Citrus Sinensis ID: 015904

---

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-------40
Protein Sequence
MFSLFSCSDILLVVVPLWCFWWRYFLWFSGPLRVVHLMQGIWAVDQGSSYIGYLPFCLYMEAEDVIDLLASSPSGCEEENNEMPGRDGEPGKSDFQPNDSEKKEDDSNGESMELNELNVEIEDGQLIEEGEVGKDVVDDSNVNVEGTTTVELAETIVESDSRIHVQNGCLEVGNRSPNHNRMKDVSSTSGVKRARMTLDEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGVS
Secondary Structure (PSIPRED)
cccccccccEEEEEHHHHHHHHHHHHHHcccHHHHHHHHcccHHcccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccEEEEccccccccccEEEccccccccccccccccccccccccccccccccEEEEEEccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccEEEEEEEccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccHHHHHHHHHHHHHHcccccccccccEEEEccccccccccccccccHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccEcHccEEEEHHHHHHHHHHHHHHHccccEEEEEHccEEEEcccccHEEcccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccEEEEccccccccEEccccEccccccEEEEEEEEEEEEEEEEccccEccccEEEccccccccccccccccccccEEcEEEccccccEEEEEEccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHcccccccccEEEEcccccccEEEEEEcccccccccccEEcccccccccccEEEEccccccccccccccEEEcccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccEccccccccccccccccccHHHHHHHccccc
Coil and Loop (DISEMBL)
mfslfscsdILLVVVPLWCFWWRYflwfsgplRVVHLMQGIWavdqgssyigylpfcLYMEAEDVIDLlasspsgceeennempgrdgepgksdfqpndsekkeddsngesmelnelnveiedgqlieegevgkdvvddsnvnvegtTTVELAETIvesdsrihvqngclevgnrspnhnrmkdvsstsgvkrarmtldeeqpsvHVIYNSLTRASKQKLEELLQQWSEWQaqfgsssndpnegiefgeqtffpairvgkakgpavsFWIDnqtrnqqnknfipsdshgtplydrgyalgltsgdgssnleggleiiddasrcfncgsyshslkecpkprdkdavNNARKQHkskrnqnsasrnpmryyqnsaggkydglrpgaldaETRQLLGLGVS
Flexible Loop (DISEMBL)
mfslfscsDILLVVVPLWCFWWRYFLWFSGPLRVVHLMQGIWAVDQGSSYIGYLPFCLYMEAEDVIDLLASSPSGCEEENnempgrdgepgksdfqpndsekkeddsngesmELNELNVEIEDGQLIEEGevgkdvvddsnvnvegTTTVELaetivesdsrihVQNGClevgnrspnhnrmkdvsstsgvkrarmtldeeqpsvhVIYNSLTRASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQtrnqqnknfipsdshgtpLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSyshslkecpkprdkdavnnarkqhkskrnqnsasrnpmRYYQNSAGGKYDGLRPGALDAETrqllglgvs
Low Complexity Region (SEG)
MFSLFSCSDILLVVVPLWCFWWRYFLWFSGPLRVVHLMQGIWAVDQGSSYIGYLPFCLYMEAEDVIDLLASSPSGCEEENNEMPGRDGEPGKSDFQPNDSEKKEDDSNGESMELNELNVEIEDGQLIEEGEVGKDVVDDSNVNVEGTTTVELAETIVESDSRIHVQNGCLEVGNRSPNHNRMKDVSSTSGVKRARMTLDEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGVS
Disordered region (IsUnstruct)
***LFSCSDILLVVVPLWCFWWRYFLWFSGPLRVVHLMQGIWAVDQGSSYIGYLPFCLYMEAEDVIDLL******************************************************************VVD**NVNVEGTTTVELAETIVESDSRIHVQNGCL***********************************HVIYNSL**********LLQQWSEW**************IEFGEQTFFPAIRVGKAKGPAVSFWIDN******************PLYDRGYALGLT*******LEGGLEIIDDASRCFNCGSY*********************************************************************
Disordered Region (DISOPRED)
**SLFSCSDILLVVVPLWCFWWRYFLWFSGPLRVVHLMQGIWAVDQGSSYIGYLPFCLYMEAEDVID*************************************************************************************************************************************EQPSVHVIYNSLT*********LL**************************TFFPAIRVGKAKGPAVSFWIDNQTRNQ****FIPSDSHGTPLYDRGYA************************CFNCGSYSHSLKECPKPRDKDAVN******************************Y*GLRPGALDAETRQLLGLG**
Disordered Region (DISEMBL)
MFSLFSCSDILLVVVPLWCFWWRYFLWFSGPLRVVHLMQGIWAVDQGSSYIGYLPFCLYMEAEDVIDLLASSP*************************************SMELNELNVEIEDGQLIEEGEVGKDVVDDSNVNVEGTTTVELAETIVESDSRIHVQNGCLEVGNRSPNHNR**********KRARMTLDEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHS*****************************SRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGVS
Disordered Region (DISPRO)
*FSLFSCSDILLVVVPLWCFWWRYFLWFSGPLRVVHLMQGIWAVDQGSSYIGYLPFCLYMEAEDVIDLL******************************************MELNELNVEIEDGQLIEEGEVGKDVVDDSNVNVEGTTTVELAETIVESDSRIHVQNGCLEVGN**************SGVKRARMTLDEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFG****DPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKR****************AGGKYDGLRPGALDAETRQLLGLGVS
Transmembrane Helix (TMHMM)
iHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFSLFSCSDILLVVVPLWCFWWRYFLWFSGPLRVVHLMQGIWAVDQGSSYIGYLPFCLYMEAEDVIDLLASSPSGCEEENNEMPGRDGEPGKSDFQPNDSEKKEDDSNGESMELNELNVEIEDGQLIEEGEVGKDVVDDSNVNVEGTTTVELAETIVESDSRIHVQNGCLEVGNRSPNHNRMKDVSSTSGVKRARMTLDEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGVS
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	398	2.2.26 [Sep-21-2011]
Q6DD45	743	Zinc finger CCHC domain-c	N/A	no	0.206	0.110	0.333	1e-07
Q5F3D1	613	Zinc finger CCHC domain-c	yes	no	0.188	0.122	0.32	3e-07
Q9CYA6	709	Zinc finger CCHC domain-c	yes	no	0.183	0.102	0.315	2e-06
Q2PE14	553	Zinc finger CCHC domain-c	yes	no	0.160	0.115	0.337	3e-06
Q5R789	704	Zinc finger CCHC domain-c	yes	no	0.208	0.117	0.298	8e-06
Q6NZY4	707	Zinc finger CCHC domain-c	yes	no	0.208	0.117	0.298	8e-06

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

 Score = 57.8 bits (138), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 47/87 (54%), Gaps = 5/87 (5%)

Query: 313 GLEIIDDASR----CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRY 368
           G EI   A R    CFNCGS  H +++CPKPRD+  +N  RK+      + + ++N  RY
Sbjct: 201 GQEIQVKAKRPKPCCFNCGSEEHQMRDCPKPRDQAHINMKRKEFLDACGE-AGNQNQQRY 259

Query: 369 YQNSAGGKYDGLRPGALDAETRQLLGL 395
           +      ++   +PG +  E ++ LG+
Sbjct: 260 HAEEVEERFGKYKPGVISEELQEALGI 286

Xenopus laevis (taxid: 8355)

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

 Score = 56.6 bits (135), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 38/75 (50%)

Query: 321 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGL 380
           S CFNCGS  H +K+CPKPR+   ++  RK+      + S      RY+      ++   
Sbjct: 126 SHCFNCGSEEHQIKDCPKPRNAARISEKRKEFMEAYGEASNQNFQQRYHAEEVEERFGKF 185

Query: 381 RPGALDAETRQLLGL 395
           +PG +  E +  LG+
Sbjct: 186 KPGVISGELQDALGV 200

Gallus gallus (taxid: 9031)

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

 Score = 54.3 bits (129), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 37/73 (50%)

Query: 323 CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRP 382
           CFNCGS  H +KECP PR+   ++  RK++     + S      RY+      ++   +P
Sbjct: 232 CFNCGSEEHQMKECPMPRNAARISEKRKEYMDACGEASGQSFQQRYHAEEVEERFGRFKP 291

Query: 383 GALDAETRQLLGL 395
           G +  E +  LG+
Sbjct: 292 GVISEELQDALGV 304

May be involved in pre-mRNA splicing.

