Citrus Sinensis ID: 015479

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Local Sequence Feature Prediction

Residue Number Marker
--------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------
Protein Sequence
MKNNLRCIASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASKRKMTTEFPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNHHSESISRGRYHEQRWSRDYRDDGPPGVDPVSSYPPRYGGYDYYSSHSRSPTRGRSYSDRDRDDYASHGSYSSPYSNRHTSPPDYDLDRYRDDYSREYLSRSMDEYDRFRPRGRWW
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccEEEEcEEEcccccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccccccEEEcccccccccccccccccHHHHHHHcccccccHHHHHHHHHHcccccccccccccccccEEEEcccccccccccccHHccccccccccEEcccccccccccccccHHccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHcHHHHHHHHHHHHHHHHHHccccccHHHHHccccccEEEEEEEcccccccEEEEEEcccccccccccEcccccccccEccEEEEccccccccccccccEEEEccccHcccccccccccccccccccHHHHHHHHHHHHHHcccccccccccEEEccccHHHccccccccccHHHHHHHccccccccHHHHHHHHcccccccccHHHHHccccEEEEccccccccccccccccccccccccHEEEccccccccccccccHHHccccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mknnlrciASKQKLEELLQQWSEWQaqfgsssndpnegiefgeqtffpairvgkakgpavsFWIDnqtrnqqnknfipsdshgtplydrgyalgltsgdgssnleggleiiddasrcfncgsyshslkecpkprdkdavNNARKQHkskrnqnsasrnpmryyqnsaggkydglrpgaldAETRQLlglgeldpppwlhrmrelgyppgyldsedddqpsgitiyadgeikegqedgeiietgrpaskrkmttefpginapipenaderlwaarpsssdssrdrshhrlnhhsesisrgryheqrwsrdyrddgppgvdpvssyppryggydyysshsrsptrgrsysdrdrddyashgsysspysnrhtsppdydldryrddYSREYLSRsmdeydrfrprgrww
Flexible Loop (DISEMBL)
mknnlrciASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQtrnqqnknfipsdshgtpLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSyshslkecpkprdkdavnnarkqhkskrnqnsasrnpmRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADgeikegqedgeiietgrpaskrkmttefpginapipenadeRLWAARPSssdssrdrshhrlnhhsesisrgryhEQRWSrdyrddgppgvDPVSSYPPRYGGydyysshsrsptrgrsysdrdrddyashgsysspysnrhtsppdydldrYRDDYSReylsrsmdeydrfrprgrww
Low Complexity Region (SEG)
MKNNLRCIASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASKRKMTTEFPGINAPIPENADERLWAArpsssdssrdrshhrlnhhsESISRGRYHEQRWSRDYRDDGPPGVDPVSSYPPRYGGYDYYSSHSRSPTrgrsysdrdrddyASHGSYSSPYSNRHTsppdydldryrddysreylsrsMDEYDRFRPRGRWW
Disordered region (IsUnstruct)
****************LLQQWSEW**************IEFGEQTFFPAIRVGKAKGPAVSFWIDN******************PLYDRGYALGLT*******LEGGLEIIDDASRCFNCGSY*************************************************************QLLGLGELDPPPWLHRMRELGY********************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
***********QKLEELLQQW****************************IRVGKAKGPAVSFWIDNQTRNQ*********SHGTPLYDRGY************************RCFNCGSYSHSLKECPKPRDKDAVNNARK********************NSAGGKYDGLRPGALDA**RQ**GLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGIT***************************MTTEFPGINAPIPENADERLWA**************************************************************************************************************************************
Disordered Region (DISEMBL)
MKNNLRCIASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHS*****************************SRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASKRKMTTEFPGINAPIPENADERLW********************************QRWSRDYRDDGPPGVDPVSSYPPRYGGYDYYS****************RDDYASHGSYSSPYSNRHTSPPDYDLDRYRDDYSREYLSRSMDEYDRFRPRGRWW
Disordered Region (DISPRO)
*****RCIASKQKLEELLQQWSEWQAQFGS***DPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADG***************RPASKRKMTTEFPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNHH*********************GPPGVDPVSSYPPRYGGYDYYSSH******************************RHTSPPDYDLDR***************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKNNLRCIASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASKRKMTTEFPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNHHSESISRGRYHEQRWSRDYRDDGPPGVDPVSSYPPRYGGYDYYSSHSRSPTRGRSYSDRDRDDYASHGSYSSPYSNRHTSPPDYDLDRYRDDYSREYLSRSMDEYDRFRPRGRWW
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	406	2.2.26 [Sep-21-2011]
Q6DD45	743	Zinc finger CCHC domain-c	N/A	no	0.379	0.207	0.349	2e-19
Q9CYA6	709	Zinc finger CCHC domain-c	yes	no	0.426	0.244	0.322	1e-18
Q5F3D1	613	Zinc finger CCHC domain-c	yes	no	0.440	0.292	0.309	3e-18
Q6NZY4	707	Zinc finger CCHC domain-c	yes	no	0.423	0.243	0.308	3e-17
Q5R789	704	Zinc finger CCHC domain-c	yes	no	0.423	0.244	0.308	4e-17
Q2PE14	553	Zinc finger CCHC domain-c	yes	no	0.325	0.238	0.348	4e-14

>sp|Q6DD45|ZCHC8_XENLA Zinc finger CCHC domain-containing protein 8 OS=Xenopus laevis GN=zcchc8 PE=2 SV=1

 Score = 97.4 bits (241), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 58/166 (34%), Positives = 91/166 (54%), Gaps = 12/166 (7%)

Query: 107 GLEIIDDASR----CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRY 162
           G EI   A R    CFNCGS  H +++CPKPRD+  +N  RK+      + + ++N  RY
Sbjct: 201 GQEIQVKAKRPKPCCFNCGSEEHQMRDCPKPRDQAHINMKRKEFLDACGE-AGNQNQQRY 259

Query: 163 YQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGI 222
           +      ++   +PG +  E ++ LG+ + + PP+++RMRELGYPPG+L  E + + SG+
Sbjct: 260 HAEEVEERFGKYKPGVISEELQEALGIMDKNLPPFIYRMRELGYPPGWL-KEAELENSGL 318

Query: 223 TIYADGEIKEGQEDGEIIETGRPASKR-----KMTTEFPGINAPIP 263
           ++Y DG+ +    DGEI +    A K           +PG N   P
Sbjct: 319 SLY-DGKERLDASDGEIEDRDTEAKKHVSYDVSKLVNYPGFNISAP 363

Xenopus laevis (taxid: 8355)

>sp|Q9CYA6|ZCHC8_MOUSE Zinc finger CCHC domain-containing protein 8 OS=Mus musculus GN=Zcchc8 PE=2 SV=3

 Score = 94.7 bits (234), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 60/186 (32%), Positives = 93/186 (50%), Gaps = 13/186 (6%)

Query: 117 CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRP 176
           CFNCGS  H +KECP PR+   ++  RK++     + S      RY+      ++   +P
Sbjct: 232 CFNCGSEEHQMKECPMPRNAARISEKRKEYMDACGEASGQSFQQRYHAEEVEERFGRFKP 291

Query: 177 GALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIY-----ADGEIK 231
           G +  E +  LG+ +   PP+++RMR+LGYPPG+L  E + + SG+ +Y     ADGE  
Sbjct: 292 GVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWL-KEAELENSGLALYDGNDDADGET- 349

Query: 232 EGQEDGEIIETGRPASKRKMTTEFPGINAPIPENA-DE-RLWAARPSSSDSSRDRSHHRL 289
              E GEI          K+   +PG N   P    DE R++ + P  +   +D     L
Sbjct: 350 ---ETGEIQNKNVTYDLSKLVN-YPGFNISTPRGIPDEWRMFGSIPMQACQQKDVFASYL 405

Query: 290 NHHSES 295
           N + +S
Sbjct: 406 NSNIQS 411

May be involved in pre-mRNA splicing.

Mus musculus (taxid: 10090)

>sp|Q5F3D1|ZCHC8_CHICK Zinc finger CCHC domain-containing protein 8 OS=Gallus gallus GN=ZCCHC8 PE=2 SV=1

 Score = 93.2 bits (230), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 57/184 (30%), Positives = 90/184 (48%), Gaps = 5/184 (2%)

Query: 115 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGL 174
           S CFNCGS  H +K+CPKPR+   ++  RK+      + S      RY+      ++   
Sbjct: 126 SHCFNCGSEEHQIKDCPKPRNAARISEKRKEFMEAYGEASNQNFQQRYHAEEVEERFGKF 185

Query: 175 RPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQ 234
           +PG +  E +  LG+     PP+++RMR+LGYPPG+L  E + + SG+ +Y DG+     
Sbjct: 186 KPGVISGELQDALGVTAKSLPPFIYRMRQLGYPPGWL-KEAEMEHSGLALY-DGKDDNET 243

Query: 235 EDGEIIETGRPASKRKMTTEFPGINAPIPENA-DE-RLWAARPSSSDSSRDRSHHRL-NH 291
           ED   ++             +PG N   P    DE +++ + P      +D   H L N 
Sbjct: 244 EDEGYLQPKHVTYDVSKLINYPGFNISTPSGIPDEWQIFGSIPMQPSQQKDVFAHYLSNF 303

Query: 292 HSES 295
           H+ S
Sbjct: 304 HAPS 307

Gallus gallus (taxid: 9031)

>sp|Q6NZY4|ZCHC8_HUMAN Zinc finger CCHC domain-containing protein 8 OS=Homo sapiens GN=ZCCHC8 PE=1 SV=2

 Score = 89.7 bits (221), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 58/188 (30%), Positives = 91/188 (48%), Gaps = 16/188 (8%)

Query: 107 GLEIIDDASR----CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRY 162
           G EI   A R    CFNCGS  H +K+CP PR+   ++  RK++     + +      RY
Sbjct: 215 GQEIQVKAKRPKPHCFNCGSEEHQMKDCPMPRNAARISEKRKEYMDACGEANNQNFQQRY 274

Query: 163 YQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGI 222
           +      ++   +PG +  E +  LG+ +   PP+++RMR+LGYPPG+L  E + + SG+
Sbjct: 275 HAEEVEERFGRFKPGVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWL-KEAELENSGL 333

Query: 223 TIY-----ADGEIKEGQEDGEIIETGRPASKRKMTTEFPGINAPIPENA-DE-RLWAARP 275
            +Y      DGE     E GEI +             +PG N   P    DE R++ + P
Sbjct: 334 ALYDGKDGTDGET----EVGEIQQNKSVTYDLSKLVNYPGFNISTPRGIPDEWRIFGSIP 389

Query: 276 SSSDSSRD 283
             +   +D
Sbjct: 390 MQACQQKD 397

May be involved in pre-mRNA splicing.

Homo sapiens (taxid: 9606)

>sp|Q5R789|ZCHC8_PONAB Zinc finger CCHC domain-containing protein 8 OS=Pongo abelii GN=ZCCHC8 PE=2 SV=1

 Score = 89.7 bits (221), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 58/188 (30%), Positives = 91/188 (48%), Gaps = 16/188 (8%)

Query: 107 GLEIIDDASR----CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRY 162
           G EI   A R    CFNCGS  H +K+CP PR+   ++  RK++     + +      RY
Sbjct: 213 GQEIQVKAKRPKPHCFNCGSEEHQMKDCPMPRNAARISEKRKEYMDACGEANNQNFQQRY 272

Query: 163 YQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGI 222
           +      ++   +PG +  E +  LG+ +   PP+++RMR+LGYPPG+L  E + + SG+
Sbjct: 273 HAEEVEERFGRFKPGVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWL-KEAELENSGL 331

Query: 223 TIY-----ADGEIKEGQEDGEIIETGRPASKRKMTTEFPGINAPIPENA-DE-RLWAARP 275
            +Y      DGE     E GEI +             +PG N   P    DE R++ + P
Sbjct: 332 ALYDGKDGTDGET----EVGEIQQNKSVTYDLSKLVNYPGFNISTPRGIPDEWRIFGSIP 387

Query: 276 SSSDSSRD 283
             +   +D
Sbjct: 388 MQACQQKD 395

May be involved in pre-mRNA splicing.

