Citrus Sinensis ID: 036141

---

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
Protein Sequence
MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQASQAVVAS
Secondary Structure (PSIPRED)
ccEEcccccHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHEHccccHHHHHHHcccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcc
Coil and Loop (DISEMBL)
MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYnqdntakrSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSnlmnrdlspslDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWkskgrdmrqvqcfsckEYRHIVVKCAKKFCnyckkpghiikecptrpqncqasqavvas
Flexible Loop (DISEMBL)
MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEqskrdqflmKLRPKYEAArsnlmnrdlsPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKFCNYCKKPghiikecptrpqNCQASQAVVAS
Low Complexity Region (SEG)
MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQASQAVVAS
Disordered region (IsUnstruct)
**WIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQ*********************************SLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKEC****************
Disordered Region (DISOPRED)
MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELL***********************************************************NYCKKPGHIIKECPT**************
Disordered Region (DISEMBL)
MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAH*********QVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKECPTR*************
Disordered Region (DISPRO)
*TWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQRLATQT********************************************AKKFCNYCKKPGHIIKECPTRPQN**********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQASQAVVAS
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

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	220
147783659	845	hypothetical protein VITISV_041689 [Viti	0.954	0.248	0.539	6e-66
147793835	1303	hypothetical protein VITISV_031057 [Viti	0.954	0.161	0.536	6e-66
359484000	1689	PREDICTED: uncharacterized protein LOC10	0.954	0.124	0.534	5e-65
147780419	1308	hypothetical protein VITISV_015686 [Viti	0.968	0.162	0.528	3e-64
147806416	1162	hypothetical protein VITISV_031906 [Viti	0.940	0.178	0.528	4e-63
147866201	1157	hypothetical protein VITISV_037079 [Viti	0.9	0.171	0.513	1e-58
147839099	369	hypothetical protein VITISV_007963 [Viti	0.890	0.531	0.492	6e-58
147770281	1652	hypothetical protein VITISV_021584 [Viti	0.945	0.125	0.515	4e-57
147802545	958	hypothetical protein VITISV_007221 [Viti	0.85	0.195	0.5	6e-53
147846218	2116	hypothetical protein VITISV_033373 [Viti	0.854	0.088	0.483	2e-51

>gi|147783659|emb|CAN74794.1| hypothetical protein VITISV_041689 [Vitis vinifera]

 Score =  256 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 117/217 (53%), Positives = 158/217 (72%), Gaps = 7/217 (3%)

Query: 1   MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQN 60
           M+W++GS++  ++ +L+ H++A+ MW YLKKVY+QDN A+R  LE+ IA +  G+LSIQ+
Sbjct: 66  MSWLLGSVEPHIVTHLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIAMFQHGSLSIQD 125

Query: 61  YFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDL 120
           Y+S F  LW EY D++   VPI +L+ +Q +H  ++RDQFLMKLRP+YE+ RS+L+NR  
Sbjct: 126 YYSAFLTLWHEYADLVTADVPIAALSTIQXIHATTRRDQFLMKLRPEYESVRSSLLNRSP 185

Query: 121 SPSLDVCFKELLREEQRLATQTILQQNKMHD--NAIAYAAAHWKSKGRDM--RQVQCFSC 176
            PSLD+CF ELLREEQRL+TQ IL+Q+        +AYAA   + +G  M  + +QCF C
Sbjct: 186 VPSLDICFGELLREEQRLSTQAILEQSHGSSGTTTVAYAA---QGRGPPMHSKNLQCFCC 242

Query: 177 KEYRHIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQA 213
           KEY HI   C KKFC+YCKK GHIIKEC  RPQN QA
Sbjct: 243 KEYGHIAATCPKKFCSYCKKKGHIIKECRIRPQNRQA 279

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147793835|emb|CAN71164.1| hypothetical protein VITISV_031057 [Vitis vinifera]

 Score =  256 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 117/218 (53%), Positives = 158/218 (72%), Gaps = 8/218 (3%)

Query: 1   MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQN 60
           M+W++GS++  ++ +L+ H++A+ MW YLKKVY+QDN A+R  LE+ IA +  G+LSIQ+
Sbjct: 208 MSWLLGSVEPHIVTHLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIAMFQHGSLSIQD 267

Query: 61  YFSGFQNLWAEYVDMIYVQVP-IESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRD 119
           Y+S F  LW EY D++   VP I +L+ +Q +H  ++RDQFLMKLRP+YE+ RS+L+NR 
Sbjct: 268 YYSAFLTLWHEYADLVTADVPIIATLSTIQTIHATTRRDQFLMKLRPEYESVRSSLLNRS 327

Query: 120 LSPSLDVCFKELLREEQRLATQTILQQNKMHD--NAIAYAAAHWKSKGRDM--RQVQCFS 175
             PSLD+CF ELLREEQRL+TQ IL+Q+        +AYAA   + +G  M  + +QCF 
Sbjct: 328 PVPSLDICFGELLREEQRLSTQAILEQSHGSSGTTTVAYAA---QGRGPPMHSKNLQCFC 384

Query: 176 CKEYRHIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQA 213
           CKEY HI   C KKFC+YCKK GHIIKEC  RPQN QA
Sbjct: 385 CKEYGHIAATCPKKFCSYCKKKGHIIKECRIRPQNRQA 422

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359484000|ref|XP_003633051.1| PREDICTED: uncharacterized protein LOC100854333 [Vitis vinifera]

 Score =  253 bits (645), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 116/217 (53%), Positives = 157/217 (72%), Gaps = 7/217 (3%)

Query: 1   MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQN 60
           M+W++GS++  ++ +L+ H++A+ MW YLKKVY+QDN A+R  LE+ IA +  G+LSIQ+
Sbjct: 66  MSWLLGSVEPHIVTHLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIAMFQHGSLSIQD 125

Query: 61  YFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDL 120
           Y+S F  LW EY D++   VPI +L+ +Q +H  ++RDQFLMKLR +YE+ RS+L+NR  
Sbjct: 126 YYSAFLTLWHEYADLVTADVPIAALSTIQTIHATTRRDQFLMKLRLEYESVRSSLLNRSP 185

Query: 121 SPSLDVCFKELLREEQRLATQTILQQNKMHDNA--IAYAAAHWKSKGRDM--RQVQCFSC 176
            PSLD+CF ELLREEQRL+TQ IL+Q+        +AYAA   + +G  M  + +QCF C
Sbjct: 186 VPSLDICFGELLREEQRLSTQAILEQSHGSSGTAIVAYAA---QGRGPPMHSKNLQCFCC 242

Query: 177 KEYRHIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQA 213
           KEY HI   C KKFC+YCKK GHIIKEC  RPQN QA
Sbjct: 243 KEYGHIAATCPKKFCSYCKKKGHIIKECRIRPQNRQA 279

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147780419|emb|CAN67992.1| hypothetical protein VITISV_015686 [Vitis vinifera]

 Score =  250 bits (638), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 113/214 (52%), Positives = 152/214 (71%), Gaps = 1/214 (0%)

Query: 1   MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQN 60
           M+W++GS++  ++ +L+ H++A+ MW YLKKVY+QDN A+R  LE+ IA +  G+LSIQ+
Sbjct: 55  MSWLIGSVEPHIVTHLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIAMFQHGSLSIQD 114

Query: 61  YFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDL 120
           Y+S F  LW EY D++   VPI +L+ +Q +H  ++RDQFLMKL P+YE+ RS+L+NR  
Sbjct: 115 YYSAFLTLWHEYADLVTTDVPIAALSTIQTIHVTTRRDQFLMKLCPEYESVRSSLLNRSP 174

Query: 121 SPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYA-AAHWKSKGRDMRQVQCFSCKEY 179
            PSLD+CF ELLREEQRL+TQ IL+Q+         A AA  +      + +QCF CKEY
Sbjct: 175 VPSLDICFGELLREEQRLSTQAILEQSHGSSGTTTVAYAAQGREPPMHSKNLQCFCCKEY 234

Query: 180 RHIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQA 213
            HI   C KKFC+YCKK GHIIKEC  RPQN QA
Sbjct: 235 GHIAATCPKKFCSYCKKKGHIIKECRIRPQNRQA 268

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147806416|emb|CAN76550.1| hypothetical protein VITISV_031906 [Vitis vinifera]

 Score =  246 bits (629), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 110/208 (52%), Positives = 151/208 (72%), Gaps = 1/208 (0%)

Query: 1   MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQN 60
           ++W++GSI   ++ NL+   TAK+MWEYL+++YNQDN A    LE EIA ++QGNLSI+ 
Sbjct: 36  VSWLLGSIKPHMVNNLRSFSTAKEMWEYLRRIYNQDNNACCFQLELEIAYFTQGNLSIEQ 95

Query: 61  YFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDL 120
           Y+SGF NLW EY  +IY +VP E L+ +Q V+E+S+ DQFLMKLR +YE  ++ L+ R+ 
Sbjct: 96  YYSGFLNLWGEYSGIIYAKVPKEVLSALQTVYEESRCDQFLMKLRAEYETTQAGLLKRNP 155

Query: 121 SPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYR 180
            P+LD+C  ELLREEQRLATQ  + Q ++H   +  A A  + +GR+  Q+QC+SCKE+ 
Sbjct: 156 VPTLDICLGELLREEQRLATQAEMGQERLHSEIVNVAYAT-QGRGREKGQIQCYSCKEFG 214

Query: 181 HIVVKCAKKFCNYCKKPGHIIKECPTRP 208
           HI   C K +CNYC+K GHIIKECP RP
Sbjct: 215 HIATSCTKPYCNYCRKRGHIIKECPIRP 242

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147866201|emb|CAN81968.1| hypothetical protein VITISV_037079 [Vitis vinifera]

 Score =  232 bits (591), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 111/216 (51%), Positives = 140/216 (64%), Gaps = 18/216 (8%)

Query: 1   MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQN 60
           MTWI+ S++   +LNL+ +KT   MW YL  VYNQDN+A+R  LEYE+A ++QG+LSI+ 
Sbjct: 73  MTWILSSVEPHFVLNLRPYKTVATMWNYLHTVYNQDNSARRFQLEYEMANFTQGSLSIEE 132

Query: 61  YFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDL 120
           YFSGFQ LW +Y D++Y  VP  +L+ VQ VH  SKRDQFLMKLRP +E ARSNLMNR L
Sbjct: 133 YFSGFQTLWIDYSDIVYANVPAAALSVVQAVHATSKRDQFLMKLRPDFEIARSNLMNRHL 192

Query: 121 SPSLDVCFKELLREEQRLATQTILQQ--NKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKE 178
            PSL+ C  ELLREEQ + TQ  ++   N     ++AY                CFSCK+
Sbjct: 193 VPSLNACLSELLREEQHIVTQATMEHRANVSAPVSVAY----------------CFSCKD 236

Query: 179 YRHIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQAS 214
           +  I   C KKFCNY KK GHII  C  RP+  Q +
Sbjct: 237 FGQIARDCPKKFCNYYKKQGHIISVCLIRPKRKQGT 272

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147839099|emb|CAN61564.1| hypothetical protein VITISV_007963 [Vitis vinifera]

 Score =  229 bits (584), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 105/213 (49%), Positives = 142/213 (66%), Gaps = 17/213 (7%)

Query: 1   MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQN 60
           M+W++ S++  ++ +L+ H++A+ MW YLKKVY+QDN A+R  LE+ I  +  G+LSIQ+
Sbjct: 1   MSWLLSSVEPHIVTHLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIVMFQHGSLSIQD 60

Query: 61  YFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDL 120
           Y+S F   W EY D++   VPI++L+ +Q +H  + RDQFLMKLRP+YE+ RS+L+NR  
Sbjct: 61  YYSAFLTFWHEYADLVTADVPIDALSTIQTIHATTLRDQFLMKLRPEYESVRSSLLNRSH 120

Query: 121 SPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYR 180
            PSLD+CF ELLREEQ L+TQ I++Q+               S G       CF  KEY 
Sbjct: 121 VPSLDICFGELLREEQHLSTQAIMEQSH-------------GSSG----TATCFCYKEYE 163

