGI LT +Q+ AF K++PAI+
Sbjct: 51  ISDKRRVGISQFKKMDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAIN 105
>pdb|1PCF|A Chain A, Human Transcriptional Coactivator Pc4 C-Terminal Domain Length = 66 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 ?
Query450
1pcf_A66 P15, transcriptional coactivator PC4; transcriptio 3e-19
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-14
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 8e-08
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 4e-04
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 6e-04
>1pcf_A P15, transcriptional coactivator PC4; transcriptional cofactor, ssDNA binding, nuclear protein; 1.74A {Homo sapiens} SCOP: d.18.1.1 PDB: 2c62_A 2phe_A Length = 66 Back     alignment and structure
 Score = 80.6 bits (199), Expect = 3e-19
 Identities = 23/65 (35%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

Query: 95  ICKLSNKRTVAIQEFKGRAFVSIREYFR-RDGKLVPTAKGIALTSEQWRAFSKSLPAIDE 153
           + ++   R V++++FKG+  + IREY+   +G++ P  KGI+L  EQW    + +  ID+
Sbjct: 2   MFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDD 61

Query: 154 AVVKM 158
           AV K+
Sbjct: 62  AVRKL 66
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 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
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query450
1pcf_A66 P15, transcriptional coactivator PC4; transcriptio 99.95
4agh_A158 Mosub1, transcription cofactor; ssDNA binding prot 99.94
1q1v_A70 DEK protein; winged-helix motif, DNA binding prote 99.54
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 98.13
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 98.11
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 98.05
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 98.03
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 97.42
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 96.62
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 96.59
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 96.56
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 96.44
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 96.41
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 96.39
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 96.38
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 96.36
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 96.27
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 96.19
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 96.14
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 95.89
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 95.85
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 95.84
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 95.82
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 95.28
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 95.2
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 95.03
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 94.7
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 94.61
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 92.92
4g06_A79 Uncharacterized protein; structural genomics, PSI- 90.67
2l3a_A82 Uncharacterized protein; structural genomics, PSI- 90.21
3pm7_A80 Uncharacterized protein; structural genomics, PSI- 90.14
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 89.68
2hqh_E26 Restin; beta/BETA structure, zinc finger motif, st 82.6
>1pcf_A P15, transcriptional coactivator PC4; transcriptional cofactor, ssDNA binding, nuclear protein; 1.74A {Homo sapiens} SCOP: d.18.1.1 PDB: 2c62_A 2phe_A Back     alignment and structure
Probab=99.95  E-value=3.2e-29  Score=183.13  Aligned_cols=64  Identities=36%  Similarity=0.797  Sum_probs=61.9

Q ss_pred             EEEcCCceeeEEeeecCceeEeeEeEE-ecCCcccCCCcccccCHHHHHHHHhhhhHHHHHHHHh
Q 013049           95 ICKLSNKRTVAIQEFKGRAFVSIREYF-RRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKM  158 (450)
Q Consensus        95 ~~~~~~~~~~~~~~~~g~~~~~ir~~~-~~~~~~~p~~kgi~l~~~~~~~l~~~~~~i~~~~~~~  158 (450)
                      +|+||++|||+|++|||++|||||||| ++||+++|||||||||++||+.|++++++|++||+++
T Consensus         2 ~~~ls~~rrvtv~~fkG~~~VdIRe~Y~~kdG~~~PgkKGIsL~~~qw~~l~~~~~~I~~ai~~~   66 (66)
T 1pcf_A            2 MFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL   66 (66)
T ss_dssp             EEEEETTEEEEEEEETTEEEEEEEEEEECTTSCEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHC
T ss_pred             eEECCCCeEEEEEEeCCCEEEEEEEEEECCCCcCCCCccccccCHHHHHHHHHHHHHHHHHHHhC
Confidence            799999999999999999999999999 7899999999999999999999999999999999863
>4agh_A Mosub1, transcription cofactor; ssDNA binding protein; 1.79A {Magnaporthe oryzae} Back     alignment and structure
>1q1v_A DEK protein; winged-helix motif, DNA binding protein; NMR {Homo sapiens} SCOP: a.159.4.1 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
>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1 Back     alignment and structure
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A Back     alignment and structure
>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
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1 Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Back     alignment and structure
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} 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
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} 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
>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
>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
>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
>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
>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
>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
>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
>4g06_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium (NESG); HET: DT; 2.90A {Streptococcus pneumoniae} Back     alignment and structure
>2l3a_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Streptococcus pneumoniae} PDB: 3obh_A* Back     alignment and structure
>3pm7_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 2.00A {Enterococcus faecalis} Back     alignment and structure
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {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 450
d1pcfa_66 d.18.1.1 (A:) Transcriptional coactivator PC4 C-te 7e-18
d1q1va_70 a.159.4.1 (A:) DEK C-terminal domain {Human (Homo 6e-06
d1nc8a_29 g.40.1.1 (A:) HIV nucleocapsid {Human immunodefici 5e-04
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 0.001
>d1pcfa_ d.18.1.1 (A:) Transcriptional coactivator PC4 C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 66 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: ssDNA-binding transcriptional regulator domain
superfamily: ssDNA-binding transcriptional regulator domain
family: Transcriptional coactivator PC4 C-terminal domain
domain: Transcriptional coactivator PC4 C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.5 bits (186), Expect = 7e-18
 Identities = 23/63 (36%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 97  KLSNKRTVAIQEFKGRAFVSIREYFR-RDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAV 155
           ++   R V++++FKG+  + IREY+   +G++ P  KGI+L  EQW    + +  ID+AV
Sbjct: 4   QIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAV 63