Pongo abelii (taxid: 9601)

>sp|Q2PE14|ZCHC8_DROME Zinc finger CCHC domain-containing protein 8 homolog OS=Drosophila melanogaster GN=CG4622 PE=1 SV=2

 Score = 79.3 bits (194), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 52/149 (34%), Positives = 76/149 (51%), Gaps = 17/149 (11%)

Query: 115 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGL 174
           S CFNCG   HSL++C KPR+   +  ARK+  S+           RY+ ++   ++  +
Sbjct: 183 SSCFNCGDTEHSLRDCTKPRNNSRITRARKKMTSRTE---------RYHVDTE-QRFGHI 232

Query: 175 RPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIY-ADGE--IK 231
           RPG +  +TR  +G      P   +RMR LGYPP +L+ E   Q SGI ++ ADG    K
Sbjct: 233 RPGKISTKTRHAMGYSRGQLPFIFYRMRVLGYPPAWLE-EAKVQSSGIALFNADGSEVTK 291

Query: 232 EGQEDGEIIETGRPASKRKMTTEFPGINA 260
             +E+GE        +K     E+PG N 
Sbjct: 292 SDEEEGESETFKYDVNK---IVEYPGFNV 317

Drosophila melanogaster (taxid: 7227)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	406
255570019	693	nucleic acid binding protein, putative [	0.963	0.564	0.635	1e-137
359488397	575	PREDICTED: uncharacterized protein LOC10	0.817	0.577	0.670	1e-126
224079886	531	predicted protein [Populus trichocarpa]	0.800	0.612	0.680	1e-126
307136480	610	nucleic acid binding protein [Cucumis me	0.834	0.555	0.656	1e-123
449525630	610	PREDICTED: uncharacterized protein LOC10	0.834	0.555	0.656	1e-123
449447474	610	PREDICTED: uncharacterized protein LOC10	0.834	0.555	0.656	1e-122
356573637	660	PREDICTED: uncharacterized protein LOC10	0.940	0.578	0.590	1e-121
298204384	1165	unnamed protein product [Vitis vinifera]	0.763	0.266	0.628	1e-114
224127396	289	predicted protein [Populus trichocarpa]	0.645	0.906	0.722	1e-110
358346605	543	Zinc finger CCHC domain-containing prote	0.775	0.580	0.648	1e-107

>gi|255570019|ref|XP_002525972.1| nucleic acid binding protein, putative [Ricinus communis] gi|223534704|gb|EEF36396.1| nucleic acid binding protein, putative [Ricinus communis]

 Score =  494 bits (1272), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 261/411 (63%), Positives = 312/411 (75%), Gaps = 20/411 (4%)

Query: 9   ASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQT 68
           ASK+KLEELLQQWSEW  Q GSSS D NE +E GE+T+FPA+ VG  K  AVSFWI+NQT
Sbjct: 272 ASKRKLEELLQQWSEWHVQRGSSSQDLNEVLESGEETYFPALCVGTEKSSAVSFWIENQT 331

Query: 69  RNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLK 128
           + Q N + I SDS   PLYDRG+A+GLTS DG SN+EGGLEI+++A+RCFNCGSYSH+LK
Sbjct: 332 KKQLNNDLISSDSDSVPLYDRGFAIGLTSTDGPSNVEGGLEIVNEAARCFNCGSYSHALK 391

Query: 129 ECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLG 188
           ECPKPR+  AVNNARKQHKSKRNQN+ SRN  RYYQ+S+GGKY+GL+PG+LDAETR+LLG
Sbjct: 392 ECPKPRNNAAVNNARKQHKSKRNQNAGSRNGTRYYQSSSGGKYEGLKPGSLDAETRRLLG 451

Query: 189 LGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASK 248
           LGELDPPPWL+RMRELGYPPGYLD +D+DQPSGI I+ADG+IK+ QEDGEIIET  P   
Sbjct: 452 LGELDPPPWLNRMRELGYPPGYLDPDDEDQPSGIIIFADGDIKDEQEDGEIIETENPDPP 511

Query: 249 RKMTTEFPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNHHSESISRGRYHEQRWSR 308
           RKM  EFPGINAPIPENADERLW   PSS +S R+R   + +H SE+ISR  +HEQR SR
Sbjct: 512 RKMAVEFPGINAPIPENADERLWETGPSSYNSFRNRPFRKSDHSSETISRWHHHEQRGSR 571

Query: 309 DYRDDGPPGVDPV---SSYPPRYGGYDYYSSHSR----SPTRGRSYSDRDR------DDY 355
           D  D+GPPGVDPV   SS+PPRYG YD   S       + +  RS S++ R      +D+
Sbjct: 572 DSIDEGPPGVDPVFSPSSFPPRYGNYDSSYSSDSLRGSTASLPRSRSEKGRRSPVVYEDF 631

Query: 356 ASHGSYSSPYSNRHTSPPDYDLDRY------RDDYSR-EYLSRSMDEYDRF 399
           ASH S      N+ +SP D D DR       R +YSR +Y  RS+DE+DR+
Sbjct: 632 ASHSSSPFSSLNKRSSPKDNDSDRLESETDERWNYSRLDYSYRSIDEHDRY 682

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488397|ref|XP_002279557.2| PREDICTED: uncharacterized protein LOC100247996 [Vitis vinifera]

 Score =  458 bits (1179), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 238/355 (67%), Positives = 269/355 (75%), Gaps = 23/355 (6%)

Query: 10  SKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTR 69
           SK+KLEELLQQWSEW A++ SSS+DP   ++ GE+T+FPA+ VG  K  AVSFW+DNQTR
Sbjct: 160 SKRKLEELLQQWSEWHAKYVSSSHDPKGQLDSGEKTYFPALHVGLNKSSAVSFWVDNQTR 219

Query: 70  NQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKE 129
            QQ+K FI  D    PLYDRG+ALGL S DG S  EG LEIID ASRCFNCGSY+HS+KE
Sbjct: 220 KQQDKEFISLDGDSVPLYDRGFALGLVSEDGQSKPEGALEIID-ASRCFNCGSYNHSMKE 278

Query: 130 CPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGL 189
           CPKPRD  AVNNARKQHKS+RNQN  SRNP RYYQNS GG+YDGLRPGAL  ETR+LLGL
Sbjct: 279 CPKPRDNVAVNNARKQHKSRRNQNPGSRNPTRYYQNSPGGRYDGLRPGALGVETRELLGL 338

Query: 190 GELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASKR 249
           GELDPPPWL+RMRE+GYPPGYLD E+++QPSGITIYAD E+K+ QEDGEI+ET     +R
Sbjct: 339 GELDPPPWLNRMREMGYPPGYLDPEEEEQPSGITIYADEEVKDEQEDGEILETEYLEPQR 398

Query: 250 KMTTEFPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNHHSESISRGRYHEQRWSRD 309
           KM+ EFPGINAPIP+NADER WAA          R H RLNH  E  SR   HEQRWSRD
Sbjct: 399 KMSVEFPGINAPIPKNADERRWAA--------GSRPHRRLNHSYEPSSRRNSHEQRWSRD 450

Query: 310 YRDDGPPGVD-----PVSSYPPRYGGYD-YYSSHS--------RSPTRGRSYSDR 350
           YRDDGP   D     P SSYPPR+GG D  Y+S+S        RSP  GRS SDR
Sbjct: 451 YRDDGPCDSDMEISPPRSSYPPRHGGIDSSYTSYSTRGNIPRPRSPNFGRSLSDR 505

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224079886|ref|XP_002305958.1| predicted protein [Populus trichocarpa] gi|222848922|gb|EEE86469.1| predicted protein [Populus trichocarpa]

 Score =  458 bits (1178), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 228/335 (68%), Positives = 267/335 (79%), Gaps = 10/335 (2%)

Query: 1   MKNNLRCIASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAV 60
           M N+L   ASK+KLEELLQQWSEW AQ  SSS+D +E ++ GE T+FPA+R+G  K  AV
Sbjct: 139 MYNSL-TRASKKKLEELLQQWSEWHAQQNSSSHDSDEMLQSGEDTYFPALRIGMVKSSAV 197

Query: 61  SFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNC 120
           +FWI+NQTR QQ+   IP  S+  PLYDRGYALGLTS DG  N+E GLEI+ DA+RC+NC
Sbjct: 198 TFWIENQTRKQQDNAIIPLQSNYVPLYDRGYALGLTSADGPINIERGLEIVGDAARCYNC 257

Query: 121 GSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALD 180
            SY+HSLKECPKPRD  AVNNARKQHK KRNQNS+SRNP RYYQ+S+GGKYDGL+PG+LD
Sbjct: 258 ASYNHSLKECPKPRDNAAVNNARKQHKFKRNQNSSSRNPTRYYQSSSGGKYDGLKPGSLD 317

Query: 181 AETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEII 240
            ET++LLGLGELDPPPWL+RM+ELGYPPGYLD +D+DQPSGITI+ADG++ E QEDGEI 
Sbjct: 318 TETQKLLGLGELDPPPWLNRMQELGYPPGYLDPDDEDQPSGITIFADGDVNEEQEDGEIT 377

Query: 241 ETGRPAS-KRKMTTEFPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNHHSESISRG 299
           ET  P   +RKM+ EFPGINA IPENAD+RLW   P+SSD  R RS HRL + SE+  R 
Sbjct: 378 ETDPPPEPQRKMSVEFPGINAAIPENADQRLWEVGPTSSDPWRHRSQHRLKYSSEATGRW 437

Query: 300 RYHEQRWSRDYRDDGPPGVDPV-----SSYPPRYG 329
            +HEQ   R YRDDGPPGVD V     SSYPPRYG
Sbjct: 438 HHHEQ---RQYRDDGPPGVDSVFSPSMSSYPPRYG 469

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307136480|gb|ADN34281.1| nucleic acid binding protein [Cucumis melo subsp. melo]

 Score =  447 bits (1150), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 235/358 (65%), Positives = 272/358 (75%), Gaps = 19/358 (5%)

Query: 10  SKQKLEELLQQWSEWQAQFGSSSNDP--NEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQ 67
           SKQKL+ELL+QWSEW AQ GS S D    E +E GE+TFFPA+ VG  K  AV+FW+DNQ
Sbjct: 230 SKQKLDELLKQWSEWHAQQGSLSRDDKDTENLESGEETFFPALCVGTKKTSAVTFWMDNQ 289

Query: 68  TRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSL 127
            +++Q + F+P D +  PLYDRG+ LGLTS + SSN+EGG +IIDDASRCFNCGSY+HSL
Sbjct: 290 -KSEQQQTFVPIDDNSVPLYDRGFTLGLTSANDSSNVEGGQKIIDDASRCFNCGSYNHSL 348

Query: 128 KECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLL 187
           K+C KPRD  AVNNAR  +K K+  NSASRN  RYYQNS GGKYD LRPG LDAETRQLL
Sbjct: 349 KDCRKPRDNAAVNNAR--NKYKKQHNSASRNSTRYYQNSRGGKYDDLRPGTLDAETRQLL 406

Query: 188 GLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPAS 247
           GL ELDPPPWL+RMRELGYPPGYLD ED+DQPSGITIYAD +  E QEDGEI E      
Sbjct: 407 GLKELDPPPWLNRMRELGYPPGYLDPEDEDQPSGITIYADEKTDE-QEDGEITEAEYRKP 465

Query: 248 KRKMTTEFPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNHHSESISRGR-YHEQRW 306
           ++KM+ EFPGINAPIPENADERLWA  PSSS   R+RS+ RLNH+ E  +RG  +H+QRW
Sbjct: 466 QKKMSVEFPGINAPIPENADERLWAPEPSSSGLPRNRSNQRLNHYPEYDTRGNDHHQQRW 525

Query: 307 SRDYRDDGPPGVDPVSSYP---PRYGGYDY-YSSH--------SRSPTRGRSYSDRDR 352
           SRDYRDD PPGVD + S P   PRYGG+D+ Y S         SRSP  GR +SDR R
Sbjct: 526 SRDYRDDRPPGVDSIKSPPSFTPRYGGHDFSYDSQTPRGSFSTSRSPNLGRPHSDRGR 583

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449525630|ref|XP_004169819.1| PREDICTED: uncharacterized protein LOC101230973 [Cucumis sativus]

 Score =  447 bits (1150), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 235/358 (65%), Positives = 273/358 (76%), Gaps = 19/358 (5%)

Query: 10  SKQKLEELLQQWSEWQAQFGSSSNDP--NEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQ 67
           SKQKL+ELL+QWSEW AQ GS S D    E +E GE+TFFPA+ VG  K  AV+FW+DNQ
Sbjct: 230 SKQKLDELLKQWSEWHAQQGSLSCDDKDTENLESGEETFFPALCVGTKKTSAVTFWMDNQ 289