Query: 181 HIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQA 213
           HI   C KK C+YCKK GHIIKEC  RPQN QA
Sbjct: 164 HIAATCPKKLCSYCKKKGHIIKECLIRPQNRQA 196

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147770281|emb|CAN67539.1| hypothetical protein VITISV_021584 [Vitis vinifera]

 Score =  226 bits (577), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 113/219 (51%), Positives = 155/219 (70%), Gaps = 11/219 (5%)

Query: 1   MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQN 60
           M+W++GS++  ++ +L+ H +A+ MW YLKKVY+QDN A+R  L++ IA +  G+LSIQ+
Sbjct: 160 MSWLLGSVEPHIVTHLRPHCSAQSMWAYLKKVYHQDNDARRFQLDHAIAMFQHGSLSIQD 219

Query: 61  YFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDL 120
           Y+S F  LW EY D++   VPI +L+ +Q +H  ++RDQFLMKLR KYE+  S+L+N+  
Sbjct: 220 YYSTFLTLWHEYADLVTADVPIAALSTIQTIHTTTQRDQFLMKLRSKYESVCSSLLNKSH 279

Query: 121 SPSLDVCFKELLREEQRLATQTILQQNKMHDN----AIAYAAAHWKSKGRDM--RQVQCF 174
            PSLD+ F ELLR+EQRL+TQ IL+Q+  H N     +AYAA   + +G  M  + +QCF
Sbjct: 280 VPSLDIFFGELLRKEQRLSTQAILEQS--HGNYGTTTVAYAA---QGRGPRMHSKNLQCF 334

Query: 175 SCKEYRHIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQA 213
            CKEY HI   C KKFC+YCKK GHIIKEC  RPQN Q 
Sbjct: 335 CCKEYGHIAATCPKKFCSYCKKKGHIIKECRIRPQNRQT 373

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147802545|emb|CAN77664.1| hypothetical protein VITISV_007221 [Vitis vinifera]

 Score =  213 bits (541), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 108/216 (50%), Positives = 135/216 (62%), Gaps = 29/216 (13%)

Query: 1   MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQN 60
           MTWI+ S++  L+LN + +KT   MW YL  VYNQDN+A+R  LE E A ++QG+LSI+ 
Sbjct: 63  MTWILSSVEPHLVLNQRPYKTVAVMWNYLHTVYNQDNSARRFQLECEKANFTQGSLSIEE 122

Query: 61  YFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDL 120
           YF                            +H  SKRDQFLMKLRP +E ARSN+MNR  
Sbjct: 123 YFFA--------------------------MHATSKRDQFLMKLRPDFEIARSNMMNRHH 156

Query: 121 SPSLDVCFKELLREEQRLATQTILQQ--NKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKE 178
            PSLDVC  ELLREEQR+ TQ  ++   N     ++AYAA   ++KG+DMR VQCFSCK+
Sbjct: 157 VPSLDVCLSELLREEQRIVTQATMEHRANVSAPVSVAYAA-QGQNKGQDMRVVQCFSCKD 215

Query: 179 YRHIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQAS 214
           + HI   C KKFCNYCKK GHII  CP RP+  Q +
Sbjct: 216 FDHIARDCPKKFCNYCKKQGHIISVCPIRPERKQGT 251

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147846218|emb|CAN79492.1| hypothetical protein VITISV_033373 [Vitis vinifera]

 Score =  207 bits (528), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 102/211 (48%), Positives = 137/211 (64%), Gaps = 23/211 (10%)

Query: 1    MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQN 60
            M+W++GS+   ++  L+ H++A+ MW YLKKVY+QDN A+R  LE+ IA           
Sbjct: 885  MSWLLGSVKPHIVTYLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIAM---------- 934

Query: 61   YFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDL 120
                FQ++ A+        VPI +L+ +Q +H  ++RDQFLMKLR +YE+ RS+L+NR  
Sbjct: 935  ----FQHVTAD--------VPIAALSTIQTIHATTRRDQFLMKLRSEYESVRSSLLNRSH 982

Query: 121  SPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYA-AAHWKSKGRDMRQVQCFSCKEY 179
             PSLD+CF ELLREEQRL+TQ IL+Q+      +  A AA  +      + +QCF CKEY
Sbjct: 983  VPSLDICFGELLREEQRLSTQAILEQSHGSSGTVTVAYAAQGRGPPMHSKNLQCFCCKEY 1042

Query: 180  RHIVVKCAKKFCNYCKKPGHIIKECPTRPQN 210
             HI V C KKFC+YCKK GHIIKEC  RPQN
Sbjct: 1043 GHIAVTCPKKFCSYCKKKGHIIKECRIRPQN 1073

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	220
TAIR|locus:2014907	237	AT1G21280 "AT1G21280" [Arabido	0.572	0.531	0.289	3.2e-08
UNIPROTKB|P69730	486	gag "Gag polyprotein" [Equine	0.681	0.308	0.276	0.00051

TAIR|locus:2014907 AT1G21280 "AT1G21280" [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 3.2e-08, P = 3.2e-08
 Identities = 40/138 (28%), Positives = 63/138 (45%)

Query:     1 MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQN 60
             M W+M S+   L+ ++   +TA  MWE L++V+      K   L   +A   QG  S++ 
Sbjct:    87 MYWLMNSMTDKLLESVMYAETAHKMWEDLRRVFVPCVDLKIYQLRRRLATLRQGGDSVEE 146

Query:    61 YFSGFQNLWAEYVDMIYVQVP--------IESLADVQEVHEQSKRDQFLM--KLRPKYEA 110
             YF     +W E  +  Y  +P         E     +E  E+ +R +FLM  KL   +EA
Sbjct:   147 YFGKLSKVWMELSE--YAPIPECKCGGCNCECTKRAEEAREKEQRYEFLMGLKLNQGFEA 204

Query:   111 ARSNLMNRDLSPSLDVCF 128
               + +M +   PSL   F
Sbjct:   205 VTTKIMFQKPPPSLHEAF 222

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|P69730 gag "Gag polyprotein" [Equine infectious anemia virus (CLONE 1369) (taxid:11670)]

 Score = 113 (44.8 bits), Expect = 0.00051, P = 0.00051
 Identities = 44/159 (27%), Positives = 69/159 (43%)

Query:    54 GNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARS 113
             G    QN   G +  + E+VD +  Q  I+S    QE+   SK     + ++   E  R 
Sbjct:   270 GKPKAQNIRQGAKEPYPEFVDRLLSQ--IKSEGHPQEI---SKFLTDTLTIQNANEECR- 323

Query:   114 NLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQ- 172
             N M R L P   +  K     +     Q ++   K     +A        KG  ++  Q 
Sbjct:   324 NAM-RHLRPEDTLEEKMYACRDIGTTKQKMMLLAKALQTGLAGPFKGGALKGGPLKAAQT 382

Query:   173 CFSCKEYRHIVVKC-AKKFCNYCKKPGHIIKECPTRPQN 210
             C++C +  H+  +C A K C  CK+PGH  K+C + P+N
Sbjct:   383 CYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRSVPKN 421


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.131   0.398    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      220       220   0.00094  112 3  11 22  0.49    32
                                                     32  0.40    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  617 (66 KB)
  Total size of DFA:  212 KB (2118 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  24.51u 0.15s 24.66t   Elapsed:  00:00:02
  Total cpu time:  24.51u 0.15s 24.66t   Elapsed:  00:00:02
  Start:  Sat May 11 01:54:01 2013   End:  Sat May 11 01:54:03 2013

GO:0005515 "protein binding" evidence=IPI

---

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	220
pfam14244	135	pfam14244, UBN2_3, gag-polypeptide of LTR copia-ty	4e-07
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	2e-04
pfam14223	119	pfam14223, UBN2, gag-polypeptide of LTR copia-type	6e-04
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	0.004

>gnl|CDD|222621 pfam14244, UBN2_3, gag-polypeptide of LTR copia-type

 Score = 47.4 bits (113), Expect = 4e-07
 Identities = 21/52 (40%), Positives = 35/52 (67%)

Query: 21  TAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEY 72
           TAK++W+ LK+ ++  NT++   L+ EIAR  QG LS+  Y++  ++LW E 
Sbjct: 69  TAKEVWDALKERFSDGNTSRVFELKREIARLKQGGLSVTEYYNKLKSLWEEL 120

This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type. Length = 135

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 7/49 (14%)

Query: 168 MRQVQCFSCKEYRHIVVKC-------AKKFCNYCKKPGHIIKECPTRPQ 209
            +   C+ C E  H+  +C        ++ C  C K GH+ +ECP  P 
Sbjct: 25  AKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPP 73

Length = 148

>gnl|CDD|222605 pfam14223, UBN2, gag-polypeptide of LTR copia-type

 Score = 37.9 bits (89), Expect = 6e-04
 Identities = 31/126 (24%), Positives = 54/126 (42%), Gaps = 20/126 (15%)

Query: 20  KTAKDMWEYLKKVYNQDNTAKRSHL-----EYEIARYSQGNLSIQNYFSGFQNLWAEYVD 74
           KTAK+ W+ LK +Y   +  K + L     E+E  +   G  SI +Y      +  +   
Sbjct: 1   KTAKEAWDALKTMYEGSDRVKEARLQTLRREFENLKMKDG-ESIDDYLDRLSEIVNK--- 56

Query: 75  MIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNL-MNRDLSP-SLDVCFKELL 132
                  + SL +     +  +  + L  L  KYE   +++  ++DLS  +L+     L 
Sbjct: 57  -------LRSLGEKISDEDVVE--KILRSLPEKYEQIVTSIEESKDLSTLTLEELVGRLK 107

Query: 133 REEQRL 138
             E+RL
Sbjct: 108 AHEERL 113

This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type. Length = 119

>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

 Score = 36.8 bits (85), Expect = 0.004
 Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 2/46 (4%)

Query: 168 MRQVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKECPTRPQ--NC 211
                CF+C +  H+   C    C  C   GH    CP   +  NC
Sbjct: 58  EENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNC 103

Length = 190

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	220
PF14223	119	UBN2: gag-polypeptide of LTR copia-type	99.82
PF14227	119	UBN2_2: gag-polypeptide of LTR copia-type	99.79
PF14244	152	UBN2_3: gag-polypeptide of LTR copia-type	99.44
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.79
PF03732	96	Retrotrans_gag: Retrotransposon gag protein ; Inte	98.29
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	98.22
PF13696	32	zf-CCHC_2: Zinc knuckle	98.09
PTZ00368	148	universal minicircle sequence binding protein (UMS	97.83
PTZ00368	148	universal minicircle sequence binding protein (UMS	97.59
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	97.38
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	97.33
smart00343	26	ZnF_C2HC zinc finger.	97.26
PF13917	42	zf-CCHC_3: Zinc knuckle	97.24
KOG0119	554	consensus Splicing factor 1/branch point binding p	96.95
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	96.79
PF03564	145	DUF1759: Protein of unknown function (DUF1759); In	96.72
PF14392	49	zf-CCHC_4: Zinc knuckle	96.62
PF15288	40	zf-CCHC_6: Zinc knuckle	96.56
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	95.71
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	95.64
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	95.02
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.89
PF02023	95	SCAN: SCAN domain; InterPro: IPR003309 A number of	90.63
PF00607	206	Gag_p24: gag gene protein p24 (core nucleocapsid p	84.83
PF14893	331	PNMA: PNMA	83.84
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	83.77
KOG0314	448	consensus Predicted E3 ubiquitin ligase [Posttrans	83.63
PF12353	128	eIF3g: Eukaryotic translation initiation factor 3	83.09
COG1198	730	PriA Primosomal protein N' (replication factor Y)	81.3

>PF14223 UBN2: gag-polypeptide of LTR copia-type

Probab=99.82  E-value=1.9e-19  Score=126.28  Aligned_cols=110  Identities=25%  Similarity=0.417  Sum_probs=99.2