Mus musculus (taxid: 10090)

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

 Score = 53.1 bits (126), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 10/74 (13%)

Query: 321 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGL 380
           S CFNCG   HSL++C KPR+   +  ARK+  S+           RY+ ++   ++  +
Sbjct: 183 SSCFNCGDTEHSLRDCTKPRNNSRITRARKKMTSRTE---------RYHVDTE-QRFGHI 232

Query: 381 RPGALDAETRQLLG 394
           RPG +  +TR  +G
Sbjct: 233 RPGKISTKTRHAMG 246

Drosophila melanogaster (taxid: 7227)

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

 Score = 52.0 bits (123), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/87 (29%), Positives = 42/87 (48%), Gaps = 4/87 (4%)

Query: 313 GLEIIDDASR----CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRY 368
           G EI   A R    CFNCGS  H +K+CP PR+   ++  RK++     + +      RY
Sbjct: 213 GQEIQVKAKRPKPHCFNCGSEEHQMKDCPMPRNAARISEKRKEYMDACGEANNQNFQQRY 272

Query: 369 YQNSAGGKYDGLRPGALDAETRQLLGL 395
           +      ++   +PG +  E +  LG+
Sbjct: 273 HAEEVEERFGRFKPGVISEELQDALGV 299

May be involved in pre-mRNA splicing.

Pongo abelii (taxid: 9601)

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

 Score = 52.0 bits (123), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/87 (29%), Positives = 42/87 (48%), Gaps = 4/87 (4%)

Query: 313 GLEIIDDASR----CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRY 368
           G EI   A R    CFNCGS  H +K+CP PR+   ++  RK++     + +      RY
Sbjct: 215 GQEIQVKAKRPKPHCFNCGSEEHQMKDCPMPRNAARISEKRKEYMDACGEANNQNFQQRY 274

Query: 369 YQNSAGGKYDGLRPGALDAETRQLLGL 395
           +      ++   +PG +  E +  LG+
Sbjct: 275 HAEEVEERFGRFKPGVISEELQDALGV 301

May be involved in pre-mRNA splicing.

Homo sapiens (taxid: 9606)

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	398
298204384	1165	unnamed protein product [Vitis vinifera]	0.844	0.288	0.588	1e-104
359488397	575	PREDICTED: uncharacterized protein LOC10	0.844	0.584	0.588	1e-102
255570019	693	nucleic acid binding protein, putative [	0.748	0.430	0.59	3e-93
224079886	531	predicted protein [Populus trichocarpa]	0.726	0.544	0.569	2e-86
356573637	660	PREDICTED: uncharacterized protein LOC10	0.580	0.35	0.653	1e-83
224127396	289	predicted protein [Populus trichocarpa]	0.520	0.716	0.725	3e-83
18421775	532	zinc finger CCHC domain-containing prote	0.788	0.590	0.511	7e-79
307136480	610	nucleic acid binding protein [Cucumis me	0.806	0.526	0.497	6e-76
297838459	409	proline-rich spliceosome-associated fami	0.663	0.645	0.541	9e-76
449447474	610	PREDICTED: uncharacterized protein LOC10	0.806	0.526	0.505	1e-75

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

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 200/340 (58%), Positives = 245/340 (72%), Gaps = 4/340 (1%)

Query: 60  MEAEDVIDLLASSPSGCEEENNEMPGRDGEPGKSDFQPNDSEKKEDDSNGESMELNELNV 119
           M  E++I+  A S S C  E+NE+   + EPG++D   ++SE KED  N ES+  N+++ 
Sbjct: 591 MGTEELINPPAPSGSVCGSEDNELHNSNPEPGEADSSSSNSEVKEDKLNIESLMQNKVDF 650

Query: 120 EIEDGQLIEEGEVGKDVVDD---SNVNVEGTTTVELAETIVESDSRIHVQNGCLEVGNRS 176
           E  D +L     + KD+VD    S  +VE T T+ + + I  S S +  +NGCL   +  
Sbjct: 651 EKVDSRLTPGVVLDKDLVDKQLTSQGSVEVTETIVVTKLINSSSSGVPTENGCLTAPDEG 710

Query: 177 PNHNRMKDVSSTSGVKRARMTLDEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFGS 236
           P  N M D +S SGVKRAR+T+DE+QPSVHVIYNSLTR SK+KLEELLQQWSEW A++ S
Sbjct: 711 PIGNHMIDGTSISGVKRARLTIDEQQPSVHVIYNSLTRDSKRKLEELLQQWSEWHAKYVS 770

Query: 237 SSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRG 296
           SS+DP   ++ GE+T+FPA+ VG  K  AVSFW+DNQTR QQ+K FI  D    PLYDRG
Sbjct: 771 SSHDPKGQLDSGEKTYFPALHVGLNKSSAVSFWVDNQTRKQQDKEFISLDGDSVPLYDRG 830

Query: 297 YALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKR 356
           +ALGL S DG S  EG LEII DASRCFNCGSY+HS+KECPKPRD  AVNNARKQHKS+R
Sbjct: 831 FALGLVSEDGQSKPEGALEII-DASRCFNCGSYNHSMKECPKPRDNVAVNNARKQHKSRR 889

Query: 357 NQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLG 396
           NQN  SRNP RYYQNS GG+YDGLRPGAL  ETR+LLGLG
Sbjct: 890 NQNPGSRNPTRYYQNSPGGRYDGLRPGALGVETRELLGLG 929

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 200/340 (58%), Positives = 245/340 (72%), Gaps = 4/340 (1%)

Query: 60  MEAEDVIDLLASSPSGCEEENNEMPGRDGEPGKSDFQPNDSEKKEDDSNGESMELNELNV 119
           M  E++I+  A S S C  E+NE+   + EPG++D   ++SE KED  N ES+  N+++ 
Sbjct: 1   MGTEELINPPAPSGSVCGSEDNELHNSNPEPGEADSSSSNSEVKEDKLNIESLMQNKVDF 60

Query: 120 EIEDGQLIEEGEVGKDVVDD---SNVNVEGTTTVELAETIVESDSRIHVQNGCLEVGNRS 176
           E  D +L     + KD+VD    S  +VE T T+ + + I  S S +  +NGCL   +  
Sbjct: 61  EKVDSRLTPGVVLDKDLVDKQLTSQGSVEVTETIVVTKLINSSSSGVPTENGCLTAPDEG 120

Query: 177 PNHNRMKDVSSTSGVKRARMTLDEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFGS 236
           P  N M D +S SGVKRAR+T+DE+QPSVHVIYNSLTR SK+KLEELLQQWSEW A++ S
Sbjct: 121 PIGNHMIDGTSISGVKRARLTIDEQQPSVHVIYNSLTRDSKRKLEELLQQWSEWHAKYVS 180

Query: 237 SSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRG 296
           SS+DP   ++ GE+T+FPA+ VG  K  AVSFW+DNQTR QQ+K FI  D    PLYDRG
Sbjct: 181 SSHDPKGQLDSGEKTYFPALHVGLNKSSAVSFWVDNQTRKQQDKEFISLDGDSVPLYDRG 240

Query: 297 YALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKR 356
           +ALGL S DG S  EG LEII DASRCFNCGSY+HS+KECPKPRD  AVNNARKQHKS+R
Sbjct: 241 FALGLVSEDGQSKPEGALEII-DASRCFNCGSYNHSMKECPKPRDNVAVNNARKQHKSRR 299

Query: 357 NQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLG 396
           NQN  SRNP RYYQNS GG+YDGLRPGAL  ETR+LLGLG
Sbjct: 300 NQNPGSRNPTRYYQNSPGGRYDGLRPGALGVETRELLGLG 339

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  348 bits (893), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 177/300 (59%), Positives = 220/300 (73%), Gaps = 2/300 (0%)

Query: 99  DSEKKEDDSNGESMELNELNVEIEDGQLIEEGEVGKDVVDDS--NVNVEGTTTVELAETI 156
           D+  +ED  + + + LN+  V  E  Q + E +V  D+VD     VN+E    V ++  +
Sbjct: 154 DAVTEEDTIDRDYLFLNQGVVREEGAQCLVETDVDMDLVDSPVMQVNIEVAEAVAVSGNL 213

Query: 157 VESDSRIHVQNGCLEVGNRSPNHNRMKDVSSTSGVKRARMTLDEEQPSVHVIYNSLTRAS 216
                R++ QN CL+  N S   N M      SGVKRAR+  +E+QPSVHV YNSLTRAS
Sbjct: 214 SSFGFRLNAQNSCLDTQNESLIQNHMMKGGHVSGVKRARIAYNEQQPSVHVTYNSLTRAS 273

Query: 217 KQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRN 276
           K+KLEELLQQWSEW  Q GSSS D NE +E GE+T+FPA+ VG  K  AVSFWI+NQT+ 
Sbjct: 274 KRKLEELLQQWSEWHVQRGSSSQDLNEVLESGEETYFPALCVGTEKSSAVSFWIENQTKK 333