Query: 68  TRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSL 127
            +++Q +NF+P D +  PLYDRG+ LGLTS + SSN+EGG +IIDDASRCFNCGSY+HSL
Sbjct: 290 -KSEQQQNFVPIDDNSVPLYDRGFTLGLTSANDSSNVEGGQKIIDDASRCFNCGSYNHSL 348

Query: 128 KECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLL 187
           K+C KPRD  AVNNAR  +K K+  NSASRN  RYYQNS GGKYD LRPG LDAETRQLL
Sbjct: 349 KDCRKPRDNAAVNNAR--NKYKKQHNSASRNSTRYYQNSRGGKYDDLRPGTLDAETRQLL 406

Query: 188 GLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPAS 247
           GL ELDPPPWL+RMRELGYPPGYLD ED+DQPSGITIYAD +  E QEDGEI E      
Sbjct: 407 GLKELDPPPWLNRMRELGYPPGYLDPEDEDQPSGITIYADEKTDE-QEDGEITEAEYRKP 465

Query: 248 KRKMTTEFPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNHHSESISRGR-YHEQRW 306
           ++K + EFPGINAPIPENADERLWA  PS+S  SR+RS+ RLNH+ E  +RG  +H+QRW
Sbjct: 466 RKKKSVEFPGINAPIPENADERLWAPEPSNSGLSRNRSNQRLNHYPEYDTRGNDHHQQRW 525

Query: 307 SRDYRDDGPPGVDPVSSYP---PRYGGYDY-YSSH--------SRSPTRGRSYSDRDR 352
           SRDYRDD PPGVD + S P   PRYGG+D+ Y S         SRSP  GR +SDR R
Sbjct: 526 SRDYRDDRPPGVDSIKSPPSFTPRYGGHDFSYDSQTPRGSFSTSRSPNLGRPHSDRGR 583

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447474|ref|XP_004141493.1| PREDICTED: uncharacterized protein LOC101212144 [Cucumis sativus]

 Score =  446 bits (1147), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 235/358 (65%), Positives = 272/358 (75%), Gaps = 19/358 (5%)

Query: 10  SKQKLEELLQQWSEWQAQFGSSSNDP--NEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQ 67
           SKQKL+ELL+QWSEW AQ GS S D    E +E GE+TFFPA+ VG  K  AV+FW+DNQ
Sbjct: 230 SKQKLDELLKQWSEWHAQQGSLSCDDKDTENLESGEETFFPALCVGTKKTSAVTFWMDNQ 289

Query: 68  TRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSL 127
            +++Q +NF+P D +  PLYDRG+ LGLTS + SSN EGG +IIDDASRCFNCGSY+HSL
Sbjct: 290 -KSEQQQNFVPIDDNSVPLYDRGFTLGLTSANDSSNAEGGQKIIDDASRCFNCGSYNHSL 348

Query: 128 KECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLL 187
           K+C KPRD  AVNNAR  +K K+  NSASRN  RYYQNS GGKYD LRPG LDAETRQLL
Sbjct: 349 KDCRKPRDNAAVNNAR--NKYKKQHNSASRNSTRYYQNSRGGKYDDLRPGTLDAETRQLL 406

Query: 188 GLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPAS 247
           GL ELDPPPWL+RMRELGYPPGYLD ED+DQPSGITIYAD +  E QEDGEI E      
Sbjct: 407 GLKELDPPPWLNRMRELGYPPGYLDPEDEDQPSGITIYADEKTDE-QEDGEITEAEYRKP 465

Query: 248 KRKMTTEFPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNHHSESISRGR-YHEQRW 306
           ++K + EFPGINAPIPENADERLWA  PS+S  SR+RS+ RLNH+ E  +RG  +H+QRW
Sbjct: 466 RKKKSVEFPGINAPIPENADERLWAPEPSNSGLSRNRSNQRLNHYPEYDTRGNDHHQQRW 525

Query: 307 SRDYRDDGPPGVDPVSSYP---PRYGGYDY-YSSH--------SRSPTRGRSYSDRDR 352
           SRDYRDD PPGVD + S P   PRYGG+D+ Y S         SRSP  GR +SDR R
Sbjct: 526 SRDYRDDRPPGVDSIKSPPSFTPRYGGHDFSYDSQTPRGSFSTSRSPNLGRPHSDRGR 583

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356573637|ref|XP_003554964.1| PREDICTED: uncharacterized protein LOC100805423 [Glycine max]

 Score =  442 bits (1138), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 245/415 (59%), Positives = 293/415 (70%), Gaps = 33/415 (7%)

Query: 9   ASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQT 68
           AS+QKL+ELLQ+WS W A+  SSS+D +E +E GE+TFFPA+ VG  K  AVSFW++NQT
Sbjct: 245 ASRQKLQELLQKWSAWHAKHVSSSSDASEVLESGEETFFPALHVGLEKTSAVSFWMENQT 304

Query: 69  RNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLK 128
           RN +NK+FIP   +  PLYDRGYALGLTS DGSSN++GGLEIID A+RCFNCGSY+HSL+
Sbjct: 305 RNDKNKDFIPLADNTVPLYDRGYALGLTSADGSSNVDGGLEIIDAAARCFNCGSYNHSLR 364

Query: 129 ECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLG 188
           ECP+PRD  AVNNAR + KS+RNQNS+SR+P RYYQNS  GKYDGLRPG+LD  TR+LLG
Sbjct: 365 ECPRPRDNIAVNNARDKLKSRRNQNSSSRHPTRYYQNSPAGKYDGLRPGSLDDATRKLLG 424

Query: 189 LGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASK 248
           L ELDPPPWL+RMRELGYPPGYLD +++DQPSGITI+ D EI + QEDGEI+E      K
Sbjct: 425 LRELDPPPWLNRMRELGYPPGYLDVDNEDQPSGITIFTDSEIAD-QEDGEIMEANASKPK 483

Query: 249 RKMTTEFPGINAPIPENADERLWAAR--PSSSDSSRDRS--HHRLNHHSESISRGRYHEQ 304
           RK T +FPGINAPIPE ADERLW  R  PSSSD SR+ S   HR N+ ++  SRG + E 
Sbjct: 484 RKKTVKFPGINAPIPEKADERLWGTRAGPSSSDISRNLSLPQHRSNYSTDYGSRGYHREH 543

Query: 305 RWSRDYRDDGPPGVDP-----VSSYPPRYGGYDYYSSHSRSPTRGRSYSDRDRDDYASHG 359
           R   D RD+GPPG DP     + S+ PR+GG+D   S  RSP+  RS SDR R       
Sbjct: 544 RLG-DLRDEGPPG-DPGHSSFMFSFHPRFGGHD---SALRSPSMARSQSDRSRSPMHDEE 598

Query: 360 SYSSPY---------SNRHTSPPDYDLDRYRD--------DYSREYLSRSMDEYD 397
           S S P+         S RH SP D D  R           D  R + SR MD +D
Sbjct: 599 S-SMPFSFHSLHYSSSERHFSPLDRDSGRLGSWTSESMYYDRDRVFSSRFMDRFD 652

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|298204384|emb|CBI16864.3| unnamed protein product [Vitis vinifera]

 Score =  419 bits (1076), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 220/350 (62%), Positives = 251/350 (71%), Gaps = 40/350 (11%)

Query: 10   SKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTR 69
            SK+KLEELLQQWSEW A++ SSS+DP   ++ GE+T+FPA+ VG  K  AVSFW+DNQTR
Sbjct: 750  SKRKLEELLQQWSEWHAKYVSSSHDPKGQLDSGEKTYFPALHVGLNKSSAVSFWVDNQTR 809

Query: 70   NQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKE 129
             QQ+K FI  D    PLYDRG+ALGL S DG S  EG LEIID ASRCFNCGSY+HS+KE
Sbjct: 810  KQQDKEFISLDGDSVPLYDRGFALGLVSEDGQSKPEGALEIID-ASRCFNCGSYNHSMKE 868

Query: 130  CPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGL 189
            CPKPRD  AVNNARKQHKS+RNQN  SRNP RYYQNS GG+YDGLRPGAL  ETR+LLGL
Sbjct: 869  CPKPRDNVAVNNARKQHKSRRNQNPGSRNPTRYYQNSPGGRYDGLRPGALGVETRELLGL 928

Query: 190  GELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASKR 249
            GELDPPPWL+RMRE+GYPPGYLD E+++QPSGITIYAD E+K+ QEDGEI+ET     +R
Sbjct: 929  GELDPPPWLNRMREMGYPPGYLDPEEEEQPSGITIYADEEVKDEQEDGEILETEYLEPQR 988

Query: 250  KMTTEFPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNHHSESISRGRYHEQRWSRD 309
            KM+ EFPGINAPIP+NADER WAA          R H RLNH  E  SR   HEQ     
Sbjct: 989  KMSVEFPGINAPIPKNADERRWAA--------GSRPHRRLNHSYEPSSRRNSHEQ----- 1035

Query: 310  YRDDGPPGVDPVSSYPPRYGGYD-YYSSHS--------RSPTRGRSYSDR 350
                             R+GG D  Y+S+S        RSP  GRS SDR
Sbjct: 1036 -----------------RHGGIDSSYTSYSTRGNIPRPRSPNFGRSLSDR 1068

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127396|ref|XP_002329267.1| predicted protein [Populus trichocarpa] gi|222870721|gb|EEF07852.1| predicted protein [Populus trichocarpa]

 Score =  403 bits (1036), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 190/263 (72%), Positives = 222/263 (84%), Gaps = 1/263 (0%)

Query: 9   ASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQT 68
           + KQKLEELLQQWSEW AQ  +SS+D NE ++ GE T+FPA+RVG  K  AVSFWI+NQ 
Sbjct: 27  SGKQKLEELLQQWSEWHAQ-QNSSHDSNEMLQSGEDTYFPALRVGMEKSSAVSFWIENQA 85

Query: 69  RNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLK 128
           R QQ+ + I   S+  PLYDRGY LGLTS DG  N+EGGLEI+D A+RCFNCG+Y+HSLK
Sbjct: 86  RKQQDNDLILQHSNFVPLYDRGYVLGLTSADGPINVEGGLEIVDAAARCFNCGAYNHSLK 145

Query: 129 ECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLG 188
           ECPKPRD  AVNNARKQHK KRNQNS+SRNP RYYQ+S+GGKYDGL+PG+LD ETRQLLG
Sbjct: 146 ECPKPRDNAAVNNARKQHKFKRNQNSSSRNPTRYYQSSSGGKYDGLKPGSLDTETRQLLG 205

Query: 189 LGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASK 248
           LGELDPPPWL+RMRELGYPPGYLD +D+DQPSGITI+ DG+++E QEDGEI+ET  P   
Sbjct: 206 LGELDPPPWLNRMRELGYPPGYLDPDDEDQPSGITIFDDGDVEEEQEDGEIMETDHPEPP 265

Query: 249 RKMTTEFPGINAPIPENADERLW 271
           RKM+ EFPGINAPIPENA++R W
Sbjct: 266 RKMSVEFPGINAPIPENANQRFW 288

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358346605|ref|XP_003637357.1| Zinc finger CCHC domain-containing protein [Medicago truncatula] gi|355503292|gb|AES84495.1| Zinc finger CCHC domain-containing protein [Medicago truncatula]

 Score =  395 bits (1014), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 214/330 (64%), Positives = 253/330 (76%), Gaps = 15/330 (4%)

Query: 9   ASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQT 68
           ASK KL+ELLQQWS+W A+  SSSNDP+E +E GE+TFFPAI VG     +VSFW++NQ+
Sbjct: 126 ASKNKLQELLQQWSQWHAKNVSSSNDPSEVLESGEETFFPAICVGHESKSSVSFWMENQS 185

Query: 69  RNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLK 128
            N +NK+  P D +  PLYDRGYALGLTS DGS+N + GL+IID  SRCFNCGSYSH+L+
Sbjct: 186 MNDRNKDVSPIDGNSVPLYDRGYALGLTSADGSNNADDGLKIIDAPSRCFNCGSYSHALR 245

Query: 129 ECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLG 188
           ECP+PRD  AVNNARKQ KS+RNQ+S+SRNP RYYQ+S+ GKY GLRPGALD  TRQLLG
Sbjct: 246 ECPRPRDNVAVNNARKQLKSQRNQSSSSRNPTRYYQDSSAGKYAGLRPGALDDATRQLLG 305