Q ss_pred             ccHHHHHHHHHHHhccCCh---hHHhHHHHHHHHHh-cCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHH
Q 036141           20 KTAKDMWEYLKKVYNQDNT---AKRSHLEYEIARYS-QGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQS   95 (220)
Q Consensus        20 ~ta~~~w~~L~~~f~~~~~---~~~~~l~~~~~~~~-q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~   95 (220)
                      +||+++|+.|+..|.+.+.   +++..|+.+|..++ ++++||.+|+.+|..|+++|..+ |.++++           ..
T Consensus         1 ~tA~e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~-g~~i~d-----------~~   68 (119)
T PF14223_consen    1 KTAKEAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAI-GKPISD-----------ED   68 (119)
T ss_pred             ChHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhc-CCcccc-----------hh
Confidence            5899999999999999999   99999999999998 67999999999999999999966 776654           66


Q ss_pred             HHHHHHhhccchHHHHHHhhcCCCCCC--CHHHHHHHHHHHHHHHHHH
Q 036141           96 KRDQFLMKLRPKYEAARSNLMNRDLSP--SLDVCFKELLREEQRLATQ  141 (220)
Q Consensus        96 ~~~~~l~gLp~~~~~~~~~l~~~~~~~--sl~e~~~~l~~~e~~~~~~  141 (220)
                      .|..+|.|||++|+.++..+....+..  |+++++..|..+|.++...
T Consensus        69 ~v~~iL~~Lp~~y~~~~~~i~~~~~~~~~t~~el~~~L~~~E~~~~~~  116 (119)
T PF14223_consen   69 LVSKILRSLPPSYDTFVTAIRNSKDLPKMTLEELISRLLAEEMRLKSK  116 (119)
T ss_pred             HHHHHHhcCCchhHHHHHHHHhcCCCCcCCHHHHHHHHHHHHHHHHHc
Confidence            666699999999999999999987776  9999999999999988763

>PF14227 UBN2_2: gag-polypeptide of LTR copia-type

Probab=99.79  E-value=1.6e-18  Score=121.47  Aligned_cols=111  Identities=25%  Similarity=0.357  Sum_probs=96.8

Q ss_pred             cccHHHHHHHHHHHhccCChhHHhHHHHHHHHHh-cCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHH
Q 036141           19 HKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYS-QGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKR   97 (220)
Q Consensus        19 ~~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~-q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~   97 (220)
                      ++||+++|+.|+..|...+.+....+.++|...+ .++.+|.+|+.+|..++++|..+ |.+++++.++.+         
T Consensus         1 ~~ta~~~W~~L~~~y~~~~~~~~~~l~~kl~~~k~~~~~~v~~hi~~~~~l~~~L~~~-g~~i~d~~~~~~---------   70 (119)
T PF14227_consen    1 CKTAKEMWDKLKKKYEKKSFANKIYLLRKLYSLKMDEGGSVRDHINEFRSLVNQLKSL-GVPIDDEDKVII---------   70 (119)
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhHhccchhHHHHHHHHHHHHHhhccc-cccchHHHHHHH---------
Confidence            5799999999999999999888888888877766 56889999999999999999966 887776555555         


Q ss_pred             HHHHhhccchHHHHHHhhcCCC--CCCCHHHHHHHHHHHHHHHHHH
Q 036141           98 DQFLMKLRPKYEAARSNLMNRD--LSPSLDVCFKELLREEQRLATQ  141 (220)
Q Consensus        98 ~~~l~gLp~~~~~~~~~l~~~~--~~~sl~e~~~~l~~~e~~~~~~  141 (220)
                        +|.+||++|++++.++....  ..+++++++..|..+|.++...
T Consensus        71 --lL~sLP~sy~~~~~~l~~~~~~~~~tl~~v~~~L~~ee~~~~~~  114 (119)
T PF14227_consen   71 --LLSSLPPSYDSFVTALLYSKPEDELTLEEVKSKLLQEEERRKKS  114 (119)
T ss_pred             --HHHcCCHhHHHHHHHHHccCCCCCcCHHHHHHHHHHHHHHHHhc
Confidence              99999999999999987754  7899999999999999887754

>PF14244 UBN2_3: gag-polypeptide of LTR copia-type

Probab=99.44  E-value=1.7e-13  Score=100.02  Aligned_cols=75  Identities=27%  Similarity=0.656  Sum_probs=70.8

Q ss_pred             CccccccchHHHHhhccccccHHHHHHHHHHHhccCC-hhHHhHHHHHHHHHhcCCccHHHHHHHHHHHH--HHHhhc
Q 036141            1 MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDN-TAKRSHLEYEIARYSQGNLSIQNYFSGFQNLW--AEYVDM   75 (220)
Q Consensus         1 ~s~i~~sl~~~~~~~~~~~~ta~~~w~~L~~~f~~~~-~~~~~~l~~~~~~~~q~~~sv~~y~~~~~~l~--~~L~~~   75 (220)
                      ++||+++|+++|...|..++||+++|+.|+++|...+ .+++++|+.+|...+|++.||.+|+.+|+.|+  .+|..+
T Consensus        63 ~swl~~sis~~i~~~i~~~~tak~~W~~L~~~f~~~~~~~r~~~L~~~l~~~kq~~~sv~ey~~~lk~l~~~~el~~~  140 (152)
T PF14244_consen   63 LSWLLNSISPDILSTIIFCETAKEIWDALKERFSQKSNASRVFQLRNELHSLKQGDKSVTEYFNKLKSLWQEDELDEY  140 (152)
T ss_pred             HHHHHHhhcHHHHhhhHhhhhHHHHHHHHHHHhhcccHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHhHHHHHhCc
Confidence            5799999999999999999999999999999999888 89999999999999999999999999999999  667654

>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=98.79  E-value=3e-09  Score=48.11  Aligned_cols=17  Identities=47%  Similarity=1.239  Sum_probs=16.0

Q ss_pred             cccccCCCCcccCCCCC
Q 036141          190 FCNYCKKPGHIIKECPT  206 (220)
Q Consensus       190 ~C~~Cgk~GH~~~~C~~  206 (220)
                      .||+||+.||++++||+
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            69999999999999985

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 ....

>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes

Probab=98.29  E-value=1.9e-06  Score=57.37  Aligned_cols=71  Identities=21%  Similarity=0.368  Sum_probs=54.7

Q ss_pred             cccHHHHHHHHHHHhccCChhHHhHHHHHHHHHhcCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHHH
Q 036141           19 HKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRD   98 (220)
Q Consensus        19 ~~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (220)
                      ..|..++-..|.+.|.+..  ....++.+|..++|+++||.+|+.+|+.|+..+..    ..           +++.++.
T Consensus        26 ~~~W~~~~~~~~~~f~~~~--~~~~~~~~l~~l~Q~~esv~~y~~rf~~l~~~~~~----~~-----------~e~~~v~   88 (96)
T PF03732_consen   26 FITWEEFKDAFRKRFFPPD--RKEQARQELNSLRQGNESVREYVNRFRELARRAPP----PM-----------DEEMLVE   88 (96)
T ss_pred             CCCHHHHHHHHHHHHhhhh--ccccchhhhhhhhccCCcHHHHHHHHHHHHHHCCC----Cc-----------CHHHHHH
Confidence            3466777777777776532  34567788999999999999999999999988862    11           5677788


Q ss_pred             HHHhhccc
Q 036141           99 QFLMKLRP  106 (220)
Q Consensus        99 ~~l~gLp~  106 (220)
                      .|+.||.|
T Consensus        89 ~f~~GL~~   96 (96)
T PF03732_consen   89 RFIRGLRP   96 (96)
T ss_pred             HHHHCCCC
Confidence            89999975

Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.

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

Probab=98.22  E-value=8.1e-07  Score=65.46  Aligned_cols=40  Identities=30%  Similarity=0.875  Sum_probs=33.0

Q ss_pred             CCCcccccCCCCCccccccc---------C----------ccccccCCCCcccCCC-CCC
Q 036141          168 MRQVQCFSCKEYRHIVVKCA---------K----------KFCNYCKKPGHIIKEC-PTR  207 (220)
Q Consensus       168 ~~~~~~~~~~~~g~~~~~~~---------~----------~~C~~Cgk~GH~~~~C-~~k  207 (220)
                      ..+..|++|+..||.+++|+         .          ++|++||..||++++| |.+
T Consensus        58 ~~~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~  117 (190)
T COG5082          58 EENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSK  117 (190)
T ss_pred             ccccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCccccccCccc
Confidence            34667999999999999888         1          2799999999999999 443

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=98.09  E-value=1.4e-06  Score=44.98  Aligned_cols=21  Identities=38%  Similarity=0.956  Sum_probs=18.2

Q ss_pred             ccccccCCCCcccCCCCCCCC
Q 036141          189 KFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       189 ~~C~~Cgk~GH~~~~C~~k~~  209 (220)
                      -.|+.|+++||+.++||...+
T Consensus         9 Y~C~~C~~~GH~i~dCP~~~P   29 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPTNKP   29 (32)
T ss_pred             CEeecCCCCCccHhHCCCCCC
Confidence            379999999999999998443

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

Probab=97.83  E-value=1.1e-05  Score=58.61  Aligned_cols=36  Identities=33%  Similarity=0.970  Sum_probs=21.9

Q ss_pred             ccccCCCCCcccccccCc--------cccccCCCCcccCCCCCC
Q 036141          172 QCFSCKEYRHIVVKCAKK--------FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       172 ~~~~~~~~g~~~~~~~~~--------~C~~Cgk~GH~~~~C~~k  207 (220)
                      .|+.|+..||..+.|+..        .||.|+..||++++||..
T Consensus        79 ~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~  122 (148)
T PTZ00368         79 SCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNA  122 (148)
T ss_pred             ccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCc
Confidence            466666666666655432        466666666666666653

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

Probab=97.59  E-value=6.7e-05  Score=54.41  Aligned_cols=37  Identities=35%  Similarity=0.987  Sum_probs=22.6

Q ss_pred             ccccCCCCCcccccccCc-------cccccCCCCcccCCCCCCC
Q 036141          172 QCFSCKEYRHIVVKCAKK-------FCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       172 ~~~~~~~~g~~~~~~~~~-------~C~~Cgk~GH~~~~C~~k~  208 (220)
                      .|+.|+..||....|+..       .|+.|++.||++++|+.+.
T Consensus        54 ~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~~~   97 (148)
T PTZ00368         54 SCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRA   97 (148)
T ss_pred             ccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCCcc
Confidence            466666666666555443       4666666666666666643

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A

Probab=97.38  E-value=9.7e-05  Score=38.88  Aligned_cols=25  Identities=24%  Similarity=0.457  Sum_probs=16.6

Q ss_pred             cccccCCCCcccCCCCCCCCCCcCC
Q 036141          190 FCNYCKKPGHIIKECPTRPQNCQAS  214 (220)
Q Consensus       190 ~C~~Cgk~GH~~~~C~~k~~~~~~~  214 (220)
                      .|+.|||-.|++.+|+.+.+..++.
T Consensus         4 ~CprC~kg~Hwa~~C~sk~d~~G~p   28 (36)
T PF14787_consen    4 LCPRCGKGFHWASECRSKTDVDGNP   28 (36)
T ss_dssp             C-TTTSSSCS-TTT---TCCCCCEE
T ss_pred             cCcccCCCcchhhhhhhhhcccCCC
Confidence            5999999999999999988766543

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=97.33  E-value=0.00015  Score=57.70  Aligned_cols=41  Identities=34%  Similarity=0.801  Sum_probs=36.7

Q ss_pred             cccccCCCCCccccccc---CccccccCCCCcccCCCCCCCCCC
Q 036141          171 VQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQNC  211 (220)
Q Consensus       171 ~~~~~~~~~g~~~~~~~---~~~C~~Cgk~GH~~~~C~~k~~~~  211 (220)
                      ..|+.|++.||....|+   ...|+.|++.||..++||......
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~~~~~~  187 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPSKQKSK  187 (261)
T ss_pred             CccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCcccccc
Confidence            45999999999999999   779999999999999999877553

>smart00343 ZnF_C2HC zinc finger

Probab=97.26  E-value=0.00012  Score=36.40  Aligned_cols=18  Identities=44%  Similarity=1.084  Sum_probs=16.0