Query: 277 QQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKEC 336
           Q N + I SDS   PLYDRG+A+GLTS DG SN+EGGLEI+++A+RCFNCGSYSH+LKEC
Sbjct: 334 QLNNDLISSDSDSVPLYDRGFAIGLTSTDGPSNVEGGLEIVNEAARCFNCGSYSHALKEC 393

Query: 337 PKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLG 396
           PKPR+  AVNNARKQHKSKRNQN+ SRN  RYYQ+S+GGKY+GL+PG+LDAETR+LLGLG
Sbjct: 394 PKPRNNAAVNNARKQHKSKRNQNAGSRNGTRYYQSSSGGKYEGLKPGSLDAETRRLLGLG 453

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  325 bits (833), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 177/311 (56%), Positives = 222/311 (71%), Gaps = 22/311 (7%)

Query: 100 SEKKEDDSNGESMELNELNV----EIEDGQLIE--EGEVGKDVVDDSNVNVEGTTTVELA 153
           +E KE   + ES+ELNE  V     +++G+ +E  EG VG D        ++   +VEL 
Sbjct: 25  NETKESKDDEESVELNEGAVGNDERMKNGESVELNEGAVGNDE------RMKNGESVELN 78

Query: 154 ETIVESDSRIHVQNGC-LEVG-------NRSPNHNRMKDVSSTSGVKRARMTLDEEQPSV 205
           E  V ++       G  L VG          P ++ +K  ++ SGVKR R+T +EEQPSV
Sbjct: 79  EGAVGNNEGTKNGEGFELNVGVIGNDEVTVDPGYSALK--ANVSGVKRKRITYNEEQPSV 136

Query: 206 HVIYNSLTRASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPA 265
           HV+YNSLTRASK+KLEELLQQWSEW AQ  SSS+D +E ++ GE T+FPA+R+G  K  A
Sbjct: 137 HVMYNSLTRASKKKLEELLQQWSEWHAQQNSSSHDSDEMLQSGEDTYFPALRIGMVKSSA 196

Query: 266 VSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFN 325
           V+FWI+NQTR QQ+   IP  S+  PLYDRGYALGLTS DG  N+E GLEI+ DA+RC+N
Sbjct: 197 VTFWIENQTRKQQDNAIIPLQSNYVPLYDRGYALGLTSADGPINIERGLEIVGDAARCYN 256

Query: 326 CGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGAL 385
           C SY+HSLKECPKPRD  AVNNARKQHK KRNQNS+SRNP RYYQ+S+GGKYDGL+PG+L
Sbjct: 257 CASYNHSLKECPKPRDNAAVNNARKQHKFKRNQNSSSRNPTRYYQSSSGGKYDGLKPGSL 316

Query: 386 DAETRQLLGLG 396
           D ET++LLGLG
Sbjct: 317 DTETQKLLGLG 327

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  316 bits (809), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 151/231 (65%), Positives = 185/231 (80%)

Query: 165 VQNGCLEVGNRSPNHNRMKDVSSTSGVKRARMTLDEEQPSVHVIYNSLTRASKQKLEELL 224
            +NGC+ + + S   +     +S SG KRAR+T+DE QPSVH  YNSLTRAS+QKL+ELL
Sbjct: 195 AENGCISLEDGSLKRSLETVGTSVSGAKRARITVDEYQPSVHFTYNSLTRASRQKLQELL 254

Query: 225 QQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIP 284
           Q+WS W A+  SSS+D +E +E GE+TFFPA+ VG  K  AVSFW++NQTRN +NK+FIP
Sbjct: 255 QKWSAWHAKHVSSSSDASEVLESGEETFFPALHVGLEKTSAVSFWMENQTRNDKNKDFIP 314

Query: 285 SDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDA 344
              +  PLYDRGYALGLTS DGSSN++GGLEIID A+RCFNCGSY+HSL+ECP+PRD  A
Sbjct: 315 LADNTVPLYDRGYALGLTSADGSSNVDGGLEIIDAAARCFNCGSYNHSLRECPRPRDNIA 374

Query: 345 VNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGL 395
           VNNAR + KS+RNQNS+SR+P RYYQNS  GKYDGLRPG+LD  TR+LLGL
Sbjct: 375 VNNARDKLKSRRNQNSSSRHPTRYYQNSPAGKYDGLRPGSLDDATRKLLGL 425

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  315 bits (806), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 151/208 (72%), Positives = 174/208 (83%), Gaps = 1/208 (0%)

Query: 189 SGVKRARMTLDEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFG 248
           SGVKR RM  DE+QPSVHV+YNSLTR+ KQKLEELLQQWSEW AQ  +SS+D NE ++ G
Sbjct: 1   SGVKRKRMAYDEQQPSVHVMYNSLTRSGKQKLEELLQQWSEWHAQ-QNSSHDSNEMLQSG 59

Query: 249 EQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSS 308
           E T+FPA+RVG  K  AVSFWI+NQ R QQ+ + I   S+  PLYDRGY LGLTS DG  
Sbjct: 60  EDTYFPALRVGMEKSSAVSFWIENQARKQQDNDLILQHSNFVPLYDRGYVLGLTSADGPI 119

Query: 309 NLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRY 368
           N+EGGLEI+D A+RCFNCG+Y+HSLKECPKPRD  AVNNARKQHK KRNQNS+SRNP RY
Sbjct: 120 NVEGGLEIVDAAARCFNCGAYNHSLKECPKPRDNAAVNNARKQHKFKRNQNSSSRNPTRY 179

Query: 369 YQNSAGGKYDGLRPGALDAETRQLLGLG 396
           YQ+S+GGKYDGL+PG+LD ETRQLLGLG
Sbjct: 180 YQSSSGGKYDGLKPGSLDTETRQLLGLG 207

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18421775|ref|NP_568558.1| zinc finger CCHC domain-containing protein 8 [Arabidopsis thaliana] gi|16604587|gb|AAL24150.1| unknown protein [Arabidopsis thaliana] gi|20465897|gb|AAM20101.1| unknown protein [Arabidopsis thaliana] gi|332006957|gb|AED94340.1| zinc finger CCHC domain-containing protein 8 [Arabidopsis thaliana]

 Score =  300 bits (768), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 174/340 (51%), Positives = 218/340 (64%), Gaps = 26/340 (7%)

Query: 60  MEAEDVIDLLASSPSGCEEENNEMPGRDGEPGKSDFQPNDSEKKEDDSNGESMELNELNV 119
           ME EDV+D+ ASS  G E + N +   +G P  +    ND    E+      ++L E N+
Sbjct: 1   METEDVLDIPASSNFGSEVKKNSLESGNGSPEANSLVGND----ENVKGNLDLDLTEENL 56

Query: 120 EIEDGQLIEEGEVGKDVVDDS-NVNVEGTTTVELAETIVESDSRIHVQNGCLEVGNRSPN 178
            I  GQ  E GE+  + V D  N +VE           V  D ++ +Q   L        
Sbjct: 57  RIVGGQ--ESGEILTEQVSDVFNASVES----------VAVDEKLGIQKETLV------- 97

Query: 179 HNRMKDVSSTSGVKRARMTLDEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFGSSS 238
           H+   DVSS +GVKR R + DE+QP+VHV Y  LTRASKQKLE LLQ+WSEW+A+  S +
Sbjct: 98  HSTTLDVSSKAGVKRPRTSYDEQQPTVHVTYKHLTRASKQKLESLLQKWSEWEAENTSLA 157

Query: 239 NDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYA 298
            D  +  E GE+T FPAIRVG  K  +VSFWIDNQT ++  ++F+  +S  TPLYDR +A
Sbjct: 158 QDQEQLFESGEETCFPAIRVGLQKTSSVSFWIDNQTGHKPLEDFVLVESSTTPLYDRKFA 217

Query: 299 LGLTSGDGSSNLEGGLEII-DDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRN 357
           +GL S DGS N+EGGLEII DD  RCFNCG YSHSL+ECP+P D+ AVN+ARK  KSKRN
Sbjct: 218 IGLNSADGSRNVEGGLEIIDDDPPRCFNCGGYSHSLRECPRPFDRSAVNSARKLQKSKRN 277

Query: 358 QNSAS-RNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLG 396
           QNS+  R P RYYQ +  GKYDGL+PG LDAETRQLL LG
Sbjct: 278 QNSSGPRLPSRYYQKTQTGKYDGLKPGTLDAETRQLLNLG 317

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  290 bits (743), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 170/342 (49%), Positives = 224/342 (65%), Gaps = 21/342 (6%)