Query: 189 LGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASK 248
           LGELDPPPWL+RMRELGYPPGYLD +++DQPSGITI+ D ++ E QEDGEII       K
Sbjct: 306 LGELDPPPWLNRMRELGYPPGYLDEDEEDQPSGITIFTDKDMAE-QEDGEIIGADSSKPK 364

Query: 249 RKMTTEFPGINAPIPENADERLWAAR----PSSSDSSRDRSHHRLNHHSESISRGRYHEQ 304
           RKM+ EFPG+NAPIPENADERLWAAR    P + D SR+ S  R    S   SRG  H+Q
Sbjct: 365 RKMSVEFPGLNAPIPENADERLWAARAVVSPIAIDISRNWSQQR---SSSFGSRGHQHDQ 421

Query: 305 RWSRDYRDDGPPGVDPVS-----SYPPRYG 329
           R   D RDDGPPG DP+      S+ PR+G
Sbjct: 422 RIG-DLRDDGPPG-DPMHNSSHFSFQPRFG 449

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	406
TAIR|locus:2159818	532	AT5G38600 [Arabidopsis thalian	0.778	0.593	0.590	5.2e-97
TAIR|locus:2809302	405	AT1G67210 [Arabidopsis thalian	0.640	0.641	0.615	3.4e-90
UNIPROTKB|E2QXB5	709	ZCCHC8 "Uncharacterized protei	0.396	0.227	0.335	1e-19
UNIPROTKB|Q5F3D1	613	ZCCHC8 "Zinc finger CCHC domai	0.379	0.251	0.312	1.8e-19
MGI|MGI:1917900	709	Zcchc8 "zinc finger, CCHC doma	0.374	0.214	0.320	3.2e-19
RGD|1309774	695	Zcchc8 "zinc finger, CCHC doma	0.374	0.218	0.314	4.2e-19
UNIPROTKB|F1MM78	710	ZCCHC8 "Uncharacterized protei	0.364	0.208	0.322	2.3e-18
UNIPROTKB|F1NEG3	684	F1NEG3 "Uncharacterized protei	0.379	0.225	0.314	3.9e-18
UNIPROTKB|Q6NZY4	707	ZCCHC8 "Zinc finger CCHC domai	0.396	0.227	0.329	4.2e-18
ZFIN|ZDB-GENE-060526-6	694	zcchc8 "zinc finger, CCHC doma	0.337	0.197	0.355	2.5e-17

TAIR|locus:2159818 AT5G38600 [Arabidopsis thaliana (taxid:3702)]

 Score = 964 (344.4 bits), Expect = 5.2e-97, P = 5.2e-97
 Identities = 206/349 (59%), Positives = 240/349 (68%)

Query:     9 ASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQT 68
             ASKQKLE LLQ+WSEW+A+  S + D  +  E GE+T FPAIRVG  K  +VSFWIDNQT
Sbjct:   134 ASKQKLESLLQKWSEWEAENTSLAQDQEQLFESGEETCFPAIRVGLQKTSSVSFWIDNQT 193

Query:    69 RNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDD-ASRCFNCGSYSHSL 127
              ++  ++F+  +S  TPLYDR +A+GL S DGS N+EGGLEIIDD   RCFNCG YSHSL
Sbjct:   194 GHKPLEDFVLVESSTTPLYDRKFAIGLNSADGSRNVEGGLEIIDDDPPRCFNCGGYSHSL 253

Query:   128 KECPKPRDKDAVNNARKQHKSKRNQNSAS-RNPMRYYQNSAGGKYDGLRPGALDAETRQL 186
             +ECP+P D+ AVN+ARK  KSKRNQNS+  R P RYYQ +  GKYDGL+PG LDAETRQL
Sbjct:   254 RECPRPFDRSAVNSARKLQKSKRNQNSSGPRLPSRYYQKTQTGKYDGLKPGTLDAETRQL 313

Query:   187 LGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADG-EIKEG--QEDGEIIETG 243
             L LGELDPPPWL+RMRE+GYPPGYL  EDD   SGITI+ +  E +E    EDGEI+E  
Sbjct:   314 LNLGELDPPPWLNRMREIGYPPGYLAPEDDHL-SGITIFGEEVETREEIESEDGEILEKA 372

Query:   244 R--PASKRKMTTEFPGINAPIPENADERLWAAXXXXXXXXXXXXXXXXXXXXESISRGRY 301
                P  + K T EFPGINAP PENADE LW A                     S   GR+
Sbjct:   373 NHPPEPQMKKTVEFPGINAPFPENADEWLWEAAPSHR---------------NSSRSGRW 417

Query:   302 HEQRWSR--DYRDDGPPGVDPVSSYPPRYGG-YDY------YSSHSRSP 341
              +Q+ SR  DYRDDGP GV+P SSYPPRYG  YDY      Y S SRSP
Sbjct:   418 QQQKTSRGHDYRDDGPLGVEP-SSYPPRYGSRYDYGYGSNEYGSRSRSP 465

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:2809302 AT1G67210 [Arabidopsis thaliana (taxid:3702)]

 Score = 867 (310.3 bits), Expect = 3.4e-90, Sum P(2) = 3.4e-90
 Identities = 165/268 (61%), Positives = 201/268 (75%)

Query:    10 SKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTR 69
             SKQKLE LLQQWSEW+A+  S S D  + +E G++T+FPA+RVG  K  +VSFW D QT 
Sbjct:    93 SKQKLESLLQQWSEWEAEQNSLSEDQEQVLEAGDETYFPALRVGLQKTSSVSFWFDYQTG 152

Query:    70 NQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKE 129
             +  +K  +P +S  TPLY+RG+ +GL SG  S+N+EGGLEIIDD  RCFNCG+YSHS++E
Sbjct:   153 HSSSKKSVPVESSTTPLYNRGFTIGLDSG--SNNVEGGLEIIDDPPRCFNCGAYSHSIRE 210

Query:   130 CPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGL 189
             CP+P D+ AV+NAR+QHK KRNQ   SR P RYYQ+   GKYDGL+PG+LDAETR+LLGL
Sbjct:   211 CPRPFDRSAVSNARRQHKRKRNQTPGSRLPSRYYQSLQRGKYDGLKPGSLDAETRKLLGL 270

Query:   190 GELDPPPWLHRMRELGYPPGYLD-SEDDDQPSGITIYADGEIKEGQE----DGEIIETGR 244
              ELDPPPWL+RMRE+GYPPGY    EDDD  S ITI+ + E KE +E    +GEI+E   
Sbjct:   271 KELDPPPWLNRMREIGYPPGYFAVEEDDDDHSRITIFGEEETKEEEEVKTEEGEILEKAS 330

Query:   245 PASKRK-MTTEFPGINAPIPENADERLW 271
             P   RK MT  FPGINAPIPENAD  LW
Sbjct:   331 PQEPRKIMTVGFPGINAPIPENADSWLW 358

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

UNIPROTKB|E2QXB5 ZCCHC8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 253 (94.1 bits), Expect = 1.0e-19, P = 1.0e-19
 Identities = 60/179 (33%), Positives = 94/179 (52%)

Query:   103 NLEGGLEIIDDASR----CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRN 158
             +LEG  EI   A R    CFNCGS  H +K+CP PR+   ++  RK++    ++ ++   
Sbjct:   212 SLEGQ-EIQVKAKRPKPHCFNCGSEEHQMKDCPMPRNAARISEKRKEYMDACSETNSQNF 270

Query:   159 PMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQ 218
               RY+      ++   +PG +  E +  LGL +   PP+++RMR+LGYPPG+L  E + +
Sbjct:   271 QQRYHAEEVEERFGRFKPGVISEELQDALGLTDKSLPPFIYRMRQLGYPPGWL-KEAELE 329

Query:   219 PSGITIYADGEIKEGQEDGEIIETGRPASKRKMTTE------FPGINAPIPENADERLW 271
              SG+ +Y DG  K+G  DGE  E G     + +T +      +PG N   P    +  W
Sbjct:   330 NSGLALY-DG--KDGA-DGEA-EAGETQQNKSVTYDLSKLVNYPGFNISTPRGIPDE-W 382

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q5F3D1 ZCCHC8 "Zinc finger CCHC domain-containing protein 8" [Gallus gallus (taxid:9031)]

 Score = 246 (91.7 bits), Expect = 1.8e-19, Sum P(2) = 1.8e-19
 Identities = 49/157 (31%), Positives = 77/157 (49%)

Query:   115 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGL 174
             S CFNCGS  H +K+CPKPR+   ++  RK+      + S      RY+      ++   
Sbjct:   126 SHCFNCGSEEHQIKDCPKPRNAARISEKRKEFMEAYGEASNQNFQQRYHAEEVEERFGKF 185

Query:   175 RPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQ 234
             +PG +  E +  LG+     PP+++RMR+LGYPPG+L  E + + SG+ +Y DG+     
Sbjct:   186 KPGVISGELQDALGVTAKSLPPFIYRMRQLGYPPGWL-KEAEMEHSGLALY-DGKDDNET 243

Query:   235 EDGEIIETGRPASKRKMTTEFPGINAPIPENADERLW 271
             ED   ++             +PG N   P    +  W
Sbjct:   244 EDEGYLQPKHVTYDVSKLINYPGFNISTPSGIPDE-W 279

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

MGI|MGI:1917900 Zcchc8 "zinc finger, CCHC domain containing 8" [Mus musculus (taxid:10090)]

 Score = 250 (93.1 bits), Expect = 3.2e-19, P = 3.2e-19
 Identities = 50/156 (32%), Positives = 80/156 (51%)

Query:   117 CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRP 176
             CFNCGS  H +KECP PR+   ++  RK++     + S      RY+      ++   +P
Sbjct:   232 CFNCGSEEHQMKECPMPRNAARISEKRKEYMDACGEASGQSFQQRYHAEEVEERFGRFKP 291

Query:   177 GALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQ-E 235
             G +  E +  LG+ +   PP+++RMR+LGYPPG+L  E + + SG+ +Y   +  +G+ E
Sbjct:   292 GVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWL-KEAELENSGLALYDGNDDADGETE 350

Query:   236 DGEIIETGRPASKRKMTTEFPGINAPIPENADERLW 271
              GEI          K+   +PG N   P    +  W
Sbjct:   351 TGEIQNKNVTYDLSKLVN-YPGFNISTPRGIPDE-W 384

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

RGD|1309774 Zcchc8 "zinc finger, CCHC domain containing 8" [Rattus norvegicus (taxid:10116)]

 Score = 249 (92.7 bits), Expect = 4.2e-19, P = 4.2e-19
 Identities = 49/156 (31%), Positives = 81/156 (51%)

Query:   117 CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRP 176
             CFNCGS  H +KECP PR+   ++  RK++     + ++     RY+      ++   +P
Sbjct:   231 CFNCGSEEHQMKECPMPRNAARISEKRKEYMDACGEANSQSFQQRYHAEEVEERFGRFKP 290

Query:   177 GALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQ-E 235
             G +  E +  LG+ +   PP+++RMR+LGYPPG+L  E + + SG+ +Y   +  +G+ E
Sbjct:   291 GVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWL-KEAELETSGLALYDGNDDADGETE 349

Query:   236 DGEIIETGRPASKRKMTTEFPGINAPIPENADERLW 271
              GEI          K+   +PG N   P    +  W
Sbjct:   350 TGEIQNKNVTYDLSKLVN-YPGFNISTPRGIPDE-W 383

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|F1MM78 ZCCHC8 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 244 (91.0 bits), Expect = 2.3e-18, P = 2.3e-18
 Identities = 52/161 (32%), Positives = 84/161 (52%)

Query:   117 CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRP 176
             CFNCGS  H +K+CP PR+   ++  RK++     + +      RY+      ++   +P
Sbjct:   231 CFNCGSEEHQMKDCPMPRNAARISEKRKEYMDACGETNNQNFQQRYHAEEVEERFGRFKP 290

Query:   177 GALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQED 236
             G +  E +  LG+ +   PP+++RMR+LGYPPG+L  E + + SG+ +Y DG  K+G  D
Sbjct:   291 GVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWL-KEAELENSGLALY-DG--KDGA-D 345

Query:   237 GEIIETGRPASKRKMTTE------FPGINAPIPENADERLW 271
             GE  E G     + +T +      +PG N   P    +  W
Sbjct:   346 GET-EAGEVQQNKSVTYDLSKLVNYPGFNISTPRGIPDE-W 384