Q ss_pred             cccccCCCCcccCCCCCC
Q 036141          190 FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       190 ~C~~Cgk~GH~~~~C~~k  207 (220)
                      .|++||+.||++++||..
T Consensus         1 ~C~~CG~~GH~~~~C~~~   18 (26)
T smart00343        1 KCYNCGKEGHIARDCPKX   18 (26)
T ss_pred             CCccCCCCCcchhhCCcc
Confidence            499999999999999843

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=97.24  E-value=0.0002  Score=39.67  Aligned_cols=19  Identities=37%  Similarity=0.885  Sum_probs=17.0

Q ss_pred             CccccccCCCCcccCCCCC
Q 036141          188 KKFCNYCKKPGHIIKECPT  206 (220)
Q Consensus       188 ~~~C~~Cgk~GH~~~~C~~  206 (220)
                      ...|.+|++.||+..+|++
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            3469999999999999996

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=96.95  E-value=0.0022  Score=53.93  Aligned_cols=45  Identities=27%  Similarity=0.583  Sum_probs=37.9

Q ss_pred             ccCCCCCCcccccCCCCCcccccccCc------cccccCCCCcccCCCCCC
Q 036141          163 SKGRDMRQVQCFSCKEYRHIVVKCAKK------FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       163 ~~~~~~~~~~~~~~~~~g~~~~~~~~~------~C~~Cgk~GH~~~~C~~k  207 (220)
                      +..+...+..|..|+..||+.-.|+..      .|++||-.||++.+|+..
T Consensus       254 gt~r~~d~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~  304 (554)
T KOG0119|consen  254 GTLRDDDNRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVN  304 (554)
T ss_pred             CCCCccccccccccCCCccccccCCcccccccccccccCCcccccccCCCc
Confidence            444555567899999999998788765      899999999999999987

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

Probab=96.79  E-value=0.00081  Score=49.84  Aligned_cols=37  Identities=30%  Similarity=0.798  Sum_probs=31.6

Q ss_pred             cccccCCCCCcccccc-cC----ccccccCCCCcccCCCCCC
Q 036141          171 VQCFSCKEYRHIVVKC-AK----KFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       171 ~~~~~~~~~g~~~~~~-~~----~~C~~Cgk~GH~~~~C~~k  207 (220)
                      ..|+.|+..||.+++| +.    +.|+.|+..+|.+++||.-
T Consensus        98 ~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~s~~Cp~~  139 (190)
T COG5082          98 KKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSEDCPSI  139 (190)
T ss_pred             cccccccccCccccccCcccccCcceeccCCCccccccCccc
Confidence            6799999999999999 33    2699999999999999863

>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function

Probab=96.72  E-value=0.0093  Score=42.88  Aligned_cols=96  Identities=14%  Similarity=0.162  Sum_probs=64.3

Q ss_pred             cccccchHHHHhhcccc----ccHHHHHHHHHHHhccCChhHHhHHHHHHHHHh---c-CCccHHHHHHHHHHHHHHHhh
Q 036141            3 WIMGSIDQSLILNLKLH----KTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYS---Q-GNLSIQNYFSGFQNLWAEYVD   74 (220)
Q Consensus         3 ~i~~sl~~~~~~~~~~~----~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~---q-~~~sv~~y~~~~~~l~~~L~~   74 (220)
                      +|...|..+-...|..+    .+-..+|..|+++|+...... ..+..++....   + +...+..+++.+..++..|..
T Consensus        33 ~L~~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~~i~-~~~~~~l~~l~~~~~~d~~~L~~~~~~v~~~i~~L~~  111 (145)
T PF03564_consen   33 YLRSCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPRRII-QALLEELRNLPPISNDDPEALRSLVDKVNNCIRALKA  111 (145)
T ss_pred             HHHHHhcchHHHHHHcccccchhhHHHHHHHHHHhCCchHHH-HHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555543    456899999999999654322 33344444444   2 368899999999999999997


Q ss_pred             cccccCCcccHHHHHHHHHHHHHHHHHhhccchHHHH
Q 036141           75 MIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAA  111 (220)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~gLp~~~~~~  111 (220)
                      + |..+.+           ...+..|+..||+....-
T Consensus       112 l-g~~~~~-----------~~l~~~i~~KLp~~~~~~  136 (145)
T PF03564_consen  112 L-GVNVDD-----------PLLISIILSKLPPEIREK  136 (145)
T ss_pred             c-CCCCCC-----------HHHHHHHHHHCCHHHHHH
Confidence            6 765543           334555999999874443

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=96.62  E-value=0.00066  Score=39.30  Aligned_cols=17  Identities=53%  Similarity=1.110  Sum_probs=16.0

Q ss_pred             cccccCCCCcccCCCCC
Q 036141          190 FCNYCKKPGHIIKECPT  206 (220)
Q Consensus       190 ~C~~Cgk~GH~~~~C~~  206 (220)
                      .|++||..||...+||.
T Consensus        33 ~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   33 FCFHCGRIGHSDKECPK   49 (49)
T ss_pred             hhcCCCCcCcCHhHcCC
Confidence            79999999999999984

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=96.56  E-value=0.0023  Score=34.80  Aligned_cols=23  Identities=30%  Similarity=0.554  Sum_probs=18.9

Q ss_pred             ccccccCCCCccc--CCCCCCCCCC
Q 036141          189 KFCNYCKKPGHII--KECPTRPQNC  211 (220)
Q Consensus       189 ~~C~~Cgk~GH~~--~~C~~k~~~~  211 (220)
                      .+|..||..||..  +.||.+....
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~~~~   26 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYCWSG   26 (40)
T ss_pred             ccccccccccccccCccCCCCCCCC
Confidence            3799999999998  6799887553

>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=95.71  E-value=0.0092  Score=26.72  Aligned_cols=17  Identities=47%  Similarity=1.065  Sum_probs=15.1

Q ss_pred             ccccCCCCCcccccccC
Q 036141          172 QCFSCKEYRHIVVKCAK  188 (220)
Q Consensus       172 ~~~~~~~~g~~~~~~~~  188 (220)
                      .|++|++.||.+++|++
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            59999999999988874

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 ....

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=95.64  E-value=0.0046  Score=48.73  Aligned_cols=20  Identities=45%  Similarity=0.833  Sum_probs=17.9

Q ss_pred             ccccccCCCCcccCCCCCCC
Q 036141          189 KFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       189 ~~C~~Cgk~GH~~~~C~~k~  208 (220)
                      ..|+.|||.|||.++||...
T Consensus       161 ~~cyrcGkeghwskEcP~~~  180 (346)
T KOG0109|consen  161 SGCYRCGKEGHWSKECPVDR  180 (346)
T ss_pred             HHheeccccccccccCCccC
Confidence            37999999999999999754

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=95.02  E-value=0.019  Score=45.67  Aligned_cols=45  Identities=29%  Similarity=0.745  Sum_probs=35.9

Q ss_pred             CCCCcccccCCCCCccccccc--CccccccCCCCcccCCCCCCCCCC
Q 036141          167 DMRQVQCFSCKEYRHIVVKCA--KKFCNYCKKPGHIIKECPTRPQNC  211 (220)
Q Consensus       167 ~~~~~~~~~~~~~g~~~~~~~--~~~C~~Cgk~GH~~~~C~~k~~~~  211 (220)
                      ......|..|+..+|....|.  ...|++|+..||++++|+......
T Consensus        69 ~~~~~~c~~~g~~~~~~~~~~~~~~~c~~C~~~gH~~~~c~~~~~~~  115 (261)
T KOG4400|consen   69 ECPEVSCYICGEKGHLGRRCTRIAAACFNCGEGGHIERDCPEAGKEG  115 (261)
T ss_pred             CCCCceeeecCCCCchhhcCcccchhhhhCCCCccchhhCCcccCcc
Confidence            345667999999998877766  468999999999999999876554

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=94.89  E-value=0.013  Score=46.36  Aligned_cols=22  Identities=36%  Similarity=0.856  Sum_probs=19.0

Q ss_pred             ccccccCCCCcccCCCCCCCCC
Q 036141          189 KFCNYCKKPGHIIKECPTRPQN  210 (220)
Q Consensus       189 ~~C~~Cgk~GH~~~~C~~k~~~  210 (220)
                      -.||.||..|||...||..++.
T Consensus       177 Y~CyRCGqkgHwIqnCpTN~Dp  198 (427)
T COG5222         177 YVCYRCGQKGHWIQNCPTNQDP  198 (427)
T ss_pred             eeEEecCCCCchhhcCCCCCCC
Confidence            3799999999999999976643

>PF02023 SCAN: SCAN domain; InterPro: IPR003309 A number of C2H2-zinc finger proteins contain a highly conserved N-terminal motif termed the SCAN domain

Probab=90.63  E-value=3.6  Score=27.31  Aligned_cols=79  Identities=15%  Similarity=0.197  Sum_probs=50.7

Q ss_pred             HHHHHHHh-cCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHHHHHHhhccchHHHHHHhhcCCCCCCC
Q 036141           45 EYEIARYS-QGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPS  123 (220)
Q Consensus        45 ~~~~~~~~-q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~gLp~~~~~~~~~l~~~~~~~s  123 (220)
                      ++.|.... +.+++..+++.++..|+.+=-.  + .+     ....++.|-..+.+||..||++....+.   ... .-|
T Consensus         6 r~~FR~~~~~~~~~p~e~~~rL~~l~~~WL~--p-e~-----~tkeqi~ellvlEQFL~~lP~e~~~wV~---e~~-p~s   73 (95)
T PF02023_consen    6 RQRFRSFQYQEGEGPREFLSRLRELCDRWLQ--P-EV-----HTKEQILELLVLEQFLNILPPEVQTWVR---ERK-PES   73 (95)
T ss_dssp             HHHHHT--CCTTTSHHHHHHHHHHHHHHHH---T-TT-----S-HHHHHHHHHHHHHHHHS-HHHHHHHH---TCS--SS
T ss_pred             HHHHhCCCCCCCCCHHHHHHHHHHHHHHhCc--c-cc-----CcHHHHHHHHHHHHHHHHCCHHHHHHHH---hcC-CCC
Confidence            44576666 4589999999999999877631  2 11     1123346777789999999998665533   333 348


Q ss_pred             HHHHHHHHHHHH
Q 036141          124 LDVCFKELLREE  135 (220)
Q Consensus       124 l~e~~~~l~~~e  135 (220)
                      .++++..+....
T Consensus        74 ~~ea~~Lae~~~   85 (95)
T PF02023_consen   74 AEEAVALAEDYQ   85 (95)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            888877765544

The SCAN domain may play an important role in the assembly and function of this newly defined subclass of transcriptional regulators [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3LHR_B 4E6S_A 2FI2_A 1Y7Q_A.

>PF00607 Gag_p24: gag gene protein p24 (core nucleocapsid protein); InterPro: IPR000721 The Gag protein from retroviruses, also known as p24, forms the inner protein layer of the nucleocapsid

Probab=84.83  E-value=5.3  Score=30.59  Aligned_cols=40  Identities=15%  Similarity=0.287  Sum_probs=29.1

Q ss_pred             cHHHHHHHHHHHhccCChhHHhHHHHHHHHHhcC-CccHHHHHHHHHHHH
Q 036141           21 TAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQG-NLSIQNYFSGFQNLW   69 (220)
Q Consensus        21 ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q~-~~sv~~y~~~~~~l~   69 (220)
                      -+-..|..|...+.+...         |...+|| +|+..+|++||..-+
T Consensus       107 ~ai~Aw~~l~~~~~~~~~---------~~~I~QGp~Epf~dFv~rl~~a~  147 (206)
T PF00607_consen  107 WAIKAWRKLPRKGSPGES---------FTKIKQGPKEPFADFVDRLQKAI  147 (206)
T ss_dssp             HHHHHHHHHHHHHSSSST---------GGGH-S-TTSHHHHHHHHHHHHH
T ss_pred             HHHHhhhccccccccccc---------HHHhhhccccchHHHHHHHHHHH
Confidence            455788899888886532         4456788 999999999998664

This protein performs highly complex orchestrated tasks during the assembly, budding, maturation and infection stages of the viral replication cycle. During viral assembly, the proteins form membrane associations and self-associations that ultimately result in budding of an immature virion from the infected cell. Gag precursors also function during viral assembly to selectively bind and package two plus strands of genomic RNA. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.; GO: 0016032 viral reproduction; PDB: 1BMX_A 1SJH_C 1SJE_C 1U57_A 1FGL_B 1G03_A 2XT1_A 2JO0_A 2L6E_A 2HJL_C ....