Query: 60  MEAEDVIDLLASSPSGCEEENNEMPGRDGEPGKSDFQPNDSEKKEDDSNGESMELNELNV 119
           ME ED+ +L   S +    EN+E+        K++  P +S       + E ++ NEL+ 
Sbjct: 82  MEIEDLNNLPDFSKTRSRSENSEILS------KAEDLPVNSADGNILPSNEPLQQNELHT 135

Query: 120 EIEDGQLIEEGEVGKDVVDDSNVNVEGTTTVELAETIVESDSRIHVQNGC-LEVGNRSPN 178
             ED   +E     KD+VD+S+ +  G     +    ++ +    + +G  +E G+ + +
Sbjct: 136 RYEDVCHVESQNFQKDLVDNSSFSKTGGQLTVMNGVSIDFN---ELNSGAPMENGSATSH 192

Query: 179 HNRMKDVSSTSGVKRARMTL---DEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFG 235
           H+    +S   GVKR RM +   DE+QPSVH++Y SLTR SKQKL+ELL+QWSEW AQ G
Sbjct: 193 HHGGPRIS---GVKRPRMAMEAMDEQQPSVHIVYTSLTRDSKQKLDELLKQWSEWHAQQG 249

Query: 236 SSSNDP--NEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLY 293
           S S D    E +E GE+TFFPA+ VG  K  AV+FW+DNQ +++Q + F+P D +  PLY
Sbjct: 250 SLSRDDKDTENLESGEETFFPALCVGTKKTSAVTFWMDNQ-KSEQQQTFVPIDDNSVPLY 308

Query: 294 DRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHK 353
           DRG+ LGLTS + SSN+EGG +IIDDASRCFNCGSY+HSLK+C KPRD  AVNNAR  +K
Sbjct: 309 DRGFTLGLTSANDSSNVEGGQKIIDDASRCFNCGSYNHSLKDCRKPRDNAAVNNAR--NK 366

Query: 354 SKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGL 395
            K+  NSASRN  RYYQNS GGKYD LRPG LDAETRQLLGL
Sbjct: 367 YKKQHNSASRNSTRYYQNSRGGKYDDLRPGTLDAETRQLLGL 408

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297838459|ref|XP_002887111.1| proline-rich spliceosome-associated family protein [Arabidopsis lyrata subsp. lyrata] gi|297332952|gb|EFH63370.1| proline-rich spliceosome-associated family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  290 bits (742), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 150/277 (54%), Positives = 193/277 (69%), Gaps = 13/277 (4%)

Query: 119 VEIEDGQLIEEGEVGKDVVDDSNVNVEGTTTVELAETIVESDSRIHVQNGCLEVGNRSPN 178
           +E E+G++  + E   D+ +D   NV G  + E   +IVE    ++V    ++V      
Sbjct: 9   LEAEEGEISIDMEEDMDLTEDDFRNVSGQFSGEA--SIVEVRDAVNVSVETVKV------ 60

Query: 179 HNRMKDVSSTSGVKRARMTLDEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFGSSS 238
                DVSS SGVKR R    E+QPSVHV Y  LTR SKQKLE LLQQWSEW+A+  S S
Sbjct: 61  -----DVSSKSGVKRPRTISLEQQPSVHVTYKHLTRNSKQKLESLLQQWSEWEAEQNSFS 115

Query: 239 NDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYA 298
            D  + +E G++T+FPA+RVG  K  +VSFW D QT +  +K  +P +S  TPLY+RG+ 
Sbjct: 116 EDQEQVLESGDETYFPALRVGLQKTSSVSFWFDYQTGHSSSKKSVPVESSTTPLYNRGFT 175

Query: 299 LGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQ 358
           +GL S  GS+N+EGGLEIIDD  RCFNCG+YSHS++ECPKP D+ AV+NAR++HKSKRNQ
Sbjct: 176 IGLDSAGGSNNMEGGLEIIDDPPRCFNCGAYSHSIRECPKPFDRSAVSNARREHKSKRNQ 235

Query: 359 NSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGL 395
            S SR P RYYQ+  GGKYDGL+PG+LDAETR+LLGL
Sbjct: 236 TSGSRLPSRYYQSPQGGKYDGLKPGSLDAETRKLLGL 272

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  290 bits (742), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 173/342 (50%), Positives = 222/342 (64%), Gaps = 21/342 (6%)

Query: 60  MEAEDVIDLLASSPSGCEEENNEMPGRDGEPGKSDFQPNDSEKKEDDSNGESMELNELNV 119
           ME ED+ +L   S +    EN+E+  +  +       P +S       + E ++ NEL+ 
Sbjct: 82  MEIEDLNNLPDFSKTRSRSENSEILSKAAD------LPVNSADGNILPSSELLQQNELHT 135

Query: 120 EIEDGQLIEEGEVGKDVVDDSN-VNVEGTTTVELAETIVESDSRIHVQNGCLEVGNRSPN 178
             ED   +E  +  KD+VD+S+ +   G  TV    +I   D         +E G+ + +
Sbjct: 136 RYEDVCHVESKKFQKDLVDNSSFLKTGGQLTVMNGVSI---DFNELNSGAPMENGSATSH 192

Query: 179 HNRMKDVSSTSGVKRARMTL---DEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFG 235
           H+    +S   GVKR RM +   DE+QPSVH++Y SLTR SKQKL+ELL+QWSEW AQ G
Sbjct: 193 HHGGPRIS---GVKRPRMAMEAMDEQQPSVHIVYTSLTRDSKQKLDELLKQWSEWHAQQG 249

Query: 236 SSSNDP--NEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLY 293
           S S D    E +E GE+TFFPA+ VG  K  AV+FW+DNQ +++Q +NF+P D +  PLY
Sbjct: 250 SLSCDDKDTENLESGEETFFPALCVGTKKTSAVTFWMDNQ-KSEQQQNFVPIDDNSVPLY 308

Query: 294 DRGYALGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHK 353
           DRG+ LGLTS + SSN EGG +IIDDASRCFNCGSY+HSLK+C KPRD  AVNNAR  +K
Sbjct: 309 DRGFTLGLTSANDSSNAEGGQKIIDDASRCFNCGSYNHSLKDCRKPRDNAAVNNAR--NK 366

Query: 354 SKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGL 395
            K+  NSASRN  RYYQNS GGKYD LRPG LDAETRQLLGL
Sbjct: 367 YKKQHNSASRNSTRYYQNSRGGKYDDLRPGTLDAETRQLLGL 408

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	398
TAIR|locus:2159818	532	AT5G38600 [Arabidopsis thalian	0.758	0.567	0.498	2.3e-71
TAIR|locus:2809302	405	AT1G67210 [Arabidopsis thalian	0.658	0.646	0.530	9.9e-71
UNIPROTKB|Q5F3D1	613	ZCCHC8 "Zinc finger CCHC domai	0.188	0.122	0.32	2.8e-06
UNIPROTKB|F1NEG3	684	F1NEG3 "Uncharacterized protei	0.188	0.109	0.32	3.3e-06
UNIPROTKB|E2QXB5	709	ZCCHC8 "Uncharacterized protei	0.216	0.121	0.318	5.8e-06
RGD|1309774	695	Zcchc8 "zinc finger, CCHC doma	0.183	0.105	0.301	2.5e-05
UNIPROTKB|F1MM78	710	ZCCHC8 "Uncharacterized protei	0.183	0.102	0.287	4.4e-05
MGI|MGI:1917900	709	Zcchc8 "zinc finger, CCHC doma	0.183	0.102	0.315	5.3e-05
UNIPROTKB|Q6NZY4	707	ZCCHC8 "Zinc finger CCHC domai	0.216	0.121	0.307	5.6e-05
FB|FBgn0035021	553	CG4622 [Drosophila melanogaste	0.160	0.115	0.337	0.00039

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

 Score = 722 (259.2 bits), Expect = 2.3e-71, P = 2.3e-71
 Identities = 156/313 (49%), Positives = 205/313 (65%)

Query:    90 PGKSDFQPNDSEKKEDDSNGESMELNELNVEIEDGQLIEEGEVGKDVVDDSNVNVEGTTT 149
             P  S+F     +   +  NG S E N L   + + + ++ G +  D+ +++   V G  +
Sbjct:    10 PASSNFGSEVKKNSLESGNG-SPEANSL---VGNDENVK-GNLDLDLTEENLRIVGGQES 64

Query:   150 VELAETIVESDSRIHVQNGCLE--VGNRSPN--HNRMKDVSSTSGVKRARMTLDEEQPSV 205
              E+    V       V++  ++  +G +     H+   DVSS +GVKR R + DE+QP+V
Sbjct:    65 GEILTEQVSDVFNASVESVAVDEKLGIQKETLVHSTTLDVSSKAGVKRPRTSYDEQQPTV 124