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1NEG3 F1NEG3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 242 (90.2 bits), Expect = 3.9e-18, P = 3.9e-18
 Identities = 50/159 (31%), Positives = 80/159 (50%)

Query:   115 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGL 174
             S CFNCGS  H +K+CPKPR+   ++  RK+      + S      RY+      ++   
Sbjct:   222 SHCFNCGSEEHQIKDCPKPRNAARISEKRKEFMEAYGEASNQNFQQRYHAEEVEERFGKF 281

Query:   175 RPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGE-IKEG 233
             +PG +  E +  LG+     PP+++RMR+LGYPPG+L  E + + SG+ +Y DG+ I + 
Sbjct:   282 KPGVISGELQDALGVTAKSLPPFIYRMRQLGYPPGWL-KEAEMEHSGLALY-DGKGIDDN 339

Query:   234 Q-EDGEIIETGRPASKRKMTTEFPGINAPIPENADERLW 271
             + ED   ++             +PG N   P    +  W
Sbjct:   340 ETEDEGYLQPKHVTYDVSKLINYPGFNISTPSGIPDE-W 377

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

UNIPROTKB|Q6NZY4 ZCCHC8 "Zinc finger CCHC domain-containing protein 8" [Homo sapiens (taxid:9606)]

 Score = 242 (90.2 bits), Expect = 4.2e-18, P = 4.2e-18
 Identities = 59/179 (32%), Positives = 92/179 (51%)

Query:   103 NLEGGLEIIDDASR----CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRN 158
             +LEG  EI   A R    CFNCGS  H +K+CP PR+   ++  RK++     + +    
Sbjct:   212 SLEGQ-EIQVKAKRPKPHCFNCGSEEHQMKDCPMPRNAARISEKRKEYMDACGEANNQNF 270

Query:   159 PMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQ 218
               RY+      ++   +PG +  E +  LG+ +   PP+++RMR+LGYPPG+L  E + +
Sbjct:   271 QQRYHAEEVEERFGRFKPGVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWL-KEAELE 329

Query:   219 PSGITIYADGEIKEGQEDGEIIETGRPASKRKMTTE------FPGINAPIPENADERLW 271
              SG+ +Y DG  K+G  DGE  E G     + +T +      +PG N   P    +  W
Sbjct:   330 NSGLALY-DG--KDGT-DGET-EVGEIQQNKSVTYDLSKLVNYPGFNISTPRGIPDE-W 382

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

ZFIN|ZDB-GENE-060526-6 zcchc8 "zinc finger, CCHC domain containing 8" [Danio rerio (taxid:7955)]

 Score = 236 (88.1 bits), Expect = 2.5e-17, P = 2.5e-17
 Identities = 53/149 (35%), Positives = 80/149 (53%)

Query:   117 CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRP 176
             CFNC S  H L++CPKP+D   +N  RK+     +QN+  R+  RY+      ++   +P
Sbjct:   221 CFNCCSEDHQLRDCPKPKDMARINEKRKEF----SQNN--RSNQRYHAEEVEERFAKYKP 274

Query:   177 GALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQED 236
             G +  +    LG+     PP+++RMRELGYPPG+L  E + + SG+ +Y DG   +G E+
Sbjct:   275 GIMSQDLLDALGMTTNTLPPFIYRMRELGYPPGWL-KEAELENSGLMLY-DGS-NDGDEN 331

Query:   237 GEIIETGRPASKRKMTTEFPGINAPIPEN 265
                 +     SK     +FPG N   P N
Sbjct:   332 NHSQKISYDVSK---LVDFPGFNVNAPPN 357

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

---

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	Length	Definition	E-value
Query	406
pfam04046	48	pfam04046, PSP, PSP	8e-14
smart00581	54	smart00581, PSP, proline-rich domain in spliceosom	3e-11
COG5182	429	COG5182, CUS1, Splicing factor 3b, subunit 2 [RNA	2e-05
pfam14392	49	pfam14392, zf-CCHC_4, Zinc knuckle	9e-04

>gnl|CDD|202864 pfam04046, PSP, PSP

 Score = 64.9 bits (159), Expect = 8e-14
 Identities = 23/36 (63%), Positives = 27/36 (75%)

Query: 175 RPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGY 210
           +PG L  E R+ LG+ E DPPPWL+RMR LGYPP Y
Sbjct: 1   KPGVLSDELREALGMPEGDPPPWLYRMRRLGYPPSY 36

Proline rich domain found in numerous spliceosome associated proteins. Length = 48

>gnl|CDD|128850 smart00581, PSP, proline-rich domain in spliceosome associated proteins

 Score = 57.7 bits (140), Expect = 3e-11
 Identities = 23/50 (46%), Positives = 30/50 (60%)

Query: 175 RPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITI 224
           +PG +  E R+ LGL    PPPWL+RMR LGYPPGY   +     + I +
Sbjct: 5   KPGRISDELREALGLPPGQPPPWLYRMRRLGYPPGYPRLKIPGLNAPIPL 54

Length = 54

>gnl|CDD|227509 COG5182, CUS1, Splicing factor 3b, subunit 2 [RNA processing and modification]

 Score = 46.1 bits (109), Expect = 2e-05
 Identities = 20/38 (52%), Positives = 25/38 (65%)

Query: 175 RPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLD 212
           RPGA+ AE R+ LG+    PPPWL  M++ G PP Y D
Sbjct: 279 RPGAISAELREALGIDSGTPPPWLFNMQKHGMPPSYPD 316

Length = 429

>gnl|CDD|222730 pfam14392, zf-CCHC_4, Zinc knuckle

 Score = 36.5 bits (85), Expect = 9e-04
 Identities = 11/17 (64%), Positives = 12/17 (70%)

Query: 116 RCFNCGSYSHSLKECPK 132
            CF+CG   HS KECPK
Sbjct: 33  FCFHCGRLGHSDKECPK 49

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. This particular family is found in plant proteins. Length = 49

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	406
KOG2673	485	consensus Uncharacterized conserved protein, conta	100.0
KOG2330	500	consensus Splicing factor 3b, subunit 2 [RNA proce	99.9
smart00581	54	PSP proline-rich domain in spliceosome associated	99.89
PF04046	48	PSP: PSP; InterPro: IPR006568 PSP is a proline-ric	99.84
COG5182	429	CUS1 Splicing factor 3b, subunit 2 [RNA processing	99.78
KOG2673	485	consensus Uncharacterized conserved protein, conta	98.59
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	97.35
PF14392	49	zf-CCHC_4: Zinc knuckle	91.83
smart00343	26	ZnF_C2HC zinc finger.	90.69
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	90.41
PF13696	32	zf-CCHC_2: Zinc knuckle	87.4
PTZ00368	148	universal minicircle sequence binding protein (UMS	86.26
PTZ00368	148	universal minicircle sequence binding protein (UMS	86.03

>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]

Probab=100.00  E-value=1.1e-46  Score=381.08  Aligned_cols=286  Identities=32%  Similarity=0.535  Sum_probs=225.0

Q ss_pred             CCccccccccccccceeccCCCCCceeEEEecccccccCCCCCCCCCCCCCccccccccccccCCCCCCcCCCcccccCC
Q 015479           35 PNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDA  114 (406)
Q Consensus        35 ~~~~~e~G~~t~~Pal~vg~~~~~a~~F~iD~~~~~~~n~~~~~~d~~~VPlYdr~~~~~L~s~Dg~s~~e~~~Ei~~~~  114 (406)
                      ..+++++++.+|+| +++++.+...++||++++....--+++.+.+...    ||.++.+|.+.+++.+++++..|.. .
T Consensus        55 qqd~l~~te~a~~~-fr~~~qe~~t~s~wl~~~~~ek~gedl~~~e~~t----dr~~a~~l~sq~~s~tvek~~~v~~-~  128 (485)
T KOG2673|consen   55 QQDLLGVTEKAFPP-FRYRMQELGTPSFWLKNAELEKSGEDLYLGEDST----DRETAVGLISQNKSVTVEKSKLVNK-C  128 (485)
T ss_pred             HHHHhhcccccccc-hhhhHHhhcCchhhhhhcccccChhhhccccccc----cccceecccccccchhhhhhhhhcc-C
Confidence            46788888888888 8999999999999999999887767777666553    9999999999999999998877644 4


Q ss_pred             CccccCCCCCCCCCCCCCccCHHHHHHHHHHHHHhhccCCCCCCCceeeecccCCccCCCCCCcCCHHHHHHhCCCCCCC
Q 015479          115 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDP  194 (406)
Q Consensus       115 ~~CFNCG~~~HsLrdCP~Prd~a~In~~Rk~f~~~r~q~~~sr~GdrYye~k~e~k~~~~kPG~LS~eLReALGm~~~dp  194 (406)
                      -.|||||++.|+|+|||+|+|+++|+++||+++..++|        |||.....+++++||||+||.+||.|||+.+++|
T Consensus       129 ~~CFNC~g~~hsLrdC~rp~d~s~I~r~rkek~~~rnq--------ry~~~teq~re~h~KPG~lS~~~R~al~l~~~d~  200 (485)
T KOG2673|consen  129 DPCFNCGGTPHSLRDCPRPFDFSRIQRARKEKMVFRNQ--------RYYQDTEQGREDHFKPGVLSGNTRSALGLSPGDP  200 (485)
T ss_pred             ccccccCCCCCccccCCCccccHHHHHHHHhhccccce--------eeeeecchhhhcccCCcccchhHHHhhcCCCCCc
Confidence            45999999999999999999999999999999887774        8998876669999999999999999999999999


Q ss_pred             hHHHHHHHhcCCCCCCCCCCCCCCCCCceeecCCCccCCCCCcchhccCCCCCCCeeeeecCCCCCC-CCCCCchhcccc
Q 015479          195 PPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEGQEDGEIIETGRPASKRKMTTEFPGINAP-IPENADERLWAA  273 (406)
Q Consensus       195 PPWL~rMr~~GyPPgY~~~a~~~q~SGl~if~Dg~~~~~~EDgEi~e~~~~~~~~kk~v~fPGFNaP-iP~gad~~~W~~  273 (406)
                      |+|+||||++||||||+.++ ..+.+||+||+.... .++|+  +.....++++.+|+|.|||||.+ .|++..++.|..
T Consensus       201 P~~~yRMR~lGYPPg~L~~s-~~e~s~i~if~eet~-~~dee--~ese~PP~~~~~K~~~f~gfn~~~~p~~~~e~~ke~  276 (485)
T KOG2673|consen  201 PEWKYRMRRLGYPPGYLRKS-DMEVSGIKIFSEETF-QFDEE--LESETPPEPQGTKPVVFPGFNPKGTPPNDREDSKEA  276 (485)
T ss_pred             hHHHHHHhhccCCchhhhhh-hcccccceeeccccc-ccCcc--cCCCCCCCCCCCCCcccCCCCCCCCCCCChhhcccc
Confidence            99999999999999999987 568999999972221 22232  32334678899999999999999 999999888876


Q ss_pred             CCCCCCcccccccccccCCCCccccccchhhccccccccCCCCCCCCCCCCCCCccc-ccc-CCCC-CCCCCCCCCCCCC
Q 015479          274 RPSSSDSSRDRSHHRLNHHSESISRGRYHEQRWSRDYRDDGPPGVDPVSSYPPRYGG-YDY-YSSH-SRSPTRGRSYSDR  350 (406)
Q Consensus       274 ~P~~~d~~~~~~~~~~~~~~e~~~r~~~~~~~~~~d~~d~g~~g~~~~ss~~pr~~~-~d~-y~~~-~~~p~~~rs~sdr  350 (406)
                      +   .++|+..-+..             .......++++|+|-|++...++|+++|. +|. |+.- .+|-...++++-+
T Consensus       277 ~---r~~s~s~~q~~-------------l~~~~l~~k~~dl~~~~e~s~~~~~~~~t~~D~~~~~~~~~s~~~~~sl~~p  340 (485)
T KOG2673|consen  277 P---RDASCSVDQDA-------------LTLSRLEKKQRDLPAGLEQSESAPSDSGTEVDDPLTENEVASEPRPNSLDLP  340 (485)
T ss_pred             c---chhhhhhhHHH-------------hhhhHHHHHhhhcccccccccCCCcccCCcccccccccccccccCCcccCCC
Confidence            2   34443211111             11111237778999999999999999998 555 3331 1122222556655