>PF14893 PNMA: PNMA

Probab=83.84  E-value=17  Score=30.10  Aligned_cols=53  Identities=23%  Similarity=0.330  Sum_probs=41.8

Q ss_pred             cccHHHHHHHHHHHhccCChhHHhHHHHHHHHHhc-CCccHHHHHHHHHHHHHHHh
Q 036141           19 HKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQ-GNLSIQNYFSGFQNLWAEYV   73 (220)
Q Consensus        19 ~~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q-~~~sv~~y~~~~~~l~~~L~   73 (220)
                      ..|+.+..+.|...|..+..  ...+..+|..+.| .+|+|.+|+.++..++++.-
T Consensus       229 ~~t~~~~l~aL~~~Fg~~es--~~~~~~kf~~~~Q~~~E~ls~yv~RlE~lLqkav  282 (331)
T PF14893_consen  229 KQTAQDCLKALGQVFGSSES--RETLEAKFLNTFQEPGEKLSAYVKRLESLLQKAV  282 (331)
T ss_pred             CCCHHHHHHHHHHhcCCccc--HHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHH
Confidence            45888999999999985544  3455666766666 59999999999999999863

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]

Probab=83.77  E-value=0.37  Score=40.19  Aligned_cols=23  Identities=39%  Similarity=0.806  Sum_probs=19.5

Q ss_pred             ccccccCCCCcccCCCCCCCCCC
Q 036141          189 KFCNYCKKPGHIIKECPTRPQNC  211 (220)
Q Consensus       189 ~~C~~Cgk~GH~~~~C~~k~~~~  211 (220)
                      +.|-|||-.||...+||+....+
T Consensus       571 kGCayCgGLGHRItdCPKle~~~  593 (610)
T KOG0341|consen  571 KGCAYCGGLGHRITDCPKLEAQQ  593 (610)
T ss_pred             cccccccCCCcccccCchhhhhc
Confidence            36999999999999999876443

>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=83.63  E-value=0.75  Score=39.14  Aligned_cols=38  Identities=34%  Similarity=0.791  Sum_probs=29.0

Q ss_pred             cccccCCCCCcccccccC-------ccccccCCCCcccCCCCCCC
Q 036141          171 VQCFSCKEYRHIVVKCAK-------KFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       171 ~~~~~~~~~g~~~~~~~~-------~~C~~Cgk~GH~~~~C~~k~  208 (220)
                      ..|..|...+|+...+..       .+|+.|+.+|||...||.-.
T Consensus       134 ~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv~  178 (448)
T KOG0314|consen  134 YVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTVS  178 (448)
T ss_pred             ceeeecccCccccccccccCCCCCCcceecCCCCCccceeccccC
Confidence            347777777777665443       38999999999999998644

>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes

Probab=83.09  E-value=0.64  Score=32.72  Aligned_cols=20  Identities=35%  Similarity=0.776  Sum_probs=16.8

Q ss_pred             CccccccCCCCcccCCCCCCC
Q 036141          188 KKFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       188 ~~~C~~Cgk~GH~~~~C~~k~  208 (220)
                      ...|.+|+ -.||...||-|-
T Consensus       106 ~v~CR~Ck-GdH~T~~CPyKd  125 (128)
T PF12353_consen  106 KVKCRICK-GDHWTSKCPYKD  125 (128)
T ss_pred             eEEeCCCC-CCcccccCCccc
Confidence            34799996 999999999764

Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=81.30  E-value=1.1  Score=40.98  Aligned_cols=40  Identities=23%  Similarity=0.554  Sum_probs=27.2

Q ss_pred             CcccccCCCCCcccccc----------cCccccccCCCCcccCCCCCCCCC
Q 036141          170 QVQCFSCKEYRHIVVKC----------AKKFCNYCKKPGHIIKECPTRPQN  210 (220)
Q Consensus       170 ~~~~~~~~~~g~~~~~~----------~~~~C~~Cgk~GH~~~~C~~k~~~  210 (220)
                      ...|..||..-.- +.|          ....|||||........||.--..
T Consensus       435 ~l~C~~Cg~v~~C-p~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~  484 (730)
T COG1198         435 LLLCRDCGYIAEC-PNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE  484 (730)
T ss_pred             eeecccCCCcccC-CCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence            3447777664432 122          233899999999999999986544

---

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	220
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	3e-08
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	5e-08
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	1e-06
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	3e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	9e-05
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	2e-04
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	4e-04
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	3e-04
3gv2_A	342	Ca, fusion protein consisting of capsid protein P2	7e-04
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	7e-04
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	8e-04

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

 Score = 48.4 bits (115), Expect = 3e-08
 Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 4/58 (6%)

Query: 162 KSKGRDMRQVQCFSCKEYRHIVVKC----AKKFCNYCKKPGHIIKECPTRPQNCQASQ 215
             + R  +  +C++C    H   +C      K C++C+   H++  CP + Q   ++Q
Sbjct: 16  SMQKRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQGPSAQ 73

>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 = 47.3 bits (112), Expect = 5e-08
 Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 4/51 (7%)

Query: 169 RQVQCFSCKEYRHIVVKC----AKKFCNYCKKPGHIIKECPTRPQNCQASQ 215
              +C++C    H   +C      K C++C+   H++  CP + Q   ++Q
Sbjct: 6   SGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQGPSAQ 56

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A* Length = 148

 Score = 45.4 bits (107), Expect = 1e-06
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 4/57 (7%)

Query: 163 SKGRDMRQVQCFSCKEYRHIVVKCAK----KFCNYCKKPGHIIKECPTRPQNCQASQ 215
           S+ R     +C++C    H   +C      K C++C+   H++  CP + Q   +SQ
Sbjct: 90  SERRPKGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQQGPSSQ 146

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 39.5 bits (92), Expect = 3e-05
 Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 8/46 (17%)

Query: 173 CFSCKEYRHIVVKC--------AKKFCNYCKKPGHIIKECPTRPQN 210
           C++C    H   +C        +++ C  C   GH  K+C  R  N
Sbjct: 7   CYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGN 52

>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 = 43.3 bits (101), Expect = 3e-05
 Identities = 28/186 (15%), Positives = 63/186 (33%), Gaps = 51/186 (27%)

Query: 11  SLILNLK--------LHKTAKDMWEYLKKVYNQDNTAKR------SHLEYEIARYSQGNL 56
           S+ L LK        LH++  D +   K   + D           SH+ + +        
Sbjct: 430 SIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPER 489

Query: 57  SIQNYFSGFQNLWAEYVDMIYVQVPIE----------SLADVQEVHEQSKRDQFLMKLRP 106
                 + F+ +   ++D  +++  I           S+ +   + +      ++    P
Sbjct: 490 -----MTLFRMV---FLDFRFLEQKIRHDSTAWNASGSILNT--LQQLKFYKPYICDNDP 539

Query: 107 KYEAARSNLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGR 166
           KYE   + +++      L    + L+  +       +L+   M ++   +  AH      
Sbjct: 540 KYERLVNAILD-----FLPKIEENLICSKYT----DLLRIALMAEDEAIFEEAH------ 584

Query: 167 DMRQVQ 172
             +QVQ
Sbjct: 585 --KQVQ 588

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1 Length = 49

 Score = 38.0 bits (88), Expect = 9e-05
 Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 3/46 (6%)

Query: 165 GRDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTR 207
            +  + ++C++C +  H   +C    ++ C  C K GH++ +CP R
Sbjct: 1   AQQRKVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPER 46

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 39.0 bits (90), Expect = 2e-04
 Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 3/46 (6%)

Query: 170 QVQCFSCKEYRHIVVKCAKKFCNYC-KKPGHIIKECPTRPQ--NCQ 212
             +C +C +  H+   C    C+YC     H  + CP   Q   C 
Sbjct: 4   APKCNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKAIQCSKCD 49

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 37.8 bits (87), Expect = 4e-04
 Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 4/47 (8%)

Query: 169 RQVQCFSCKEYRHIVVKCAKKF----CNYCKKPGHIIKECPTRPQNC 211
           + +QC  C E  H   +C  K+    C  CK   H  + CP+  +  
Sbjct: 41  KAIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPSIWRAY 87

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 37.2 bits (86), Expect = 3e-04
 Identities = 12/49 (24%), Positives = 17/49 (34%), Gaps = 11/49 (22%)

Query: 173 CFSCKEYRHIVVKCAKK-----------FCNYCKKPGHIIKECPTRPQN 210
           CF C +  H    C +             C  CK+  H   EC ++  N
Sbjct: 4   CFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKTDN 52

>3gv2_A Ca, fusion protein consisting of capsid protein P24, linker and carbon dioxide-concentrating...; hexameric retroviral capsid; 7.00A {Human immunodeficiency virus type 1} Length = 342

 Score = 38.7 bits (90), Expect = 7e-04
 Identities = 4/48 (8%), Positives = 11/48 (22%), Gaps = 1/48 (2%)

Query: 169 RQVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKECPTRPQNCQASQA 216
             V+        +I    + +F    +     +K       +      
Sbjct: 252 AMVKAGRITIVGYIRAG-SARFTLNIRGDVQEVKTAMAAGIDAINRTE 298

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Length = 37

 Score = 35.3 bits (81), Expect = 7e-04
 Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)

Query: 172 QCFSCKEYRHIVVKC-AKKFCNYCKKPGHIIKECPT 206
            C++C +  H+  +C A K C  CK+PGH  K+C +
Sbjct: 2   TCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Length = 39

 Score = 35.3 bits (81), Expect = 8e-04
 Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 3/38 (7%)

Query: 171 VQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECP 205
           + CF+C +  H    C    ++ C  C    H   +CP
Sbjct: 1   LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCP 38

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	220
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	99.13
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	99.01
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.01
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	98.99
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	98.98
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	98.97
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	98.97
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	98.95
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	98.94
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.66
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.64
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	98.59
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.58
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	98.56
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	98.24
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	98.2
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	98.02
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.83
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.7
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.66
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.65
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.64
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.35
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.31
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.22
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.85
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	96.5
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	95.34
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	94.98
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	94.46
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	94.06
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	92.84
3alr_A	106	Nanos protein; zinc-finger, translational repressi	90.82
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	89.96
2pzo_E	42	CAP-Gly domain-containing linker protein 1; struct	85.62

>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=99.13  E-value=5e-11  Score=68.67  Aligned_cols=42  Identities=29%  Similarity=0.780  Sum_probs=36.7

Q ss_pred             CCCcccccCCCCCcccccccCc---cccccCCCCcccCCCCCCCC
Q 036141          168 MRQVQCFSCKEYRHIVVKCAKK---FCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       168 ~~~~~~~~~~~~g~~~~~~~~~---~C~~Cgk~GH~~~~C~~k~~  209 (220)
                      .+...|++|+..||.+++|+..   .||.||+.||++++||.++.
T Consensus         4 ~r~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~~~~   48 (49)
T 2ec7_A            4 RKVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPERQA   48 (49)
T ss_dssp             CCCCBCTTTCCBTCCTTTCCCSSCCSCSSSCCSSCCGGGCCSSCC
T ss_pred             CCcCeeeecCCCCcChhhCcCCCCCeeCcCCCcCCccCCCcCCCC
Confidence            3456799999999999999864   79999999999999998764

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

Probab=99.01  E-value=2e-10  Score=69.31  Aligned_cols=42  Identities=31%  Similarity=0.711  Sum_probs=35.2