Query:   206 HVIYNSLTRASKQKLEELLQQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPA 265
             HV Y  LTRASKQKLE LLQ+WSEW+A+  S + D  +  E GE+T FPAIRVG  K  +
Sbjct:   125 HVTYKHLTRASKQKLESLLQKWSEWEAENTSLAQDQEQLFESGEETCFPAIRVGLQKTSS 184

Query:   266 VSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDD-ASRCF 324
             VSFWIDNQT ++  ++F+  +S  TPLYDR +A+GL S DGS N+EGGLEIIDD   RCF
Sbjct:   185 VSFWIDNQTGHKPLEDFVLVESSTTPLYDRKFAIGLNSADGSRNVEGGLEIIDDDPPRCF 244

Query:   325 NCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSAS-RNPMRYYQNSAGGKYDGLRPG 383
             NCG YSHSL+ECP+P D+ AVN+ARK  KSKRNQNS+  R P RYYQ +  GKYDGL+PG
Sbjct:   245 NCGGYSHSLRECPRPFDRSAVNSARKLQKSKRNQNSSGPRLPSRYYQKTQTGKYDGLKPG 304

Query:   384 ALDAETRQLLGLG 396
              LDAETRQLL LG
Sbjct:   305 TLDAETRQLLNLG 317

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 = 716 (257.1 bits), Expect = 9.9e-71, P = 9.9e-71
 Identities = 147/277 (53%), Positives = 191/277 (68%)

Query:   119 VEIEDGQLIEEGEVGKDVVDDSNVNVEGTTTVELAETIVESDSRIHVQNGCLEVGNRSPN 178
             +E E+G++  + E   D+ +D   NV G  + + +  IVE    + V+   ++V      
Sbjct:     9 LEAEEGEISIDMEEDMDLTEDDFRNVSGQFSGQAS--IVEVGDAVDVRVETVKV------ 60

Query:   179 HNRMKDVSSTSGVKRARMTLDEEQPSVHVIYNSLTRASKQKLEELLQQWSEWQAQFGSSS 238
                  DVSS SGVKRAR    E+QPSVHV Y  LTR SKQKLE LLQQWSEW+A+  S S
Sbjct:    61 -----DVSSKSGVKRARTISLEQQPSVHVTYKHLTRDSKQKLESLLQQWSEWEAEQNSLS 115

Query:   239 NDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYA 298
              D  + +E G++T+FPA+RVG  K  +VSFW D QT +  +K  +P +S  TPLY+RG+ 
Sbjct:   116 EDQEQVLEAGDETYFPALRVGLQKTSSVSFWFDYQTGHSSSKKSVPVESSTTPLYNRGFT 175

Query:   299 LGLTSGDGSSNLEGGLEIIDDASRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQ 358
             +GL SG  S+N+EGGLEIIDD  RCFNCG+YSHS++ECP+P D+ AV+NAR+QHK KRNQ
Sbjct:   176 IGLDSG--SNNVEGGLEIIDDPPRCFNCGAYSHSIRECPRPFDRSAVSNARRQHKRKRNQ 233

Query:   359 NSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGL 395
                SR P RYYQ+   GKYDGL+PG+LDAETR+LLGL
Sbjct:   234 TPGSRLPSRYYQSLQRGKYDGLKPGSLDAETRKLLGL 270

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

 Score = 140 (54.3 bits), Expect = 2.8e-06, P = 2.8e-06
 Identities = 24/75 (32%), Positives = 38/75 (50%)

Query:   321 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGL 380
             S CFNCGS  H +K+CPKPR+   ++  RK+      + S      RY+      ++   
Sbjct:   126 SHCFNCGSEEHQIKDCPKPRNAARISEKRKEFMEAYGEASNQNFQQRYHAEEVEERFGKF 185

Query:   381 RPGALDAETRQLLGL 395
             +PG +  E +  LG+
Sbjct:   186 KPGVISGELQDALGV 200

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 140 (54.3 bits), Expect = 3.3e-06, P = 3.3e-06
 Identities = 24/75 (32%), Positives = 38/75 (50%)

Query:   321 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGL 380
             S CFNCGS  H +K+CPKPR+   ++  RK+      + S      RY+      ++   
Sbjct:   222 SHCFNCGSEEHQIKDCPKPRNAARISEKRKEFMEAYGEASNQNFQQRYHAEEVEERFGKF 281

Query:   381 RPGALDAETRQLLGL 395
             +PG +  E +  LG+
Sbjct:   282 KPGVISGELQDALGV 296

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

 Score = 138 (53.6 bits), Expect = 5.8e-06, P = 5.8e-06
 Identities = 29/91 (31%), Positives = 47/91 (51%)

Query:   309 NLEGGLEIIDDASR----CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRN 364
             +LEG  EI   A R    CFNCGS  H +K+CP PR+   ++  RK++    ++ ++   
Sbjct:   212 SLEGQ-EIQVKAKRPKPHCFNCGSEEHQMKDCPMPRNAARISEKRKEYMDACSETNSQNF 270

Query:   365 PMRYYQNSAGGKYDGLRPGALDAETRQLLGL 395
               RY+      ++   +PG +  E +  LGL
Sbjct:   271 QQRYHAEEVEERFGRFKPGVISEELQDALGL 301

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 133 (51.9 bits), Expect = 2.5e-05, Sum P(2) = 2.5e-05
 Identities = 22/73 (30%), Positives = 38/73 (52%)

Query:   323 CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRP 382
             CFNCGS  H +KECP PR+   ++  RK++     + ++     RY+      ++   +P
Sbjct:   231 CFNCGSEEHQMKECPMPRNAARISEKRKEYMDACGEANSQSFQQRYHAEEVEERFGRFKP 290

Query:   383 GALDAETRQLLGL 395
             G +  E +  LG+
Sbjct:   291 GVISEELQDALGV 303

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 = 130 (50.8 bits), Expect = 4.4e-05, P = 4.4e-05
 Identities = 21/73 (28%), Positives = 37/73 (50%)

Query:   323 CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRP 382
             CFNCGS  H +K+CP PR+   ++  RK++     + +      RY+      ++   +P
Sbjct:   231 CFNCGSEEHQMKDCPMPRNAARISEKRKEYMDACGETNNQNFQQRYHAEEVEERFGRFKP 290

Query:   383 GALDAETRQLLGL 395
             G +  E +  LG+
Sbjct:   291 GVISEELQDALGV 303

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 135 (52.6 bits), Expect = 5.3e-05, Sum P(2) = 5.3e-05
 Identities = 23/73 (31%), Positives = 37/73 (50%)

Query:   323 CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRP 382
             CFNCGS  H +KECP PR+   ++  RK++     + S      RY+      ++   +P
Sbjct:   232 CFNCGSEEHQMKECPMPRNAARISEKRKEYMDACGEASGQSFQQRYHAEEVEERFGRFKP 291

Query:   383 GALDAETRQLLGL 395
             G +  E +  LG+
Sbjct:   292 GVISEELQDALGV 304

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

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

 Score = 129 (50.5 bits), Expect = 5.6e-05, P = 5.6e-05
 Identities = 28/91 (30%), Positives = 45/91 (49%)

Query:   309 NLEGGLEIIDDASR----CFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRN 364
             +LEG  EI   A R    CFNCGS  H +K+CP PR+   ++  RK++     + +    
Sbjct:   212 SLEGQ-EIQVKAKRPKPHCFNCGSEEHQMKDCPMPRNAARISEKRKEYMDACGEANNQNF 270

Query:   365 PMRYYQNSAGGKYDGLRPGALDAETRQLLGL 395
               RY+      ++   +PG +  E +  LG+
Sbjct:   271 QQRYHAEEVEERFGRFKPGVISEELQDALGV 301

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

FB|FBgn0035021 CG4622 [Drosophila melanogaster (taxid:7227)]

 Score = 120 (47.3 bits), Expect = 0.00039, P = 0.00039
 Identities = 25/74 (33%), Positives = 40/74 (54%)

Query:   321 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGL 380
             S CFNCG   HSL++C KPR+   +  ARK+  S+           RY+ ++   ++  +
Sbjct:   183 SSCFNCGDTEHSLRDCTKPRNNSRITRARKKMTSRTE---------RYHVDTEQ-RFGHI 232

Query:   381 RPGALDAETRQLLG 394
             RPG +  +TR  +G
Sbjct:   233 RPGKISTKTRHAMG 246

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

Your Input: fgenesh4_pg.C_LG_IV000890 hypothetical protein (531 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	398
pfam14392	49	pfam14392, zf-CCHC_4, Zinc knuckle	0.001

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 11/17 (64%), Positives = 12/17 (70%)