Q ss_pred             CCCc
Q 015479          351 DRDD  354 (406)
Q Consensus       351 ~~~~  354 (406)
                      +-++
T Consensus       341 ~~ed  344 (485)
T KOG2673|consen  341 VPED  344 (485)
T ss_pred             CCCC
Confidence            5544

>KOG2330 consensus Splicing factor 3b, subunit 2 [RNA processing and modification]

Probab=99.90  E-value=2.4e-24  Score=218.06  Aligned_cols=107  Identities=32%  Similarity=0.551  Sum_probs=90.7

Q ss_pred             CCCCCceeeecc-cCCccCCCCCCcCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCCCCCCCCCCCceeecCCCccCC
Q 015479          155 ASRNPMRYYQNS-AGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEG  233 (406)
Q Consensus       155 ~sr~GdrYye~k-~e~k~~~~kPG~LS~eLReALGm~~~dpPPWL~rMr~~GyPPgY~~~a~~~q~SGl~if~Dg~~~~~  233 (406)
                      -+.+|+.||+++ .+..+++.+||.||+|||.||||+.+.|||||++||++|+|||||+                     
T Consensus       251 lt~~Ge~yyegke~e~~~k~k~PG~iS~eLr~aLgmp~g~pPPWl~aMqryGpPpsYPd---------------------  309 (500)
T KOG2330|consen  251 LTKFGELYYEGKELEAMVKEKKPGDISDELRIALGMPVGTPPPWLIAMQRYGPPPSYPD---------------------  309 (500)
T ss_pred             eeecceeeecchhHHHHHhhcCccchhHHHHHHhCCCCCCCChHHHHhhhcCCCCCCCc---------------------
Confidence            468999999998 5677899999999999999999999999999999999999999997                     


Q ss_pred             CCCcchhccCCCCCCCeeeeecCCCCCCCCCCCch----hccc-----cCCCCCCcccccccccccCCCCcc-ccccc
Q 015479          234 QEDGEIIETGRPASKRKMTTEFPGINAPIPENADE----RLWA-----ARPSSSDSSRDRSHHRLNHHSESI-SRGRY  301 (406)
Q Consensus       234 ~EDgEi~e~~~~~~~~kk~v~fPGFNaPiP~gad~----~~W~-----~~P~~~d~~~~~~~~~~~~~~e~~-~r~~~  301 (406)
                                         ++|||+|+|||+|+.+    ++||     ..|.++||||.....-.+...+++ .|.++
T Consensus       310 -------------------lkIpGLNapIPeg~s~Gyh~gGWGpVDe~g~PLygDVfG~~~p~~~~~t~es~~~rn~w  368 (500)
T KOG2330|consen  310 -------------------LKIPGLNAPIPEGCSFGYHAGGWGPVDEFGKPLYGDVFGLNIPEHHNGTKESEIERNHW  368 (500)
T ss_pred             -------------------ccCCCCCCCCCcccccccccCCCccccccCCccchhccccccccccccccccccccccc
Confidence                               7899999999999987    5888     247788999987754444443333 35554

>smart00581 PSP proline-rich domain in spliceosome associated proteins

Probab=99.89  E-value=9.2e-24  Score=161.47  Aligned_cols=42  Identities=52%  Similarity=1.112  Sum_probs=40.8

Q ss_pred             cCCCCCCcCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCC
Q 015479          171 YDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLD  212 (406)
Q Consensus       171 ~~~~kPG~LS~eLReALGm~~~dpPPWL~rMr~~GyPPgY~~  212 (406)
                      |++||||+||++||+||||.++++||||++||++|||||||+
T Consensus         1 ~~~~kPG~lS~~LR~ALG~~~~~pPPWl~~Mq~~G~PPsYp~   42 (54)
T smart00581        1 FKHFKPGRISDELREALGLPPGQPPPWLYRMRRLGYPPGYPR   42 (54)
T ss_pred             CCCccCCcCCHHHHHHcCCCCCCCChHHHHHHHHCCCCCCcc
Confidence            578999999999999999999999999999999999999997

>PF04046 PSP: PSP; InterPro: IPR006568 PSP is a proline-rich domain of unknown function found in spliceosome associated proteins

Probab=99.84  E-value=1.9e-21  Score=145.72  Aligned_cols=38  Identities=66%  Similarity=1.307  Sum_probs=37.1

Q ss_pred             CCCcCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCC
Q 015479          175 RPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLD  212 (406)
Q Consensus       175 kPG~LS~eLReALGm~~~dpPPWL~rMr~~GyPPgY~~  212 (406)
                      |||+||++||+||||.++++||||++||++||||||++
T Consensus         1 kPG~lS~~LR~ALg~~~~~~PPwl~~M~~~G~PP~y~~   38 (48)
T PF04046_consen    1 KPGKLSDELREALGMQENDPPPWLYRMRRLGYPPGYPD   38 (48)
T ss_pred             CCcccCHHHHHHcCCCCCCCChHHHHHHhcCCCCCCcc
Confidence            79999999999999999999999999999999999975

>COG5182 CUS1 Splicing factor 3b, subunit 2 [RNA processing and modification]

Probab=99.78  E-value=1.7e-19  Score=179.06  Aligned_cols=96  Identities=31%  Similarity=0.468  Sum_probs=76.5

Q ss_pred             CCCCCceeeecc-cCCccCCCCCCcCCHHHHHHhCCCCCCChHHHHHHHhcCCCCCCCCCCCCCCCCCceeecCCCccCC
Q 015479          155 ASRNPMRYYQNS-AGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGYPPGYLDSEDDDQPSGITIYADGEIKEG  233 (406)
Q Consensus       155 ~sr~GdrYye~k-~e~k~~~~kPG~LS~eLReALGm~~~dpPPWL~rMr~~GyPPgY~~~a~~~q~SGl~if~Dg~~~~~  233 (406)
                      -+.||+.||+++ .....++.+||.||+|||+||||.+++|||||.+||++|+|||||+                     
T Consensus       258 L~~fGe~y~e~~n~~~~vk~krPG~IS~eLrealgi~~g~pPPWlf~Mq~~G~PpsYPD---------------------  316 (429)
T COG5182         258 LSKFGEFYEEVDNDYRFVKKKRPGAISAELREALGIDSGTPPPWLFNMQKHGMPPSYPD---------------------  316 (429)
T ss_pred             cccccceeeccchHHHHHhccCCcchHHHHHHHhCCCCCCCChHHHhhhhcCCCCCCcc---------------------
Confidence            468999999998 4445689999999999999999999999999999999999999996                     


Q ss_pred             CCCcchhccCCCCCCCeeeeecCCCCCCCCCCCchhccccCCCCCCcccccccccccCCCCccccccc
Q 015479          234 QEDGEIIETGRPASKRKMTTEFPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNHHSESISRGRY  301 (406)
Q Consensus       234 ~EDgEi~e~~~~~~~~kk~v~fPGFNaPiP~gad~~~W~~~P~~~d~~~~~~~~~~~~~~e~~~r~~~  301 (406)
                                         ++|||+|           |+..|..+||||.+...-...+.+.+++.+.
T Consensus       317 -------------------lkIpGlN-----------W~~~pL~GdvyG~~~p~~h~~~~~~~~~~~~  354 (429)
T COG5182         317 -------------------LKIPGLN-----------WAPIPLEGDVYGYQPPGWHEPLFEVGPETAE  354 (429)
T ss_pred             -------------------ccCCCCC-----------CCCcccccccccccCCCcCCccCCcCcchhh
Confidence                               7899999           6666666666666553333334445555443

>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]

Probab=98.59  E-value=2.3e-08  Score=103.51  Aligned_cols=137  Identities=22%  Similarity=0.360  Sum_probs=101.9

Q ss_pred             CCCCCCccCHHHHHHHHHHHHHhhccCCCCCCCceeeecccCCccCCCCCCcCCHHHHHHhCCCCCCChHHHHHHHhcCC
Q 015479          127 LKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLHRMRELGY  206 (406)
Q Consensus       127 LrdCP~Prd~a~In~~Rk~f~~~r~q~~~sr~GdrYye~k~e~k~~~~kPG~LS~eLReALGm~~~dpPPWL~rMr~~Gy  206 (406)
                      +++||.|+| ++|+..|.+++.+-..-...-++.+++..........+.+|.|| ++.++|+-.+...+|++++||++|+
T Consensus         1 ~~~cp~~~n-~~i~~~~d~~~e~~~eis~q~~~e~~~d~~~d~~~~r~esg~i~-~qqd~l~~te~a~~~fr~~~qe~~t   78 (485)
T KOG2673|consen    1 MKDCPMPRN-ARISEKRDEYMEACGEISNQNFQERLHDELVDERRGRFESGVIS-EQQDLLGVTEKAFPPFRYRMQELGT   78 (485)
T ss_pred             CCcCCCccc-cccCcchhHHHHHhhhcCCcchhhhccchhhhhhhccccccccc-hHHHHhhcccccccchhhhHHhhcC
Confidence            579999999 99999999998764432333456788877777888999999999 8899999999999999999999999


Q ss_pred             CCCCCCCCCCCCCCCceeecCCC-ccCCCCCcchhccCCCCCCCeeeeecC--CCCC-CCCCCC
Q 015479          207 PPGYLDSEDDDQPSGITIYADGE-IKEGQEDGEIIETGRPASKRKMTTEFP--GINA-PIPENA  266 (406)
Q Consensus       207 PPgY~~~a~~~q~SGl~if~Dg~-~~~~~EDgEi~e~~~~~~~~kk~v~fP--GFNa-PiP~ga  266 (406)
                      |+.|++.+. .+.+|..||.-.. .+-..+.|.+..+.....+.++.|.++  =||. -.|.++
T Consensus        79 ~s~wl~~~~-~ek~gedl~~~e~~tdr~~a~~l~sq~~s~tvek~~~v~~~~~CFNC~g~~hsL  141 (485)
T KOG2673|consen   79 PSFWLKNAE-LEKSGEDLYLGEDSTDRETAVGLISQNKSVTVEKSKLVNKCDPCFNCGGTPHSL  141 (485)
T ss_pred             chhhhhhcc-cccChhhhccccccccccceecccccccchhhhhhhhhccCccccccCCCCCcc
Confidence            999998654 4578888884222 223455666655555555566666665  4554 455554

>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

Probab=97.35  E-value=0.0001  Score=45.36  Aligned_cols=18  Identities=50%  Similarity=1.315  Sum_probs=16.5

Q ss_pred             CccccCCCCCCCCCCCCC
Q 015479          115 SRCFNCGSYSHSLKECPK  132 (406)
Q Consensus       115 ~~CFNCG~~~HsLrdCP~  132 (406)
                      ..|||||+.+|..++||+
T Consensus         1 ~~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    1 RKCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             SBCTTTSCSSSCGCTSSS
T ss_pred             CcCcCCCCcCcccccCcc
Confidence            379999999999999995

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=91.83  E-value=0.063  Score=40.04  Aligned_cols=19  Identities=58%  Similarity=1.183  Sum_probs=17.5

Q ss_pred             CCccccCCCCCCCCCCCCC
Q 015479          114 ASRCFNCGSYSHSLKECPK  132 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~  132 (406)
                      ...||+||..+|..++||+
T Consensus        31 p~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   31 PRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             ChhhcCCCCcCcCHhHcCC
Confidence            4789999999999999985

>smart00343 ZnF_C2HC zinc finger

Probab=90.69  E-value=0.12  Score=33.57  Aligned_cols=18  Identities=44%  Similarity=1.309  Sum_probs=16.1

Q ss_pred             ccccCCCCCCCCCCCCCc
Q 015479          116 RCFNCGSYSHSLKECPKP  133 (406)
Q Consensus       116 ~CFNCG~~~HsLrdCP~P  133 (406)
                      .||+||..+|..++||..
T Consensus         1 ~C~~CG~~GH~~~~C~~~   18 (26)
T smart00343        1 KCYNCGKEGHIARDCPKX   18 (26)
T ss_pred             CCccCCCCCcchhhCCcc
Confidence            499999999999999944

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=90.41  E-value=0.16  Score=48.42  Aligned_cols=20  Identities=40%  Similarity=1.154  Sum_probs=18.2

Q ss_pred             cCCCccccCCCCCCCCCCCC
Q 015479          112 DDASRCFNCGSYSHSLKECP  131 (406)
Q Consensus       112 ~~~~~CFNCG~~~HsLrdCP  131 (406)
                      .....|||||+.+|..+|||
T Consensus        58 ~~~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          58 EENPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             ccccccchhcccCcccccCC
Confidence            34689999999999999999