Q ss_pred             CcccccCCCCCcccccccC--------ccccccCCCCcccCCCCCCCCCC
Q 036141          170 QVQCFSCKEYRHIVVKCAK--------KFCNYCKKPGHIIKECPTRPQNC  211 (220)
Q Consensus       170 ~~~~~~~~~~g~~~~~~~~--------~~C~~Cgk~GH~~~~C~~k~~~~  211 (220)
                      ...|++|+..||.+++|+.        ..||.|++.||++++||.++...
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~~~~   53 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGNQ   53 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTTSSSCCCSBCTTTCCBSSCGGGCCCCC---
T ss_pred             CCcccccCCCCeehhhCcCCcCCCCCCCeeCCCCCCCCCcCCCcCCCcCC
Confidence            4569999999999999987        35999999999999999987654

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

Probab=99.01  E-value=3e-10  Score=71.00  Aligned_cols=43  Identities=26%  Similarity=0.793  Sum_probs=37.3

Q ss_pred             CCCcccccCCCCCcccccccC----ccccccCCCCcccCCCCCCCCC
Q 036141          168 MRQVQCFSCKEYRHIVVKCAK----KFCNYCKKPGHIIKECPTRPQN  210 (220)
Q Consensus       168 ~~~~~~~~~~~~g~~~~~~~~----~~C~~Cgk~GH~~~~C~~k~~~  210 (220)
                      .+...|++|+..||..+.|+.    ..||.||+.||++++||.++..
T Consensus        22 ~r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~~~~   68 (74)
T 2li8_A           22 SKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQ   68 (74)
T ss_dssp             STTSCCTTTCCSSSCTTTCSSCCCCCCCTTTCCTTSCGGGCTTGGGT
T ss_pred             CCCCcccccCCcCcCcccCCCCCCCCccCCcCCcCCccCcCcCCcCC
Confidence            345679999999999999984    5899999999999999987743

>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=98.99  E-value=2.3e-10  Score=67.63  Aligned_cols=41  Identities=39%  Similarity=0.865  Sum_probs=35.9

Q ss_pred             CCcccccCCCCCcccccccC---ccccccCCCCcccCCCCCCCC
Q 036141          169 RQVQCFSCKEYRHIVVKCAK---KFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       169 ~~~~~~~~~~~g~~~~~~~~---~~C~~Cgk~GH~~~~C~~k~~  209 (220)
                      +...|+.|+..||.++.|+.   ..||.||+.||++++||.++.
T Consensus        11 ~~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~~~~   54 (55)
T 1a1t_A           11 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA   54 (55)
T ss_dssp             GTCBCTTTCCBSSCGGGCSSCSCCBCTTTCCBSSCGGGCSSSCC
T ss_pred             CCcceeeeCCCCcChhhcCCCCCCEeCCCCCcCCccCCCcCcCC
Confidence            34679999999999999976   479999999999999998654

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

Probab=98.98  E-value=2.9e-10  Score=62.15  Aligned_cols=35  Identities=29%  Similarity=0.744  Sum_probs=32.1

Q ss_pred             ccccCCCCCcccccccC---ccccccCCCCcccCCCCC
Q 036141          172 QCFSCKEYRHIVVKCAK---KFCNYCKKPGHIIKECPT  206 (220)
Q Consensus       172 ~~~~~~~~g~~~~~~~~---~~C~~Cgk~GH~~~~C~~  206 (220)
                      .|++|++.||.+++|+.   ..||.||+.||++++||+
T Consensus         2 ~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSCCCSSCTTTCCSSSCTTTSCC
T ss_pred             eeeccCCCCcccccCCCCCCCccccCCCCCCccCcCcC
Confidence            58999999999999986   489999999999999985

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

Probab=98.97  E-value=3.1e-10  Score=61.30  Aligned_cols=35  Identities=37%  Similarity=1.009  Sum_probs=32.2

Q ss_pred             ccccCCCCCcccccccC-ccccccCCCCcccCCCCC
Q 036141          172 QCFSCKEYRHIVVKCAK-KFCNYCKKPGHIIKECPT  206 (220)
Q Consensus       172 ~~~~~~~~g~~~~~~~~-~~C~~Cgk~GH~~~~C~~  206 (220)
                      .|++|++.||.+++|+. ..||.||++||++++||.
T Consensus         2 ~C~~Cg~~GH~~~~C~~~~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCBTTCSSCCCTTGGGGTTCC
T ss_pred             cccccCCCCcchhhCcCcCeEccCCCcCCccCcCcC
Confidence            58999999999999987 589999999999999984

>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=98.97  E-value=5.3e-10  Score=67.83  Aligned_cols=40  Identities=28%  Similarity=0.835  Sum_probs=35.4

Q ss_pred             CcccccCCCCCcccccccC----ccccccCCCCcccCCCCCCCC
Q 036141          170 QVQCFSCKEYRHIVVKCAK----KFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       170 ~~~~~~~~~~g~~~~~~~~----~~C~~Cgk~GH~~~~C~~k~~  209 (220)
                      ...|++|+..||.+++|+.    ..||.|++.||++++||.++.
T Consensus         7 ~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~~~   50 (63)
T 2cqf_A            7 GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQ   50 (63)
T ss_dssp             CCCCSSSCCSSSCTTTCCSCCCSSCCTTTCCSSSCTTTCTGGGC
T ss_pred             CCcccccCCCCcChhhCCCCCCCCccCCcCCcCCccCcCCCccc
Confidence            4569999999999999983    589999999999999998653

>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=98.95  E-value=5.7e-10  Score=79.57  Aligned_cols=45  Identities=24%  Similarity=0.710  Sum_probs=38.0

Q ss_pred             CCCCcccccCCCCCcccccccC----ccccccCCCCcccCCCCCCCCCC
Q 036141          167 DMRQVQCFSCKEYRHIVVKCAK----KFCNYCKKPGHIIKECPTRPQNC  211 (220)
Q Consensus       167 ~~~~~~~~~~~~~g~~~~~~~~----~~C~~Cgk~GH~~~~C~~k~~~~  211 (220)
                      +.+...|++|+..||.++.|+.    ..||.||+.||++++||.+.+..
T Consensus        94 p~~~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp~~~~~~  142 (148)
T 3ts2_A           94 PKGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQQG  142 (148)
T ss_dssp             CCCSCCCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCTTTTC--
T ss_pred             cCCCCcccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCcCCCCCC
Confidence            3445679999999999999987    58999999999999999886654

>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=98.94  E-value=3.6e-10  Score=68.08  Aligned_cols=42  Identities=29%  Similarity=0.744  Sum_probs=21.3

Q ss_pred             ccccCCCCCcccccccC-----------ccccccCCCCcccCCCCCCCCCCcC
Q 036141          172 QCFSCKEYRHIVVKCAK-----------KFCNYCKKPGHIIKECPTRPQNCQA  213 (220)
Q Consensus       172 ~~~~~~~~g~~~~~~~~-----------~~C~~Cgk~GH~~~~C~~k~~~~~~  213 (220)
                      .|++|+..||.+++|+.           ..||.||+.||++++|+.+....++
T Consensus         3 ~Cf~Cg~~GH~a~~C~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~~~~G~   55 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKTDNQGN   55 (60)
T ss_dssp             --------------------------CCCSCSSCSSCSSCSTTCCCTTSSSSC
T ss_pred             ccccCCCCCcCHhhCcCCCCCccccCCCcceeECCCCCCccCcCCCccccCCC
Confidence            59999999999998865           4699999999999999998865544

>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=98.66  E-value=1.2e-08  Score=55.38  Aligned_cols=24  Identities=42%  Similarity=1.097  Sum_probs=20.2

Q ss_pred             CccccccCCCCcccCCCCCCCCCC
Q 036141          188 KKFCNYCKKPGHIIKECPTRPQNC  211 (220)
Q Consensus       188 ~~~C~~Cgk~GH~~~~C~~k~~~~  211 (220)
                      ...||+||+.||++++||.+....
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~~~~~   33 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKKPRGP   33 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCCCT
T ss_pred             CCeeeECCCCCcchhhCcCCcccC
Confidence            347999999999999999876543

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

Probab=98.59  E-value=3.9e-08  Score=62.67  Aligned_cols=36  Identities=14%  Similarity=0.348  Sum_probs=20.4

Q ss_pred             cccCCCCCcccccccC----ccccccCCCCcccCCCCCCC
Q 036141          173 CFSCKEYRHIVVKCAK----KFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       173 ~~~~~~~g~~~~~~~~----~~C~~Cgk~GH~~~~C~~k~  208 (220)
                      |+.|+..||.++.|..    ..||+||+.||+.++||...
T Consensus        27 cY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~~r   66 (83)
T 3nyb_B           27 AYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKR   66 (83)
T ss_dssp             CCCBC-------------CCCBCSSSSCBSSCGGGCSSCC
T ss_pred             ccccccCCcccccccCCCCCCeecccCCCCcCcccCCccc
Confidence            4455555554433322    37999999999999999865

>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=98.58  E-value=2.9e-08  Score=50.23  Aligned_cols=21  Identities=29%  Similarity=0.578  Sum_probs=18.1

Q ss_pred             CccccccCCCCcccCCCCCCC
Q 036141          188 KKFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       188 ~~~C~~Cgk~GH~~~~C~~k~  208 (220)
                      ..+||+||++||++++|+...
T Consensus         6 ~~~C~nCgk~GH~ar~C~~pr   26 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSS
T ss_pred             CCEEEECCccccCHhHCcccc
Confidence            346999999999999998754

>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=98.56  E-value=3e-08  Score=57.95  Aligned_cols=25  Identities=40%  Similarity=1.050  Sum_probs=20.7

Q ss_pred             cCccccccCCCCcccCCCCCCCCCC
Q 036141          187 AKKFCNYCKKPGHIIKECPTRPQNC  211 (220)
Q Consensus       187 ~~~~C~~Cgk~GH~~~~C~~k~~~~  211 (220)
                      ....||+||+.|||+++||.+....
T Consensus        22 ~~~~C~~Cge~GH~ardCp~~~~~~   46 (56)
T 1u6p_A           22 DRDQCAYCKEKGHWAKDCPKKPRGP   46 (56)
T ss_dssp             CTTBCSSSCCBSSCGGGCTTCCCSS
T ss_pred             CCCcceeCCCCCcccccCcCCcccc
Confidence            3457999999999999999876543

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

Probab=98.24  E-value=3.6e-07  Score=53.16  Aligned_cols=21  Identities=52%  Similarity=0.994  Sum_probs=17.7

Q ss_pred             CccccccCCCCcccCCCCCCC
Q 036141          188 KKFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       188 ~~~C~~Cgk~GH~~~~C~~k~  208 (220)
                      ...||.||++||++++||...
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            346999999999999999543

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

Probab=98.20  E-value=8.6e-07  Score=61.32  Aligned_cols=36  Identities=31%  Similarity=0.748  Sum_probs=22.5

Q ss_pred             ccccCCCC-CcccccccC-ccccccCCCCcccCCCCCC
Q 036141          172 QCFSCKEY-RHIVVKCAK-KFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       172 ~~~~~~~~-g~~~~~~~~-~~C~~Cgk~GH~~~~C~~k  207 (220)
                      .|+.|+.. ||..+.|+. ..|++|++.||++++||..
T Consensus        24 ~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~   61 (124)
T 2lli_A           24 ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHK   61 (124)
T ss_dssp             CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCC
T ss_pred             cCcCCCCcCCccCcccCCcccccccCCCCCccccCcCc
Confidence            46666665 666666655 3566666666666666653

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

Probab=98.02  E-value=4e-06  Score=57.93  Aligned_cols=38  Identities=32%  Similarity=0.719  Sum_probs=34.3

Q ss_pred             cccccCCCCCcccccccC----ccccccCCCCcccCCCCCCC
Q 036141          171 VQCFSCKEYRHIVVKCAK----KFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       171 ~~~~~~~~~g~~~~~~~~----~~C~~Cgk~GH~~~~C~~k~  208 (220)
                      ..|+.|+..||..+.|+.    ..|+.||+.||++++||...
T Consensus        43 ~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~~~~Cp~~~   84 (124)
T 2lli_A           43 IQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPSIW   84 (124)
T ss_dssp             SCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCCTTTCCCST
T ss_pred             ccccccCCCCCccccCcCcccCccCCCCCcCCcchhhCCCcc
Confidence            579999999999999886    47999999999999999764