Query: 322 RCFNCGSYSHSLKECPK 338
            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	398
KOG2673	485	consensus Uncharacterized conserved protein, conta	99.93
smart00581	54	PSP proline-rich domain in spliceosome associated	97.83
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	97.47
PF04046	48	PSP: PSP; InterPro: IPR006568 PSP is a proline-ric	97.18
KOG2673	485	consensus Uncharacterized conserved protein, conta	96.33
PF14392	49	zf-CCHC_4: Zinc knuckle	92.68
smart00343	26	ZnF_C2HC zinc finger.	91.74
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	91.0
PTZ00368	148	universal minicircle sequence binding protein (UMS	88.93
PTZ00368	148	universal minicircle sequence binding protein (UMS	88.75
COG5182	429	CUS1 Splicing factor 3b, subunit 2 [RNA processing	88.48
PF13696	32	zf-CCHC_2: Zinc knuckle	87.55
KOG2330	500	consensus Splicing factor 3b, subunit 2 [RNA proce	81.38

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

Probab=99.93  E-value=7.3e-27  Score=235.83  Aligned_cols=143  Identities=33%  Similarity=0.598  Sum_probs=122.7

Q ss_pred             CCcccccccceeccceecCCCCCCccceEEecCCccccCCCCCCCCCCCCCcccccccccccCCCCCCCCCCCcccccCC
Q 015904          241 PNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIPSDSHGTPLYDRGYALGLTSGDGSSNLEGGLEIIDDA  320 (398)
Q Consensus       241 ~~evlesGeetyfPal~vg~~kssa~sF~IDkq~~~~~Ne~~q~~~~~eVPlYdR~y~~~L~s~Dg~sdteg~lEi~~~~  320 (398)
                      ..+++++++.+|+| +++.+.+...++||++++.....-+.+-+.+...    +|.++.+|++.+++-.++++..|.+ .
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            45677788888888 9999999999999999998876556555554442    8999999999988877776655544 4


Q ss_pred             CccccCCCCCCCCCCCCCCCCHHHHHHHHHHHHhhhccCCCCCCCcceEecCCCCcCCCCCCCCCCHHHHHhhCCCC
Q 015904          321 SRCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGV  397 (398)
Q Consensus       321 ~rCFNCGs~eHsLrDCP~PRD~arIs~~RkeF~~krnq~~g~r~~~RYh~~e~eqrf~~fKPG~LS~eLReALGL~~  397 (398)
                      -+||||||+.|+|+|||+|+|+++|+++||+++..||        +|||++...+||+|||||+||++||+||||++
T Consensus       129 ~~CFNC~g~~hsLrdC~rp~d~s~I~r~rkek~~~rn--------qry~~~teq~re~h~KPG~lS~~~R~al~l~~  197 (485)
T KOG2673|consen  129 DPCFNCGGTPHSLRDCPRPFDFSRIQRARKEKMVFRN--------QRYYQDTEQGREDHFKPGVLSGNTRSALGLSP  197 (485)
T ss_pred             ccccccCCCCCccccCCCccccHHHHHHHHhhccccc--------eeeeeecchhhhcccCCcccchhHHHhhcCCC
Confidence            4599999999999999999999999999999998876        49999987779999999999999999999987

>smart00581 PSP proline-rich domain in spliceosome associated proteins

Probab=97.83  E-value=1e-05  Score=62.67  Aligned_cols=21  Identities=33%  Similarity=0.702  Sum_probs=19.8

Q ss_pred             CCCCCCCCCCHHHHHhhCCCC
Q 015904          377 YDGLRPGALDAETRQLLGLGV  397 (398)
Q Consensus       377 f~~fKPG~LS~eLReALGL~~  397 (398)
                      |.+||||+||++||+|||+.+
T Consensus         1 ~~~~kPG~lS~~LR~ALG~~~   21 (54)
T smart00581        1 FKHFKPGRISDELREALGLPP   21 (54)
T ss_pred             CCCccCCcCCHHHHHHcCCCC
Confidence            689999999999999999986

>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=97.47  E-value=6.4e-05  Score=46.36  Aligned_cols=18  Identities=50%  Similarity=1.315  Sum_probs=16.6

Q ss_pred             CccccCCCCCCCCCCCCC
Q 015904          321 SRCFNCGSYSHSLKECPK  338 (398)
Q Consensus       321 ~rCFNCGs~eHsLrDCP~  338 (398)
                      ..|||||..+|..++||+
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            479999999999999995

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 ....

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

Probab=97.18  E-value=0.00021  Score=54.29  Aligned_cols=18  Identities=39%  Similarity=0.733  Sum_probs=16.6

Q ss_pred             CCCCCCHHHHHhhCCCCC
Q 015904          381 RPGALDAETRQLLGLGVS  398 (398)
Q Consensus       381 KPG~LS~eLReALGL~~~  398 (398)
                      |||+||++||+||||++.
T Consensus         1 kPG~lS~~LR~ALg~~~~   18 (48)
T PF04046_consen    1 KPGKLSDELREALGMQEN   18 (48)
T ss_pred             CCcccCHHHHHHcCCCCC
Confidence            799999999999999873

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

Probab=96.33  E-value=0.0017  Score=67.74  Aligned_cols=63  Identities=21%  Similarity=0.401  Sum_probs=51.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhhhccCCCCCCCcceEecCCCCcCCCCCCCCCCHHHHHhhCCCC
Q 015904          333 LKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQNSAGGKYDGLRPGALDAETRQLLGLGV  397 (398)
Q Consensus       333 LrDCP~PRD~arIs~~RkeF~~krnq~~g~r~~~RYh~~e~eqrf~~fKPG~LS~eLReALGL~~  397 (398)
                      +++||.|+| ++|+..|++++..-..-+....+.|||......+++.+++|.|| +..++|+.++
T Consensus         1 ~~~cp~~~n-~~i~~~~d~~~e~~~eis~q~~~e~~~d~~~d~~~~r~esg~i~-~qqd~l~~te   63 (485)
T KOG2673|consen    1 MKDCPMPRN-ARISEKRDEYMEACGEISNQNFQERLHDELVDERRGRFESGVIS-EQQDLLGVTE   63 (485)
T ss_pred             CCcCCCccc-cccCcchhHHHHHhhhcCCcchhhhccchhhhhhhccccccccc-hHHHHhhccc
Confidence            579999999 99999999999864422233466899888888999999999999 6778887665

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=92.68  E-value=0.043  Score=40.63  Aligned_cols=20  Identities=55%  Similarity=1.057  Sum_probs=18.2

Q ss_pred             CCCccccCCCCCCCCCCCCC
Q 015904          319 DASRCFNCGSYSHSLKECPK  338 (398)
Q Consensus       319 ~~~rCFNCGs~eHsLrDCP~  338 (398)
                      ....||+||..+|..++||+
T Consensus        30 lp~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   30 LPRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             cChhhcCCCCcCcCHhHcCC
Confidence            46889999999999999995

>smart00343 ZnF_C2HC zinc finger

Probab=91.74  E-value=0.084  Score=34.22  Aligned_cols=19  Identities=42%  Similarity=1.235  Sum_probs=16.5

Q ss_pred             ccccCCCCCCCCCCCCCCC
Q 015904          322 RCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       322 rCFNCGs~eHsLrDCP~PR  340 (398)
                      .||+||..+|..++||+..
T Consensus         1 ~C~~CG~~GH~~~~C~~~~   19 (26)
T smart00343        1 KCYNCGKEGHIARDCPKXX   19 (26)
T ss_pred             CCccCCCCCcchhhCCccc
Confidence            5999999999999999543

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

Probab=91.00  E-value=0.11  Score=49.27  Aligned_cols=22  Identities=41%  Similarity=1.073  Sum_probs=18.7

Q ss_pred             cccCCCccccCCCCCCCCCCCC
Q 015904          316 IIDDASRCFNCGSYSHSLKECP  337 (398)
Q Consensus       316 i~~~~~rCFNCGs~eHsLrDCP  337 (398)
                      +....+.|||||.-+|..+|||
T Consensus        56 ~~~~~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          56 IREENPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             ccccccccchhcccCcccccCC
Confidence            3445689999999999999999

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

Probab=88.93  E-value=0.26  Score=43.01  Aligned_cols=22  Identities=36%  Similarity=0.925  Sum_probs=14.4

Q ss_pred             CCccccCCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPRD  341 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PRD  341 (398)
                      ...||||+..+|..++||.+++
T Consensus        27 ~~~C~~Cg~~GH~~~~Cp~~~~   48 (148)
T PTZ00368         27 ARPCYKCGEPGHLSRECPSAPG   48 (148)
T ss_pred             CccCccCCCCCcCcccCcCCCC
Confidence            4567777766677777766653

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

Probab=88.75  E-value=0.23  Score=43.28  Aligned_cols=20  Identities=35%  Similarity=1.022  Sum_probs=18.2