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=87.40  E-value=0.25  Score=34.99  Aligned_cols=21  Identities=29%  Similarity=0.828  Sum_probs=18.5

Q ss_pred             CCCccccCCCCCCCCCCCCCc
Q 015479          113 DASRCFNCGSYSHSLKECPKP  133 (406)
Q Consensus       113 ~~~~CFNCG~~~HsLrdCP~P  133 (406)
                      ..-.|+-|+..+|-++|||.-
T Consensus         7 ~~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    7 PGYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCCEeecCCCCCccHhHCCCC
Confidence            346899999999999999983

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=86.26  E-value=0.59  Score=41.31  Aligned_cols=22  Identities=36%  Similarity=0.925  Sum_probs=17.4

Q ss_pred             CCccccCCCCCCCCCCCCCccC
Q 015479          114 ASRCFNCGSYSHSLKECPKPRD  135 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Prd  135 (406)
                      ...||||+..+|..++||.+++
T Consensus        27 ~~~C~~Cg~~GH~~~~Cp~~~~   48 (148)
T PTZ00368         27 ARPCYKCGEPGHLSRECPSAPG   48 (148)
T ss_pred             CccCccCCCCCcCcccCcCCCC
Confidence            5678888888888888888764

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=86.03  E-value=0.41  Score=42.32  Aligned_cols=20  Identities=35%  Similarity=1.022  Sum_probs=18.1

Q ss_pred             CccccCCCCCCCCCCCCCcc
Q 015479          115 SRCFNCGSYSHSLKECPKPR  134 (406)
Q Consensus       115 ~~CFNCG~~~HsLrdCP~Pr  134 (406)
                      +.||||+..+|..++||.+.
T Consensus         1 ~~C~~C~~~GH~~~~c~~~~   20 (148)
T PTZ00368          1 MVCYRCGGVGHQSRECPNSA   20 (148)
T ss_pred             CcCCCCCCCCcCcccCcCCC
Confidence            47999999999999999964

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	406
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-09

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 57.9 bits (139), Expect = 4e-09
 Identities = 64/393 (16%), Positives = 101/393 (25%), Gaps = 137/393 (34%)

Query: 62  FWI-------DNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNL---------E 105
           FW+                K     D + T   D    + L      + L         E
Sbjct: 185 FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE 244

Query: 106 GGLEIIDDAS-----RCFNCGSYSHSLKECP---KPRDK---DAVNNARKQHKSKRNQNS 154
             L ++ +         FN          C      R K   D ++ A   H S      
Sbjct: 245 NCLLVLLNVQNAKAWNAFNLS--------CKILLTTRFKQVTDFLSAATTTHIS------ 290

Query: 155 ASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGELDPPPWLH-RMRELGYPPGYLDS 213
                            D         E + LL         +L  R ++L  P      
Sbjct: 291 ----------------LDHHSMTLTPDEVKSLLLK-------YLDCRPQDL--PR----E 321

Query: 214 EDDDQPSGITIYADGEIKEG----------QED--GEIIETG----RPASKRKMTTE--- 254
                P  ++I A+  I++G            D    IIE+      PA  RKM      
Sbjct: 322 VLTTNPRRLSIIAE-SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380

Query: 255 FPGINAPIPENADERLWAARPSSSDSSRDRSHHRLNH-HSESISRGRYHEQRWSRDYRDD 313
           FP  +A IP      +W       D  +      +N  H  S+       ++  ++    
Sbjct: 381 FPP-SAHIPTILLSLIW------FDVIKSDVMVVVNKLHKYSLV------EKQPKEST-- 425

Query: 314 GPPGVDPVSSYPPRYGGYDYYSSHSRSPTRGRSYSDRDRDDYASHGSYSSPYSNRHTSPP 373
                               Y               +  ++YA H S    Y+   T   
Sbjct: 426 --------------ISIPSIY----------LELKVKLENEYALHRSIVDHYNIPKTFDS 461

Query: 374 DYDLDRYRDDYSREYLSRSM------DEYDRFR 400
           D  +  Y D Y   ++   +      +    FR
Sbjct: 462 DDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFR 494

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	406
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.32
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	97.21
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	96.69
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	96.1
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	96.09
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	95.79
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	95.63
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	95.51
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	95.32
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	95.1
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	94.85
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	94.76
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	94.68
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	94.38
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	94.35
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	94.22
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	94.1
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	93.86
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	93.37
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	93.33
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	93.17
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	92.24
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	91.18
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	91.08
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	88.86
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	87.8
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	86.87

>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

Probab=97.32  E-value=6.9e-05  Score=49.51  Aligned_cols=22  Identities=45%  Similarity=1.081  Sum_probs=19.6

Q ss_pred             CCccccCCCCCCCCCCCCCccC
Q 015479          114 ASRCFNCGSYSHSLKECPKPRD  135 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Prd  135 (406)
                      ...|||||..+|..++||.|+-
T Consensus         6 ~~~C~nCgk~GH~ar~C~~prk   27 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAPRR   27 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSSS
T ss_pred             CCEEEECCccccCHhHCccccc
Confidence            3679999999999999999973

>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

Probab=96.69  E-value=0.00082  Score=48.06  Aligned_cols=23  Identities=35%  Similarity=0.735  Sum_probs=20.8

Q ss_pred             CCCccccCCCCCCCCCCCCCccC
Q 015479          113 DASRCFNCGSYSHSLKECPKPRD  135 (406)
Q Consensus       113 ~~~~CFNCG~~~HsLrdCP~Prd  135 (406)
                      ....|||||..+|-.++||.++.
T Consensus         9 ~~~~C~~Cgk~GH~ardCP~~~~   31 (40)
T 1a6b_B            9 DRDQCAYCKEKGHWAKDCPKKPR   31 (40)
T ss_dssp             CSSSCSSSCCTTCCTTSCSSSCC
T ss_pred             CCCeeeECCCCCcchhhCcCCcc
Confidence            46899999999999999999874

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=96.10  E-value=0.0023  Score=44.39  Aligned_cols=19  Identities=47%  Similarity=1.209  Sum_probs=16.2

Q ss_pred             ccccCCCCCCCCCCCCCcc
Q 015479          116 RCFNCGSYSHSLKECPKPR  134 (406)
Q Consensus       116 ~CFNCG~~~HsLrdCP~Pr  134 (406)
                      .|||||..+|..++||.|+
T Consensus         2 ~C~~Cg~~GH~a~~C~~~~   20 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQPR   20 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSCC
T ss_pred             eeeccCCCCcccccCCCCC
Confidence            5899998899999998874

>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

Probab=96.09  E-value=0.0026  Score=46.17  Aligned_cols=21  Identities=48%  Similarity=1.137  Sum_probs=16.3

Q ss_pred             CCccccCCCCCCCCCCCCCcc
Q 015479          114 ASRCFNCGSYSHSLKECPKPR  134 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Pr  134 (406)
                      ...|||||..+|..++||.|+
T Consensus         6 ~~~C~~Cg~~GH~a~~C~~~~   26 (49)
T 2ec7_A            6 VIRCWNCGKEGHSARQCRAPR   26 (49)
T ss_dssp             CCBCTTTCCBTCCTTTCCCSS
T ss_pred             cCeeeecCCCCcChhhCcCCC
Confidence            357888888888888888774

>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

Probab=95.79  E-value=0.0032  Score=47.89  Aligned_cols=24  Identities=33%  Similarity=0.649  Sum_probs=21.1

Q ss_pred             cCCCccccCCCCCCCCCCCCCccC
Q 015479          112 DDASRCFNCGSYSHSLKECPKPRD  135 (406)
Q Consensus       112 ~~~~~CFNCG~~~HsLrdCP~Prd  135 (406)
                      .....|||||..+|-.+|||.+..
T Consensus        21 ~~~~~C~~Cge~GH~ardCp~~~~   44 (56)
T 1u6p_A           21 LDRDQCAYCKEKGHWAKDCPKKPR   44 (56)
T ss_dssp             CCTTBCSSSCCBSSCGGGCTTCCC
T ss_pred             CCCCcceeCCCCCcccccCcCCcc
Confidence            346899999999999999999864

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=95.63  E-value=0.0053  Score=42.05  Aligned_cols=18  Identities=39%  Similarity=1.056  Sum_probs=13.4

Q ss_pred             ccccCCCCCCCCCCCCCc
Q 015479          116 RCFNCGSYSHSLKECPKP  133 (406)
Q Consensus       116 ~CFNCG~~~HsLrdCP~P  133 (406)
                      .|||||..+|..++||.|
T Consensus         2 ~C~~Cg~~GH~~~~C~~~   19 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAP   19 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCB
T ss_pred             cccccCCCCcchhhCcCc
Confidence            477777777777777765

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=95.51  E-value=0.0049  Score=46.56  Aligned_cols=20  Identities=45%  Similarity=1.050  Sum_probs=10.6

Q ss_pred             CccccCCCCCCCCCCCCCcc
Q 015479          115 SRCFNCGSYSHSLKECPKPR  134 (406)
Q Consensus       115 ~~CFNCG~~~HsLrdCP~Pr  134 (406)
                      ..||||+...|..++||.++
T Consensus         5 ~~C~~Cg~~GH~a~~C~~~~   24 (61)
T 2ihx_A            5 GLCYTCGSPGHYQAQCPKKR   24 (61)
T ss_dssp             TBCSSSCCBTCCGGGCTTTT
T ss_pred             CcccccCCCCeehhhCcCCc
Confidence            34555555555555555544

>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

Probab=95.32  E-value=0.0063  Score=44.72  Aligned_cols=20  Identities=45%  Similarity=1.089  Sum_probs=14.2

Q ss_pred             CCccccCCCCCCCCCCCCCc
Q 015479          114 ASRCFNCGSYSHSLKECPKP  133 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~P  133 (406)
                      ...|||||..+|..++||.|
T Consensus        12 ~~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           12 TVKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             TCBCTTTCCBSSCGGGCSSC
T ss_pred             CcceeeeCCCCcChhhcCCC
Confidence            35677777777777777766

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.10  E-value=0.011  Score=45.08  Aligned_cols=19  Identities=53%  Similarity=1.268  Sum_probs=12.5

Q ss_pred             CccccCCCCCCCCCCCCCc
Q 015479          115 SRCFNCGSYSHSLKECPKP  133 (406)
Q Consensus       115 ~~CFNCG~~~HsLrdCP~P  133 (406)
                      ..|||||..+|..++||.+
T Consensus         8 ~~C~~Cg~~GH~a~~C~~~   26 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKLP   26 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCSC
T ss_pred             CcccccCCCCcChhhCCCC
Confidence            4566666666666666655

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.85  E-value=0.0077  Score=45.63  Aligned_cols=21  Identities=38%  Similarity=0.967  Sum_probs=18.1

Q ss_pred             CCccccCCCCCCCCCCCCCcc
Q 015479          114 ASRCFNCGSYSHSLKECPKPR  134 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Pr  134 (406)
                      ...||.||..+|.+++||...
T Consensus         7 ~~~C~kCGk~GH~~k~Cp~~~   27 (55)
T 2ysa_A            7 GYTCFRCGKPGHYIKNCPTNG   27 (55)
T ss_dssp             SCCCTTTCCTTSCGGGCSGGG
T ss_pred             CCccccCCCcCcccccCCCCC
Confidence            467999999999999998543

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=94.76  E-value=0.014  Score=40.32  Aligned_cols=19  Identities=47%  Similarity=1.186  Sum_probs=17.4

Q ss_pred             CCccccCCCCCCCCCCCCC
Q 015479          114 ASRCFNCGSYSHSLKECPK  132 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~  132 (406)
                      ...|||||..+|..++||+
T Consensus        21 ~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           21 QEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             CSSCTTTCCSSSCTTTSCC
T ss_pred             CCccccCCCCCCccCcCcC
Confidence            4689999999999999995

>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

Probab=94.68  E-value=0.016  Score=43.20  Aligned_cols=22  Identities=27%  Similarity=0.510  Sum_probs=19.9

Q ss_pred             CCccccCCCCCCCCCCCCCccC
Q 015479          114 ASRCFNCGSYSHSLKECPKPRD  135 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Prd  135 (406)
                      ...||+||..+|..++||.+.+
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~~   51 (60)
T 1cl4_A           30 PGLCPRCKRGKHWANECKSKTD   51 (60)
T ss_dssp             CCSCSSCSSCSSCSTTCCCTTS
T ss_pred             CcceeECCCCCCccCcCCCccc
Confidence            4789999999999999999865