Query: 156 VKM 158
            K+
Sbjct: 64  RKL 66
>d1q1va_ a.159.4.1 (A:) DEK C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 70 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
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query450
d1pcfa_66 Transcriptional coactivator PC4 C-terminal domain 99.95
d1q1va_70 DEK C-terminal domain {Human (Homo sapiens) [TaxId 99.56
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 98.45
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 97.84
d1a6bb_40 Zinc finger protein ncp10 {Moloney murine leukemia 97.66
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 97.17
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 96.95
d1cl4a_32 Nucleocapsid protein from mason-pfizer monkey viru 93.88
d1dsva_31 Nucleic acid binding protein p14 {Mouse mammary tu 93.66
>d1pcfa_ d.18.1.1 (A:) Transcriptional coactivator PC4 C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: ssDNA-binding transcriptional regulator domain
superfamily: ssDNA-binding transcriptional regulator domain
family: Transcriptional coactivator PC4 C-terminal domain
domain: Transcriptional coactivator PC4 C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=2e-29  Score=182.13  Aligned_cols=64  Identities=36%  Similarity=0.797  Sum_probs=61.8

Q ss_pred             EEEcCCceeeEEeeecCceeEeeEeEE-ecCCcccCCCcccccCHHHHHHHHhhhhHHHHHHHHh
Q 013049           95 ICKLSNKRTVAIQEFKGRAFVSIREYF-RRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKM  158 (450)
Q Consensus        95 ~~~~~~~~~~~~~~~~g~~~~~ir~~~-~~~~~~~p~~kgi~l~~~~~~~l~~~~~~i~~~~~~~  158 (450)
                      +|+||++|||||++|||++|||||||| ++||+|+|||||||||.+||..|++++++|++||++|
T Consensus         2 ~~~L~~~rrvtV~~FkG~~~vdIReyY~dkdGe~~PgkKGIsL~~~qw~~l~~~~~~i~~ai~~l   66 (66)
T d1pcfa_           2 MFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL   66 (66)
T ss_dssp             EEEEETTEEEEEEEETTEEEEEEEEEEECTTSCEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHC
T ss_pred             eeecCCcEEEEEEEECCcEEEEEEEEEECCCCCCCCCCCeEEECHHHHHHHHHHHHHHHHHHHhC
Confidence            799999999999999999999999999 5799999999999999999999999999999999874
>d1q1va_ a.159.4.1 (A:) DEK C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} 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
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [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
>d1cl4a_ g.40.1.1 (A:) Nucleocapsid protein from mason-pfizer monkey virus (MPMV) {Mason-pfizer monkey virus [TaxId: 11855]} Back     information, alignment and structure
>d1dsva_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]} Back     information, alignment and structure