Q ss_pred             CccccCCCCCCCCCCCCCCC
Q 015904          321 SRCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       321 ~rCFNCGs~eHsLrDCP~PR  340 (398)
                      +.||||+...|..++||.+.
T Consensus         1 ~~C~~C~~~GH~~~~c~~~~   20 (148)
T PTZ00368          1 MVCYRCGGVGHQSRECPNSA   20 (148)
T ss_pred             CcCCCCCCCCcCcccCcCCC
Confidence            47999999999999999965

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

Probab=88.48  E-value=0.23  Score=51.12  Aligned_cols=21  Identities=43%  Similarity=0.710  Sum_probs=19.2

Q ss_pred             CCCCCCCCCHHHHHhhCCCCC
Q 015904          378 DGLRPGALDAETRQLLGLGVS  398 (398)
Q Consensus       378 ~~fKPG~LS~eLReALGL~~~  398 (398)
                      .+=+||.||++||+||||.++
T Consensus       276 k~krPG~IS~eLrealgi~~g  296 (429)
T COG5182         276 KKKRPGAISAELREALGIDSG  296 (429)
T ss_pred             hccCCcchHHHHHHHhCCCCC
Confidence            778999999999999999874

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=87.55  E-value=0.24  Score=35.13  Aligned_cols=21  Identities=29%  Similarity=0.882  Sum_probs=18.5

Q ss_pred             CCccccCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PR  340 (398)
                      .-.|+-|+..+|.++|||.-+
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~~~   28 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPTNK   28 (32)
T ss_pred             CCEeecCCCCCccHhHCCCCC
Confidence            468999999999999999843

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

Probab=81.38  E-value=0.64  Score=49.16  Aligned_cols=25  Identities=28%  Similarity=0.453  Sum_probs=21.0

Q ss_pred             CCcCCCCCCCCCCHHHHHhhCCCCC
Q 015904          374 GGKYDGLRPGALDAETRQLLGLGVS  398 (398)
Q Consensus       374 eqrf~~fKPG~LS~eLReALGL~~~  398 (398)
                      +-+..+=+||.||++||.||||.+.
T Consensus       265 e~~~k~k~PG~iS~eLr~aLgmp~g  289 (500)
T KOG2330|consen  265 EAMVKEKKPGDISDELRIALGMPVG  289 (500)
T ss_pred             HHHHhhcCccchhHHHHHHhCCCCC
Confidence            3446888999999999999999753

---

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	398
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	3e-04
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	4e-04

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 10/25 (40%), Positives = 11/25 (44%)

Query: 318 DDASRCFNCGSYSHSLKECPKPRDK 342
               RC+NCG   H  KEC  P   
Sbjct: 5   SSGDRCYNCGGLDHHAKECKLPPQP 29

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 1/45 (2%)

Query: 322 RCFNCGSYSHSLKECPKPRDKDAVNNARKQ-HKSKRNQNSASRNP 365
           RC+NCG   H  KEC  P      +  +   H        A + P
Sbjct: 26  RCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQGP 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	398
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.5
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	97.39
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	96.92
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	96.54
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	96.53
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	96.33
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	96.07
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	96.03
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	95.86
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	95.72
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	95.4
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	95.26
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	95.14
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	95.08
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	95.03
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	95.02
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	94.92
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	94.84
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	94.49
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	94.22
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	94.05
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	93.37
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	92.79
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	92.24
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	90.78
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	90.33
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	89.62

>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=97.50  E-value=3.6e-05  Score=50.68  Aligned_cols=22  Identities=45%  Similarity=1.081  Sum_probs=19.7

Q ss_pred             CCccccCCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPRD  341 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PRD  341 (398)
                      ...|||||.+.|..++||.||-
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=96.92  E-value=0.00043  Score=49.37  Aligned_cols=23  Identities=35%  Similarity=0.735  Sum_probs=21.0

Q ss_pred             CCCccccCCCCCCCCCCCCCCCC
Q 015904          319 DASRCFNCGSYSHSLKECPKPRD  341 (398)
Q Consensus       319 ~~~rCFNCGs~eHsLrDCP~PRD  341 (398)
                      ....|||||..+|-.+|||+++.
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            46899999999999999999974

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

Probab=96.54  E-value=0.00095  Score=46.00  Aligned_cols=19  Identities=47%  Similarity=1.209  Sum_probs=16.8

Q ss_pred             ccccCCCCCCCCCCCCCCC
Q 015904          322 RCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       322 rCFNCGs~eHsLrDCP~PR  340 (398)
                      .|||||.++|..++||.|+
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            6999999999999999884

>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=96.53  E-value=0.0011  Score=47.73  Aligned_cols=21  Identities=48%  Similarity=1.137  Sum_probs=15.9

Q ss_pred             CCccccCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PR  340 (398)
                      ...|||||..+|..++||.|+
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            356888888888888888774

>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=96.33  E-value=0.0013  Score=49.78  Aligned_cols=25  Identities=32%  Similarity=0.598  Sum_probs=21.6

Q ss_pred             ccCCCccccCCCCCCCCCCCCCCCC
Q 015904          317 IDDASRCFNCGSYSHSLKECPKPRD  341 (398)
Q Consensus       317 ~~~~~rCFNCGs~eHsLrDCP~PRD  341 (398)
                      ......|||||..+|--+|||+++.
T Consensus        20 ~~~~~~C~~Cge~GH~ardCp~~~~   44 (56)
T 1u6p_A           20 QLDRDQCAYCKEKGHWAKDCPKKPR   44 (56)
T ss_dssp             TCCTTBCSSSCCBSSCGGGCTTCCC
T ss_pred             CCCCCcceeCCCCCcccccCcCCcc
Confidence            3446899999999999999999864

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

Probab=96.07  E-value=0.0025  Score=43.39  Aligned_cols=18  Identities=39%  Similarity=1.056  Sum_probs=12.9

Q ss_pred             ccccCCCCCCCCCCCCCC
Q 015904          322 RCFNCGSYSHSLKECPKP  339 (398)
Q Consensus       322 rCFNCGs~eHsLrDCP~P  339 (398)
                      .|||||..+|..++||.|
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=96.03  E-value=0.0024  Score=47.89  Aligned_cols=19  Identities=47%  Similarity=1.099  Sum_probs=9.8

Q ss_pred             ccccCCCCCCCCCCCCCCC
Q 015904          322 RCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       322 rCFNCGs~eHsLrDCP~PR  340 (398)
                      .|||||.+.|..++||.++
T Consensus         6 ~C~~Cg~~GH~a~~C~~~~   24 (61)
T 2ihx_A            6 LCYTCGSPGHYQAQCPKKR   24 (61)
T ss_dssp             BCSSSCCBTCCGGGCTTTT
T ss_pred             cccccCCCCeehhhCcCCc
Confidence            4555555555555555543

>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=95.86  E-value=0.0033  Score=45.81  Aligned_cols=20  Identities=45%  Similarity=1.089  Sum_probs=13.9

Q ss_pred             CCccccCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKP  339 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~P  339 (398)
                      ...|||||..+|..++||.|
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=95.72  E-value=0.005  Score=46.55  Aligned_cols=19  Identities=53%  Similarity=1.268  Sum_probs=11.3

Q ss_pred             CccccCCCCCCCCCCCCCC
Q 015904          321 SRCFNCGSYSHSLKECPKP  339 (398)
Q Consensus       321 ~rCFNCGs~eHsLrDCP~P  339 (398)
                      ..|||||.+.|..++||.|
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            4466666666666666654

>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=95.40  E-value=0.0077  Score=44.54  Aligned_cols=22  Identities=27%  Similarity=0.510  Sum_probs=19.9

Q ss_pred             CCccccCCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPRD  341 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PRD  341 (398)
                      ...||+||...|..+|||.+++
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

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

Probab=95.26  E-value=0.0085  Score=41.18  Aligned_cols=19  Identities=47%  Similarity=1.186  Sum_probs=17.4

Q ss_pred             CCccccCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPK  338 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~  338 (398)
                      ...|||||..+|..++||+
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

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

Probab=95.14  E-value=0.0069  Score=48.66  Aligned_cols=22  Identities=32%  Similarity=0.800  Sum_probs=20.3

Q ss_pred             CCCccccCCCCCCCCCCCCCCC
Q 015904          319 DASRCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       319 ~~~rCFNCGs~eHsLrDCP~PR  340 (398)
                      ....|+|||..+|.-+|||++|
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            3578999999999999999998

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

Probab=95.08  E-value=0.01  Score=46.59  Aligned_cols=21  Identities=48%  Similarity=1.141  Sum_probs=16.1

Q ss_pred             CCccccCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PR  340 (398)
                      ...|||||.+.|..++||.++
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            467888888888888888664