>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

Probab=94.38  E-value=0.0072  Score=45.15  Aligned_cols=22  Identities=32%  Similarity=0.806  Sum_probs=0.0

Q ss_pred             CccccCCCCCCCCCCCCCccCH
Q 015479          115 SRCFNCGSYSHSLKECPKPRDK  136 (406)
Q Consensus       115 ~~CFNCG~~~HsLrdCP~Prd~  136 (406)
                      ..|||||..+|..++||.+++.
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~~~~   23 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEHAHN   23 (60)
T ss_dssp             ----------------------
T ss_pred             CccccCCCCCcCHhhCcCCCCC
Confidence            3699999999999999988653

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=94.35  E-value=0.02  Score=45.33  Aligned_cols=21  Identities=48%  Similarity=1.141  Sum_probs=16.2

Q ss_pred             CCccccCCCCCCCCCCCCCcc
Q 015479          114 ASRCFNCGSYSHSLKECPKPR  134 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Pr  134 (406)
                      ...|||||..+|..++||.+.
T Consensus        24 ~~~C~~Cg~~GH~a~~C~~~~   44 (74)
T 2li8_A           24 GDRCYNCGGLDHHAKECKLPP   44 (74)
T ss_dssp             TSCCTTTCCSSSCTTTCSSCC
T ss_pred             CCcccccCCcCcCcccCCCCC
Confidence            467888888888888888654

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=94.22  E-value=0.015  Score=43.93  Aligned_cols=23  Identities=30%  Similarity=0.679  Sum_probs=19.3

Q ss_pred             CCccccCCCCCCCCCCCCCccCH
Q 015479          114 ASRCFNCGSYSHSLKECPKPRDK  136 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Prd~  136 (406)
                      ...|||||...|..++||.++..
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~~~   52 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCRKRDGN   52 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCCCCC--
T ss_pred             CCeeCCCCCCCCCcCCCcCCCcC
Confidence            36799999999999999998754

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=94.10  E-value=0.017  Score=46.78  Aligned_cols=22  Identities=32%  Similarity=0.800  Sum_probs=20.2

Q ss_pred             CCCccccCCCCCCCCCCCCCcc
Q 015479          113 DASRCFNCGSYSHSLKECPKPR  134 (406)
Q Consensus       113 ~~~~CFNCG~~~HsLrdCP~Pr  134 (406)
                      ....|+|||..+|.-+|||++|
T Consensus        45 ~~~~CYnCG~~GH~~rdC~~~r   66 (83)
T 3nyb_B           45 HTIYCYNCGGKGHFGDDCKEKR   66 (83)
T ss_dssp             CCCBCSSSSCBSSCGGGCSSCC
T ss_pred             CCCeecccCCCCcCcccCCccc
Confidence            3578999999999999999988

>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

Probab=93.86  E-value=0.021  Score=41.88  Aligned_cols=21  Identities=29%  Similarity=0.933  Sum_probs=19.0

Q ss_pred             CCccccCCCCCCCCCCCCCcc
Q 015479          114 ASRCFNCGSYSHSLKECPKPR  134 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Pr  134 (406)
                      ...||+||..+|..++||..+
T Consensus        33 ~~~C~~Cg~~GH~~~~C~~~~   53 (55)
T 1a1t_A           33 KKGCWKCGKEGHQMKDCTERQ   53 (55)
T ss_dssp             CCBCTTTCCBSSCGGGCSSSC
T ss_pred             CCEeCCCCCcCCccCCCcCcC
Confidence            468999999999999999865

>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*

Probab=93.37  E-value=0.028  Score=49.41  Aligned_cols=22  Identities=45%  Similarity=1.103  Sum_probs=18.4

Q ss_pred             CCccccCCCCCCCCCCCCCccC
Q 015479          114 ASRCFNCGSYSHSLKECPKPRD  135 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Prd  135 (406)
                      ..+|||||..+|..++||.|..
T Consensus        97 ~~~C~~Cg~~GH~a~~C~~~~~  118 (148)
T 3ts2_A           97 GDRCYNCGGLDHHAKECKLPPQ  118 (148)
T ss_dssp             SCCCTTTCCSSCCGGGCCSCCC
T ss_pred             CCcccEeCCccchhhhCCCCCC
Confidence            3579999999999999998654

>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

Probab=93.33  E-value=0.031  Score=40.49  Aligned_cols=21  Identities=29%  Similarity=0.963  Sum_probs=18.5

Q ss_pred             CCccccCCCCCCCCCCCCCcc
Q 015479          114 ASRCFNCGSYSHSLKECPKPR  134 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Pr  134 (406)
                      ...||+||..+|..++||...
T Consensus        27 ~~~C~~Cg~~GH~~~~C~~~~   47 (49)
T 2ec7_A           27 RQGCWKCGKTGHVMAKCPERQ   47 (49)
T ss_dssp             CCSCSSSCCSSCCGGGCCSSC
T ss_pred             CCeeCcCCCcCCccCCCcCCC
Confidence            367999999999999999754

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=93.17  E-value=0.037  Score=42.12  Aligned_cols=21  Identities=33%  Similarity=0.755  Sum_probs=19.0

Q ss_pred             CCccccCCCCCCCCCCCCCcc
Q 015479          114 ASRCFNCGSYSHSLKECPKPR  134 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Pr  134 (406)
                      ...||||+..+|..++||...
T Consensus        29 ~~~C~~Cg~~GH~ar~Cp~~~   49 (63)
T 2cqf_A           29 PKKCHFCQSISHMVASCPLKA   49 (63)
T ss_dssp             SSCCTTTCCSSSCTTTCTGGG
T ss_pred             CCccCCcCCcCCccCcCCCcc
Confidence            478999999999999999764

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=92.24  E-value=0.041  Score=37.55  Aligned_cols=18  Identities=33%  Similarity=0.778  Sum_probs=16.7

Q ss_pred             CccccCCCCCCCCCCCCC
Q 015479          115 SRCFNCGSYSHSLKECPK  132 (406)
Q Consensus       115 ~~CFNCG~~~HsLrdCP~  132 (406)
                      ..||+||..+|..++||.
T Consensus        20 ~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           20 KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             TTCSSCCCTTGGGGTTCC
T ss_pred             CeEccCCCcCCccCcCcC
Confidence            689999999999999984

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=91.18  E-value=0.084  Score=41.67  Aligned_cols=21  Identities=33%  Similarity=0.755  Sum_probs=18.8

Q ss_pred             CCccccCCCCCCCCCCCCCcc
Q 015479          114 ASRCFNCGSYSHSLKECPKPR  134 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Pr  134 (406)
                      ...||+||..+|..++||...
T Consensus        46 ~~~C~~Cg~~GH~ar~Cp~~~   66 (74)
T 2li8_A           46 PKKCHFCQSISHMVASCPLKA   66 (74)
T ss_dssp             CCCCTTTCCTTSCGGGCTTGG
T ss_pred             CCccCCcCCcCCccCcCcCCc
Confidence            478999999999999999764

>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*

Probab=91.08  E-value=0.081  Score=46.41  Aligned_cols=23  Identities=26%  Similarity=0.706  Sum_probs=19.4

Q ss_pred             CCccccCCCCCCCCCCCCCccCH
Q 015479          114 ASRCFNCGSYSHSLKECPKPRDK  136 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~Prd~  136 (406)
                      ...||+||..+|..++||...-.
T Consensus       119 ~~~C~~Cg~~GH~~r~Cp~~~~~  141 (148)
T 3ts2_A          119 PKKCHFCQSINHMVASCPLKAQQ  141 (148)
T ss_dssp             CCCCTTTCCSSCCGGGCTTTTC-
T ss_pred             CCcccccCCcCCEeccCcCCCCC
Confidence            46899999999999999976544

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=88.86  E-value=0.11  Score=42.05  Aligned_cols=21  Identities=33%  Similarity=0.664  Sum_probs=17.2

Q ss_pred             CCCccccCCCCCCCCCCCCCc
Q 015479          113 DASRCFNCGSYSHSLKECPKP  133 (406)
Q Consensus       113 ~~~~CFNCG~~~HsLrdCP~P  133 (406)
                      +...||||++.+|..++||..
T Consensus         4 k~~~C~~Cg~~GH~~~~Cp~~   24 (83)
T 3nyb_B            4 KKVQCTLCKSKKHSKERCPSI   24 (83)
T ss_dssp             ---CCSSSCCSSSCGGGCGGG
T ss_pred             ccCCCCCCCCCCCccccCCCc
Confidence            357899999999999999986

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=87.80  E-value=0.25  Score=41.27  Aligned_cols=20  Identities=30%  Similarity=0.811  Sum_probs=18.2

Q ss_pred             CCCccccCCCCCCCCCCCCC
Q 015479          113 DASRCFNCGSYSHSLKECPK  132 (406)
Q Consensus       113 ~~~~CFNCG~~~HsLrdCP~  132 (406)
                      ....|||||+.+|..+|||+
T Consensus       104 ~~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A          104 HTIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CCCCTTTTSSSCTTTTTSCC
T ss_pred             CCCCcCCCCCCCcCcccCcC
Confidence            35799999999999999997

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=86.87  E-value=0.28  Score=41.04  Aligned_cols=19  Identities=37%  Similarity=0.891  Sum_probs=13.0

Q ss_pred             CccccCCCCCCCCCCCCCc
Q 015479          115 SRCFNCGSYSHSLKECPKP  133 (406)
Q Consensus       115 ~~CFNCG~~~HsLrdCP~P  133 (406)
                      ..||||+..+|..++||.+
T Consensus         5 ~~C~~C~~~GH~~~~Cp~~   23 (124)
T 2lli_A            5 PKCNNCSQRGHLKKDCPHI   23 (124)
T ss_dssp             SCCSSCSSSSCCTTTTTSC
T ss_pred             CcccCCCCCCcCcccCcCC
Confidence            4577777777777777763

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	406
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	1e-04

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

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 = 37.1 bits (86), Expect = 1e-04
 Identities = 10/21 (47%), Positives = 13/21 (61%)

Query: 116 RCFNCGSYSHSLKECPKPRDK 136
           +CFNCG   H+ + C  PR K
Sbjct: 3   KCFNCGKEGHTARNCRAPRKK 23

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	406
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.17
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	96.92
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	93.34
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	91.55

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

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 2 [TaxId: 11709]

Probab=97.17  E-value=6.5e-05  Score=48.92  Aligned_cols=23  Identities=43%  Similarity=1.041  Sum_probs=20.3

Q ss_pred             CCCccccCCCCCCCCCCCCCccC
Q 015479          113 DASRCFNCGSYSHSLKECPKPRD  135 (406)
Q Consensus       113 ~~~~CFNCG~~~HsLrdCP~Prd  135 (406)
                      +...|||||-++|..++|--||-
T Consensus         5 ~~ikCfNCGkeGH~ar~CrAPRk   27 (29)
T d1nc8a_           5 KVIRCWNCGKEGHSARQCRAPRR   27 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSSSS
T ss_pred             ceeEeecCCccchhhhhccCccc
Confidence            35789999999999999999974

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

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=96.92  E-value=0.00017  Score=49.96  Aligned_cols=21  Identities=43%  Similarity=1.154  Sum_probs=16.2

Q ss_pred             CccccCCCCCCCCCCCCCccC
Q 015479          115 SRCFNCGSYSHSLKECPKPRD  135 (406)
Q Consensus       115 ~~CFNCG~~~HsLrdCP~Prd  135 (406)
                      .+|||||..+|..++||.|+.
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~~   22 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPRK   22 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCCC
T ss_pred             CccccCCCcCcCcccCcCCCc
Confidence            468888888888888887753

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

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=93.34  E-value=0.018  Score=39.38  Aligned_cols=20  Identities=30%  Similarity=0.954  Sum_probs=17.7

Q ss_pred             CCccccCCCCCCCCCCCCCc
Q 015479          114 ASRCFNCGSYSHSLKECPKP  133 (406)
Q Consensus       114 ~~~CFNCG~~~HsLrdCP~P  133 (406)
                      ...||+||..+|..++||+.
T Consensus        22 ~~~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1          22 KKGCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             CSSCSSSCCSSSCTTTCCSS
T ss_pred             cCccccCCCCCeecccCCCC
Confidence            35799999999999999974