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

Probab=97.83  E-value=5.4e-06  Score=51.54  Aligned_cols=20  Identities=30%  Similarity=0.509  Sum_probs=17.5

Q ss_pred             CccccccCCCCcccCCCCCC
Q 036141          188 KKFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       188 ~~~C~~Cgk~GH~~~~C~~k  207 (220)
                      ...||+||+.||++++|+..
T Consensus        24 ~~~C~~Cg~~GH~a~~C~~~   43 (74)
T 2li8_A           24 GDRCYNCGGLDHHAKECKLP   43 (74)
T ss_dssp             TSCCTTTCCSSSCTTTCSSC
T ss_pred             CCcccccCCcCcCcccCCCC
Confidence            34799999999999999963

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

Probab=97.70  E-value=1.4e-05  Score=43.26  Aligned_cols=18  Identities=39%  Similarity=0.881  Sum_probs=16.7

Q ss_pred             cccccCCCCcccCCCCCC
Q 036141          190 FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       190 ~C~~Cgk~GH~~~~C~~k  207 (220)
                      .||+||+.||++++||..
T Consensus         2 ~C~~Cg~~GH~a~~C~~~   19 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQP   19 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSC
T ss_pred             eeeccCCCCcccccCCCC
Confidence            599999999999999975

>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=97.66  E-value=2.2e-05  Score=44.74  Aligned_cols=20  Identities=30%  Similarity=0.622  Sum_probs=17.9

Q ss_pred             CccccccCCCCcccCCCCCC
Q 036141          188 KKFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       188 ~~~C~~Cgk~GH~~~~C~~k  207 (220)
                      ...||+||+.||++++||..
T Consensus         6 ~~~C~~Cg~~GH~a~~C~~~   25 (49)
T 2ec7_A            6 VIRCWNCGKEGHSARQCRAP   25 (49)
T ss_dssp             CCBCTTTCCBTCCTTTCCCS
T ss_pred             cCeeeecCCCCcChhhCcCC
Confidence            35799999999999999975

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

Probab=97.65  E-value=1.8e-05  Score=42.27  Aligned_cols=18  Identities=39%  Similarity=0.988  Sum_probs=16.5

Q ss_pred             cccccCCCCcccCCCCCC
Q 036141          190 FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       190 ~C~~Cgk~GH~~~~C~~k  207 (220)
                      .||+|+++||++++||..
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            599999999999999874

>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=97.64  E-value=2.6e-05  Score=45.65  Aligned_cols=22  Identities=36%  Similarity=0.649  Sum_probs=18.9

Q ss_pred             ccCccccccCCCCcccCCCCCC
Q 036141          186 CAKKFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       186 ~~~~~C~~Cgk~GH~~~~C~~k  207 (220)
                      .....||+||+.||++++||..
T Consensus        10 ~~~~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           10 RKTVKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             GGTCBCTTTCCBSSCGGGCSSC
T ss_pred             CCCcceeeeCCCCcChhhcCCC
Confidence            4446799999999999999875

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

Probab=97.35  E-value=7.1e-05  Score=44.71  Aligned_cols=21  Identities=33%  Similarity=0.967  Sum_probs=18.3

Q ss_pred             ccccccCCCCcccCCCCCCCC
Q 036141          189 KFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       189 ~~C~~Cgk~GH~~~~C~~k~~  209 (220)
                      ..||+|++.||++++||....
T Consensus         5 ~~C~~Cg~~GH~a~~C~~~~~   25 (61)
T 2ihx_A            5 GLCYTCGSPGHYQAQCPKKRK   25 (61)
T ss_dssp             TBCSSSCCBTCCGGGCTTTTS
T ss_pred             CcccccCCCCeehhhCcCCcC
Confidence            469999999999999998643

>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=97.31  E-value=3.4e-05  Score=45.99  Aligned_cols=19  Identities=37%  Similarity=0.782  Sum_probs=0.0

Q ss_pred             cccccCCCCcccCCCCCCC
Q 036141          190 FCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       190 ~C~~Cgk~GH~~~~C~~k~  208 (220)
                      .||+|++.||++++||...
T Consensus         3 ~Cf~Cg~~GH~a~~C~~~~   21 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHEHA   21 (60)
T ss_dssp             -------------------
T ss_pred             ccccCCCCCcCHhhCcCCC
Confidence            5999999999999999864

>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=97.22  E-value=0.00013  Score=43.80  Aligned_cols=19  Identities=32%  Similarity=0.555  Sum_probs=17.1

Q ss_pred             ccccccCCCCcccCCCCCC
Q 036141          189 KFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       189 ~~C~~Cgk~GH~~~~C~~k  207 (220)
                      ..||+|++.||++++|+..
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            4699999999999999964

>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=96.85  E-value=0.00063  Score=48.18  Aligned_cols=20  Identities=30%  Similarity=0.509  Sum_probs=17.7

Q ss_pred             CccccccCCCCcccCCCCCC
Q 036141          188 KKFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       188 ~~~C~~Cgk~GH~~~~C~~k  207 (220)
                      ..+||+||+.||++++|+..
T Consensus        97 ~~~C~~Cg~~GH~a~~C~~~  116 (148)
T 3ts2_A           97 GDRCYNCGGLDHHAKECKLP  116 (148)
T ss_dssp             SCCCTTTCCSSCCGGGCCSC
T ss_pred             CCcccEeCCccchhhhCCCC
Confidence            35799999999999999973

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

Probab=96.50  E-value=0.00071  Score=42.85  Aligned_cols=39  Identities=21%  Similarity=0.272  Sum_probs=22.7

Q ss_pred             CCcccccCCCCCcccccccCc-cccccCCCCcccCCCCCC
Q 036141          169 RQVQCFSCKEYRHIVVKCAKK-FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       169 ~~~~~~~~~~~g~~~~~~~~~-~C~~Cgk~GH~~~~C~~k  207 (220)
                      ....|+.|+..||..+.|+.. .||+|+.+||.+++|+..
T Consensus         4 k~~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p   43 (83)
T 3nyb_B            4 KKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLP   43 (83)
T ss_dssp             ---CCSSSCCSSSCGGGCGGGTCCCCBC------------
T ss_pred             ccCCCCCCCCCCCccccCCCcccccccccCCcccccccCC
Confidence            345799999999999999987 799999999999999754

>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=95.34  E-value=0.015  Score=31.15  Aligned_cols=25  Identities=36%  Similarity=0.631  Sum_probs=20.6

Q ss_pred             CCCCCCcccccCCCCCcccccccCc
Q 036141          165 GRDMRQVQCFSCKEYRHIVVKCAKK  189 (220)
Q Consensus       165 ~~~~~~~~~~~~~~~g~~~~~~~~~  189 (220)
                      +.......|+.|+..||++++|+..
T Consensus         5 ~~~~~~~~C~~Cgk~GH~ardCP~~   29 (40)
T 1a6b_B            5 RSQLDRDQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             CCSCCSSSCSSSCCTTCCTTSCSSS
T ss_pred             cCCCCCCeeeECCCCCcchhhCcCC
Confidence            3455567899999999999999874

>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=94.98  E-value=0.019  Score=33.21  Aligned_cols=26  Identities=35%  Similarity=0.641  Sum_probs=21.2

Q ss_pred             cCCCCCCcccccCCCCCcccccccCc
Q 036141          164 KGRDMRQVQCFSCKEYRHIVVKCAKK  189 (220)
Q Consensus       164 ~~~~~~~~~~~~~~~~g~~~~~~~~~  189 (220)
                      ++.......|+.|+..||++++|+..
T Consensus        17 ~~~~~~~~~C~~Cge~GH~ardCp~~   42 (56)
T 1u6p_A           17 RRSQLDRDQCAYCKEKGHWAKDCPKK   42 (56)
T ss_dssp             CSTTCCTTBCSSSCCBSSCGGGCTTC
T ss_pred             CCCCCCCCcceeCCCCCcccccCcCC
Confidence            34455677899999999999999875

>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=94.46  E-value=0.029  Score=27.69  Aligned_cols=21  Identities=19%  Similarity=0.689  Sum_probs=17.5

Q ss_pred             CCcccccCCCCCcccccccCc
Q 036141          169 RQVQCFSCKEYRHIVVKCAKK  189 (220)
Q Consensus       169 ~~~~~~~~~~~g~~~~~~~~~  189 (220)
                      ++..|++|+..||..++|+.+
T Consensus         5 ~~~~C~nCgk~GH~ar~C~~p   25 (29)
T 1nc8_A            5 KVIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSS
T ss_pred             CCCEEEECCccccCHhHCccc
Confidence            456799999999998888754

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1

Probab=94.06  E-value=0.027  Score=27.06  Aligned_cols=19  Identities=37%  Similarity=0.814  Sum_probs=16.5

Q ss_pred             cccccCCCCCcccccccCc
Q 036141          171 VQCFSCKEYRHIVVKCAKK  189 (220)
Q Consensus       171 ~~~~~~~~~g~~~~~~~~~  189 (220)
                      ..|+.|+..||.+++|+..
T Consensus         3 ~~Cf~CG~~GH~ardC~~~   21 (26)
T 1dsq_A            3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CeeEeCCCCCcccccCCCc
Confidence            4699999999999988764

>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}

Probab=92.84  E-value=0.03  Score=26.48  Aligned_cols=19  Identities=26%  Similarity=0.842  Sum_probs=16.2

Q ss_pred             CccccccCCCCcccCCCCC
Q 036141          188 KKFCNYCKKPGHIIKECPT  206 (220)
Q Consensus       188 ~~~C~~Cgk~GH~~~~C~~  206 (220)
                      ++.|-.|.--||+..+|..
T Consensus         3 RpYCe~CE~FGH~t~~C~d   21 (26)
T 2hqh_E            3 RPYCEICEMFGHWATNCND   21 (26)
T ss_dssp             -CEETTTTEESSCGGGCCT
T ss_pred             CccchHHHHhCcccccCCc
Confidence            3569999999999999965

>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}

Probab=90.82  E-value=0.07  Score=34.49  Aligned_cols=43  Identities=28%  Similarity=0.593  Sum_probs=28.5

Q ss_pred             CCCcccccCCCCC--------ccccc------ccCc---cccccCCCC---cccCCCCCCCCC
Q 036141          168 MRQVQCFSCKEYR--------HIVVK------CAKK---FCNYCKKPG---HIIKECPTRPQN  210 (220)
Q Consensus       168 ~~~~~~~~~~~~g--------~~~~~------~~~~---~C~~Cgk~G---H~~~~C~~k~~~  210 (220)
                      .....|.+|...|        |..++      |+..   .|-.||-.|   |+.+-||..++.
T Consensus        34 ~~~~~C~FCrnNGE~~~vy~SH~LKd~~G~V~CPvLR~Y~CpiCGATGd~AHT~kYCP~~~~~   96 (106)
T 3alr_A           34 AERKFCSFCKHNGETEAVYTSHYLKNRDGDVMCPYLRQYKCPLCGATGAKAHTKRFCPMVDKN   96 (106)
T ss_dssp             ----CCHHHHHTTCCHHHHTSBCSBCTTSCBCCTTGGGCCCTTTCCCGGGCCCGGGCTTCGGG
T ss_pred             CCCCEeECCCCCCcccCccccceeECCCCCCcCCCcccccCCCCCCcCCcccceecCCCCCCc
Confidence            3455688887776        33333      4432   799999999   999999987643

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

Probab=89.96  E-value=0.2  Score=28.73  Aligned_cols=20  Identities=25%  Similarity=0.715  Sum_probs=17.1

Q ss_pred             CCcccccCCCCCcccccccC
Q 036141          169 RQVQCFSCKEYRHIVVKCAK  188 (220)
Q Consensus       169 ~~~~~~~~~~~g~~~~~~~~  188 (220)
                      ....|+.|+..||+.+.|+.
T Consensus         6 ~~~~C~kCGk~GH~~k~Cp~   25 (55)
T 2ysa_A            6 SGYTCFRCGKPGHYIKNCPT   25 (55)
T ss_dssp             SSCCCTTTCCTTSCGGGCSG
T ss_pred             CCCccccCCCcCcccccCCC
Confidence            34579999999999999983