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

Probab=95.03  E-value=0.0077  Score=45.05  Aligned_cols=23  Identities=30%  Similarity=0.679  Sum_probs=19.4

Q ss_pred             CCccccCCCCCCCCCCCCCCCCH
Q 015904          320 ASRCFNCGSYSHSLKECPKPRDK  342 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PRD~  342 (398)
                      ...|||||...|..+|||.++..
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

>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=95.02  E-value=0.004  Score=46.08  Aligned_cols=22  Identities=32%  Similarity=0.806  Sum_probs=0.0

Q ss_pred             CccccCCCCCCCCCCCCCCCCH
Q 015904          321 SRCFNCGSYSHSLKECPKPRDK  342 (398)
Q Consensus       321 ~rCFNCGs~eHsLrDCP~PRD~  342 (398)
                      ..|||||.+.|..++||.+++.
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            3699999999999999998753

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

Probab=94.92  E-value=0.0086  Score=45.20  Aligned_cols=20  Identities=40%  Similarity=1.032  Sum_probs=17.7

Q ss_pred             CCccccCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKP  339 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~P  339 (398)
                      ...||.||.++|.+++||..
T Consensus         7 ~~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            7 GYTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             SCCCTTTCCTTSCGGGCSGG
T ss_pred             CCccccCCCcCcccccCCCC
Confidence            46799999999999999953

>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=94.84  E-value=0.01  Score=43.21  Aligned_cols=22  Identities=27%  Similarity=0.886  Sum_probs=19.5

Q ss_pred             CCccccCCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPRD  341 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PRD  341 (398)
                      ...||+||..+|..++||.++.
T Consensus        33 ~~~C~~Cg~~GH~~~~C~~~~~   54 (55)
T 1a1t_A           33 KKGCWKCGKEGHQMKDCTERQA   54 (55)
T ss_dssp             CCBCTTTCCBSSCGGGCSSSCC
T ss_pred             CCEeCCCCCcCCccCCCcCcCC
Confidence            4689999999999999998763

>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=94.49  E-value=0.013  Score=50.99  Aligned_cols=22  Identities=45%  Similarity=1.103  Sum_probs=18.2

Q ss_pred             CCccccCCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPRD  341 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PRD  341 (398)
                      ..+|||||.+.|..++||.|..
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            4679999999999999998654

>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=94.22  E-value=0.017  Score=41.51  Aligned_cols=21  Identities=29%  Similarity=0.963  Sum_probs=18.7

Q ss_pred             CCccccCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PR  340 (398)
                      ...||+||..+|..++||...
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            367999999999999999864

>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=94.05  E-value=0.02  Score=43.17  Aligned_cols=21  Identities=33%  Similarity=0.755  Sum_probs=19.1

Q ss_pred             CCccccCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PR  340 (398)
                      ...|||||...|..+|||.++
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            578999999999999999764

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

Probab=93.37  E-value=0.028  Score=38.18  Aligned_cols=18  Identities=33%  Similarity=0.778  Sum_probs=16.7

Q ss_pred             CccccCCCCCCCCCCCCC
Q 015904          321 SRCFNCGSYSHSLKECPK  338 (398)
Q Consensus       321 ~rCFNCGs~eHsLrDCP~  338 (398)
                      ..||+||..+|..++||.
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

>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=92.79  E-value=0.039  Score=47.90  Aligned_cols=24  Identities=25%  Similarity=0.678  Sum_probs=19.4

Q ss_pred             CCccccCCCCCCCCCCCCCCCCHH
Q 015904          320 ASRCFNCGSYSHSLKECPKPRDKD  343 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PRD~a  343 (398)
                      ...||+||...|..++||...-.+
T Consensus       119 ~~~C~~Cg~~GH~~r~Cp~~~~~~  142 (148)
T 3ts2_A          119 PKKCHFCQSINHMVASCPLKAQQG  142 (148)
T ss_dssp             CCCCTTTCCSSCCGGGCTTTTC--
T ss_pred             CCcccccCCcCCEeccCcCCCCCC
Confidence            468999999999999999765443

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

Probab=92.24  E-value=0.052  Score=42.58  Aligned_cols=21  Identities=33%  Similarity=0.755  Sum_probs=18.8

Q ss_pred             CCccccCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PR  340 (398)
                      ...||+||...|..++||...
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

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

Probab=90.78  E-value=0.061  Score=43.15  Aligned_cols=21  Identities=33%  Similarity=0.664  Sum_probs=17.1

Q ss_pred             CCCccccCCCCCCCCCCCCCC
Q 015904          319 DASRCFNCGSYSHSLKECPKP  339 (398)
Q Consensus       319 ~~~rCFNCGs~eHsLrDCP~P  339 (398)
                      +...|||||+.+|.-++||.+
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=90.33  E-value=0.13  Score=42.59  Aligned_cols=21  Identities=29%  Similarity=0.763  Sum_probs=18.7

Q ss_pred             CCCccccCCCCCCCCCCCCCC
Q 015904          319 DASRCFNCGSYSHSLKECPKP  339 (398)
Q Consensus       319 ~~~rCFNCGs~eHsLrDCP~P  339 (398)
                      ....|||||+.+|..+|||+.
T Consensus       104 ~~~~Cy~Cg~~GH~a~dCp~~  124 (124)
T 2lli_A          104 HTIYCYNCGGKGHFGDDCKEK  124 (124)
T ss_dssp             CCCCTTTTSSSCTTTTTSCCC
T ss_pred             CCCCcCCCCCCCcCcccCcCC
Confidence            357999999999999999973

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

Probab=89.62  E-value=0.15  Score=42.16  Aligned_cols=19  Identities=37%  Similarity=0.852  Sum_probs=11.3

Q ss_pred             CccccCCCC-CCCCCCCCCC
Q 015904          321 SRCFNCGSY-SHSLKECPKP  339 (398)
Q Consensus       321 ~rCFNCGs~-eHsLrDCP~P  339 (398)
                      ..|||||.. +|..++||.+
T Consensus        23 ~~C~~Cg~~~gH~~~~C~~~   42 (124)
T 2lli_A           23 IICSYCGATDDHYSRHCPKA   42 (124)
T ss_dssp             CCCTTTCCTTTCCTTTGGGS
T ss_pred             CcCcCCCCcCCccCcccCCc
Confidence            356666665 5666666553

---

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	398
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	4e-05
d1nc8a_	29	g.40.1.1 (A:) HIV nucleocapsid {Human immunodefici	0.004

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

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 = 38.3 bits (89), Expect = 4e-05
 Identities = 10/21 (47%), Positives = 13/21 (61%)

Query: 322 RCFNCGSYSHSLKECPKPRDK 342
           +CFNCG   H+ + C  PR K
Sbjct: 3   KCFNCGKEGHTARNCRAPRKK 23

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 29

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]

 Score = 32.5 bits (74), Expect = 0.004
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 322 RCFNCGSYSHSLKECPKPRDK 342
           RC+NCG   HS ++C  PR +
Sbjct: 8   RCWNCGKEGHSARQCRAPRRQ 28

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	398
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.19
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.12
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	93.97
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	91.83

>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=97.19  E-value=6.8e-05  Score=51.82  Aligned_cols=20  Identities=45%  Similarity=1.203  Sum_probs=15.6

Q ss_pred             CccccCCCCCCCCCCCCCCC
Q 015904          321 SRCFNCGSYSHSLKECPKPR  340 (398)
Q Consensus       321 ~rCFNCGs~eHsLrDCP~PR  340 (398)
                      .+|||||..+|..+|||.||
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~   21 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPR   21 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCC
T ss_pred             CccccCCCcCcCcccCcCCC
Confidence            46888888888888888775

>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=97.12  E-value=7.5e-05  Score=48.94  Aligned_cols=22  Identities=45%  Similarity=1.081  Sum_probs=20.0

Q ss_pred             CCccccCCCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKPRD  341 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~PRD  341 (398)
                      ...|||||-+.|..|+|--||-
T Consensus         6 ~ikCfNCGkeGH~ar~CrAPRk   27 (29)
T d1nc8a_           6 VIRCWNCGKEGHSARQCRAPRR   27 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSSS
T ss_pred             eeEeecCCccchhhhhccCccc
Confidence            4689999999999999999984

>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=93.97  E-value=0.012  Score=40.11  Aligned_cols=20  Identities=30%  Similarity=0.954  Sum_probs=17.8

Q ss_pred             CCccccCCCCCCCCCCCCCC
Q 015904          320 ASRCFNCGSYSHSLKECPKP  339 (398)
Q Consensus       320 ~~rCFNCGs~eHsLrDCP~P  339 (398)
                      ...||+||..+|..++||+.
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