---

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	220
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	7e-07
d1a6bb_	40	g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney m	0.002

>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 = 42.5 bits (100), Expect = 7e-07
 Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 3/40 (7%)

Query: 171 VQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTR 207
           V+CF+C +  H    C    KK C  C K GH +K+C  R
Sbjct: 2   VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER 41

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]} Length = 40

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

 Score = 33.1 bits (75), Expect = 0.002
 Identities = 10/27 (37%), Positives = 16/27 (59%)

Query: 188 KKFCNYCKKPGHIIKECPTRPQNCQAS 214
           +  C YCK+ GH  K+CP +P+  +  
Sbjct: 10  RDQCAYCKEKGHWAKDCPKKPRGPRGP 36

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	220
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	99.29
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.86
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	98.33
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	98.31
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.97
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	96.77
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	96.26
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	96.02
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	94.62
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	91.55
d2fi2a1	92	Zinc finger protein 42 {Human (Homo sapiens) [TaxI	85.97
d1y7qa1	96	Zinc finger protein 174 {Human (Homo sapiens) [Tax	84.21

>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=99.29  E-value=1e-12  Score=71.39  Aligned_cols=39  Identities=36%  Similarity=0.819  Sum_probs=35.1

Q ss_pred             CcccccCCCCCcccccccCc---cccccCCCCcccCCCCCCC
Q 036141          170 QVQCFSCKEYRHIVVKCAKK---FCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       170 ~~~~~~~~~~g~~~~~~~~~---~C~~Cgk~GH~~~~C~~k~  208 (220)
                      +..|++|+..||.+.+|+.+   .|+.||+.||++++||.++
T Consensus         1 ni~C~~Cg~~GH~~~~Cp~~~~~~C~~Cg~~GH~~~~Cp~rq   42 (42)
T d2exfa1           1 NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQ   42 (42)
T ss_dssp             CCCCTTTCCSSSCTTTCSSCCCSSCSSSCCSSSCTTTCCSSC
T ss_pred             CCccccCCCcCcCcccCcCCCcCccccCCCCCeecccCCCCC
Confidence            35799999999999999874   7999999999999999875

>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=98.86  E-value=6.3e-10  Score=52.36  Aligned_cols=21  Identities=29%  Similarity=0.578  Sum_probs=18.1

Q ss_pred             CccccccCCCCcccCCCCCCC
Q 036141          188 KKFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       188 ~~~C~~Cgk~GH~~~~C~~k~  208 (220)
                      ..+||+|||.||++++|+...
T Consensus         6 ~ikCfNCGkeGH~ar~CrAPR   26 (29)
T d1nc8a_           6 VIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSS
T ss_pred             eeEeecCCccchhhhhccCcc
Confidence            457999999999999997643

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=98.33  E-value=1.1e-07  Score=48.11  Aligned_cols=24  Identities=42%  Similarity=1.081  Sum_probs=20.2

Q ss_pred             cccccCCCCcccCCCCCCCCCCcC
Q 036141          190 FCNYCKKPGHIIKECPTRPQNCQA  213 (220)
Q Consensus       190 ~C~~Cgk~GH~~~~C~~k~~~~~~  213 (220)
                      .|-||++.|||+++||++.....+
T Consensus        12 QCAyCke~GHW~~dCPkkprg~k~   35 (40)
T d1a6bb_          12 QCAYCKEKGHWAKDCPKKPRGPRG   35 (40)
T ss_dssp             SCSSSCCTTCCTTSCSSSCCCTTC
T ss_pred             hhHHHhhcCchhhhCccCCCCCCC
Confidence            599999999999999988755443

>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=97.97  E-value=1.9e-06  Score=45.98  Aligned_cols=20  Identities=30%  Similarity=0.655  Sum_probs=17.8

Q ss_pred             ccccccCCCCcccCCCCCCC
Q 036141          189 KFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       189 ~~C~~Cgk~GH~~~~C~~k~  208 (220)
                      .+||+||+.||++++||...
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            47999999999999999753

>d1cl4a_ g.40.1.1 (A:) Nucleocapsid protein from mason-pfizer monkey virus (MPMV) {Mason-pfizer monkey virus [TaxId: 11855]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleocapsid protein from mason-pfizer monkey virus (MPMV)
species: Mason-pfizer monkey virus [TaxId: 11855]

Probab=96.77  E-value=0.00054  Score=32.88  Aligned_cols=25  Identities=28%  Similarity=0.666  Sum_probs=21.8

Q ss_pred             cccccCCCCcccCCCCCCCCCCcCC
Q 036141          190 FCNYCKKPGHIIKECPTRPQNCQAS  214 (220)
Q Consensus       190 ~C~~Cgk~GH~~~~C~~k~~~~~~~  214 (220)
                      .|..|+|--||+++|+.+....++.
T Consensus         4 lCPrC~kG~HWa~~Crsk~~~~G~p   28 (32)
T d1cl4a_           4 LCPRCKRGKHWANECKSKTDNQGNP   28 (32)
T ss_dssp             SCSSCSSCSSCSTTCCCTTSSSSCC
T ss_pred             cCccccCcchHHHHhhhhhccCCCc
Confidence            5999999999999999998776654

>d1dsva_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=96.26  E-value=0.00072  Score=32.25  Aligned_cols=24  Identities=29%  Similarity=0.520  Sum_probs=20.5

Q ss_pred             cccccCCCCcccCCCCCCCCCCcC
Q 036141          190 FCNYCKKPGHIIKECPTRPQNCQA  213 (220)
Q Consensus       190 ~C~~Cgk~GH~~~~C~~k~~~~~~  213 (220)
                      .|..|+|--||+++|+.+....++
T Consensus         4 lCPrC~kG~HWa~~Crsk~~~~G~   27 (31)
T d1dsva_           4 LCPRCKKGYHWKSECKSKFDKDGN   27 (31)
T ss_dssp             BCTTTCSSBSCTTTCCCSEEGGGE
T ss_pred             cCccccCcchHHHHhhhhhccCCC
Confidence            699999999999999998765543

>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=96.02  E-value=0.0027  Score=29.33  Aligned_cols=23  Identities=17%  Similarity=0.618  Sum_probs=18.6

Q ss_pred             CCCCcccccCCCCCcccccccCc
Q 036141          167 DMRQVQCFSCKEYRHIVVKCAKK  189 (220)
Q Consensus       167 ~~~~~~~~~~~~~g~~~~~~~~~  189 (220)
                      .++...|++|+..||.++.|..+
T Consensus         3 qr~~ikCfNCGkeGH~ar~CrAP   25 (29)
T d1nc8a_           3 QRKVIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCCCCBCTTTSCBSSCGGGCCSS
T ss_pred             CcceeEeecCCccchhhhhccCc
Confidence            34567899999999999888754

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=94.62  E-value=0.0087  Score=26.29  Aligned_cols=18  Identities=39%  Similarity=0.837  Sum_probs=15.6

Q ss_pred             cccccCCCCCcccccccC
Q 036141          171 VQCFSCKEYRHIVVKCAK  188 (220)
Q Consensus       171 ~~~~~~~~~g~~~~~~~~  188 (220)
                      +.|++|+..||.+++|..
T Consensus         3 pvcfscgktghikkdck~   20 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKE   20 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTC
T ss_pred             CEEEecCCcccchhhhhh
Confidence            569999999999888764

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=91.55  E-value=0.094  Score=25.94  Aligned_cols=24  Identities=38%  Similarity=0.671  Sum_probs=19.7

Q ss_pred             CCCCCcccccCCCCCcccccccCc
Q 036141          166 RDMRQVQCFSCKEYRHIVVKCAKK  189 (220)
Q Consensus       166 ~~~~~~~~~~~~~~g~~~~~~~~~  189 (220)
                      .+-....|..|...||+.++|+..
T Consensus         6 ~~L~kDQCAyCke~GHW~~dCPkk   29 (40)
T d1a6bb_           6 SQLDRDQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             CSCCSSSCSSSCCTTCCTTSCSSS
T ss_pred             CcccchhhHHHhhcCchhhhCccC
Confidence            445567899999999999999864

>d2fi2a1 a.28.3.2 (A:37-128) Zinc finger protein 42 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Acyl carrier protein-like
superfamily: Retrovirus capsid dimerization domain-like
family: SCAN domain
domain: Zinc finger protein 42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.97  E-value=2.3  Score=25.59  Aligned_cols=76  Identities=14%  Similarity=0.118  Sum_probs=51.0

Q ss_pred             HHHHHHHh-cCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHHHHHHhhccchHHHHHHhhcCCCCCCC
Q 036141           45 EYEIARYS-QGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPS  123 (220)
Q Consensus        45 ~~~~~~~~-q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~gLp~~~~~~~~~l~~~~~~~s  123 (220)
                      ++.|.... +++.+..+++.+++.|+..=-  .+. +..     ..++.+-..+.+||..||++....+.   . ....|
T Consensus         8 rq~FR~f~y~e~~~p~e~l~rL~eLc~~WL--~pe-~~t-----keqilelLVLEQFl~~lP~e~~~~V~---e-~~p~s   75 (92)
T d2fi2a1           8 RLRFRCFHYEEATGPQEALAQLRELCRQWL--RPE-VRS-----KEQMLELLVLEQFLGALPPEIQARVQ---G-QRPGS   75 (92)
T ss_dssp             HHHHHSCCCCTTTCHHHHHHHHHHHHHHHH--CTT-TCC-----HHHHHHHHHHHHHHHHSCHHHHHHHH---H-HCCCS
T ss_pred             HHHHhcCCCcccCCHHHHHHHHHHHHHHHc--CCc-ccC-----HHHHHHHHHHHHHHHHCCHHHHHHHH---H-hCCCC
Confidence            44466665 568999999999999988763  122 111     12346777789999999998555532   2 23357


Q ss_pred             HHHHHHHHH
Q 036141          124 LDVCFKELL  132 (220)
Q Consensus       124 l~e~~~~l~  132 (220)
                      .++++..+.
T Consensus        76 ~~eav~L~E   84 (92)
T d2fi2a1          76 PEEAAALVD   84 (92)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            787777654

>d1y7qa1 a.28.3.2 (A:37-132) Zinc finger protein 174 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Acyl carrier protein-like
superfamily: Retrovirus capsid dimerization domain-like
family: SCAN domain
domain: Zinc finger protein 174
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.21  E-value=2.9  Score=25.27  Aligned_cols=79  Identities=15%  Similarity=0.076  Sum_probs=52.6

Q ss_pred             HHHHHHHh-cCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHHHHHHhhccchHHHHHHhhcCCCCCCC
Q 036141           45 EYEIARYS-QGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPS  123 (220)
Q Consensus        45 ~~~~~~~~-q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~gLp~~~~~~~~~l~~~~~~~s  123 (220)
                      ++.|.... +++.+..+++.+++.|+.+=-  .+...+.      .++.|-....+||..||++....   +.. ...-|
T Consensus        10 rqrFR~f~~~e~~~P~eal~rL~eLc~~WL--rPe~~tK------EqilelLVLEQFl~~lP~e~q~w---V~e-~~p~s   77 (96)
T d1y7qa1          10 RQSFRRFCYQEVSGPQEALSQLRQLCRQWL--QPELHTK------EQILELLVMEQFLTILPEEIQAR---VRH-RCLMS   77 (96)
T ss_dssp             HHHHHTCCSCSCCSSHHHHHHHHHHHHHHH--CCSSCCH------HHHHHHHHHHHHHHHSCTHHHHH---HHT-SCCCC
T ss_pred             HHHhcCCCcccCCCHHHHHHHHHHHHHHHc--CccccCH------HHHHHHHHHHHHHHHCCHHHHHH---HHH-hCCCC
Confidence            44566665 568888999999999988763  1221221      13466677799999999985554   333 34458


Q ss_pred             HHHHHHHHHHHH
Q 036141          124 LDVCFKELLREE  135 (220)
Q Consensus       124 l~e~~~~l~~~e  135 (220)
                      .++++..+....
T Consensus        78 ~eeav~L~Edl~   89 (96)
T d1y7qa1          78 SKEIVTLVEDFH   89 (96)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            888887766543